Contacts of the strand formed by residues 85 - 103 (chain B) in PDB entry 4V1M


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with SER 85 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73B  GLN      3.6     3.6    -      -       -      -
     74B  LEU*     3.6    30.9    -      -       -      +
     75B  ALA      4.0     2.8    +      -       -      -
     83B  ASN      4.3     0.2    -      -       -      -
     84B  ILE*     1.3    73.9    +      -       -      +
     86B  ARG*     1.3    59.7    +      -       -      +
     87B  LYS*     5.8     0.2    -      -       -      -
    138B  GLU*     3.2     2.6    -      -       -      +
    139B  ALA*     2.6    54.4    +      -       -      +
    140B  ILE      5.7     0.2    -      -       -      -
    141B  ASP*     4.6    15.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 86 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71B  LEU      4.9     0.2    -      -       -      -
     72B  GLU*     3.2     1.6    -      -       -      +
     73B  GLN*     2.8    40.2    +      -       +      +
     74B  LEU*     3.7     2.1    -      -       -      +
     84B  ILE*     3.8    18.3    -      -       +      +
     85B  SER*     1.3    77.4    -      -       -      +
     87B  LYS*     1.3    69.3    +      -       -      +
     88B  TYR*     3.3    41.9    +      -       +      +
    136B  THR*     4.7     9.3    -      -       -      +
    137B  TYR      3.2    10.5    -      -       -      +
    138B  GLU*     2.9    39.2    +      -       +      +
    151B  LEU*     5.8     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 87 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70B  ILE*     5.1    14.8    -      -       +      +
     71B  LEU      3.7     6.1    -      -       -      +
     72B  GLU*     3.5    35.5    +      -       +      +
     74B  LEU*     4.6     7.0    -      -       +      -
     86B  ARG*     1.3    79.9    -      -       -      +
     88B  TYR*     1.3    62.5    +      -       -      +
     89B  GLU*     5.6     1.1    -      -       +      -
    137B  TYR*     2.8    53.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 88 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69B  LEU      4.2     0.2    -      -       -      +
     70B  ILE*     3.2     8.5    -      -       -      +
     71B  LEU*     2.9    56.1    +      -       +      +
     73B  GLN*     4.3    17.8    -      -       +      +
     86B  ARG*     3.3    41.1    +      -       +      +
     87B  LYS*     1.3    72.8    -      -       -      +
     89B  GLU*     1.3    64.6    +      -       -      +
     90B  ILE*     6.5     0.4    -      -       +      -
    134B  LYS*     5.8     3.8    -      -       +      -
    135B  ARG      3.6     6.5    -      -       -      +
    136B  THR*     3.5    35.0    -      -       +      +
    432B  MET*     5.7     5.3    -      -       -      +
    436B  VAL*     3.6    32.3    -      -       +      +
    442B  PHE*     5.6    14.6    -      +       +      -
----------------------------------------------------------
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Residues in contact with GLU 89 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68B  THR*     5.4     6.0    -      -       -      +
     69B  LEU      4.0     0.2    -      -       -      -
     70B  ILE*     3.5    23.3    -      -       +      +
     87B  LYS*     5.6     0.7    -      -       +      -
     88B  TYR*     1.3    75.9    -      -       -      +
     90B  ILE*     1.3    71.6    +      -       -      +
     91B  SER*     3.6    16.5    +      -       -      +
    133B  LYS      4.3     0.2    -      -       -      -
    134B  LYS*     3.3     6.4    -      -       -      +
    135B  ARG*     2.9    42.2    +      -       +      +
    137B  TYR*     3.5    35.0    +      -       +      -
    432B  MET*     5.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 90 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68B  THR*     3.2     7.0    -      -       -      -
     69B  LEU*     3.2    42.0    +      -       +      +
     70B  ILE*     4.9     0.4    -      -       -      +
     88B  TYR*     6.5     0.2    -      -       +      -
     89B  GLU*     1.3    80.7    -      -       -      +
     91B  SER*     1.3    62.7    +      -       -      +
     92B  PHE*     4.2    19.6    -      -       +      -
    132B  VAL*     4.1    16.8    -      -       +      -
    133B  LYS      3.3     3.4    -      -       -      -
    134B  LYS*     3.6    34.1    -      -       +      +
    428B  ILE*     4.3    13.5    -      -       +      -
    432B  MET*     3.4    33.0    -      -       +      -
    444B  MET*     5.1     7.0    -      -       +      -
    447B  ALA*     6.3     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 91 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68B  THR*     3.6    17.2    -      -       -      +
     89B  GLU*     3.6    19.8    +      -       -      +
     90B  ILE*     1.3    76.9    +      -       -      +
     92B  PHE*     1.3    64.1    +      -       -      +
     93B  GLY      4.1     0.2    -      -       -      -
    131B  ASP      3.6     0.3    -      -       -      +
    132B  VAL*     3.3    10.9    -      -       -      +
    133B  LYS*     2.8    48.3    +      -       -      +
    135B  ARG*     5.4     3.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 92 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63B  ILE*     4.1    17.1    -      -       +      +
     64B  CYS*     4.4    13.9    -      -       -      -
     67B  SER*     3.6    36.0    -      -       -      -
     68B  THR*     4.2     6.6    -      -       -      +
     69B  LEU*     3.9    13.2    -      -       +      -
     90B  ILE*     4.2    11.9    -      -       +      -
     91B  SER*     1.3    78.2    -      -       -      +
     93B  GLY*     1.3    62.7    +      -       -      +
    130B  VAL*     3.7    24.5    -      -       +      -
    131B  ASP      3.5     0.9    -      -       -      -
    132B  VAL*     3.7    25.8    -      -       +      -
    167B  ILE*     6.0     4.7    -      -       +      -
    421B  PHE*     4.1    24.9    -      +       -      -
    424B  LEU*     6.1     1.6    -      -       +      -
    425B  THR*     4.5     2.5    -      -       -      -
    428B  ILE*     4.1    25.1    -      -       +      -
    448B  ILE*     5.8     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 93 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60B  GLN*     3.2    18.2    +      -       -      -
     63B  ILE*     3.7     5.5    -      -       -      +
     64B  CYS*     5.4     1.1    -      -       -      -
     91B  SER      4.1     0.8    -      -       -      -
     92B  PHE*     1.3    75.2    -      -       -      +
     94B  LYS*     1.3    69.9    +      -       -      +
    130B  VAL*     4.2     1.8    -      -       -      +
    131B  ASP*     2.8    19.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 94 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60B  GLN*     3.6    11.4    -      -       -      +
     93B  GLY*     1.3    72.9    -      -       -      +
     95B  ILE*     1.3    72.4    -      -       -      +
     96B  TYR*     3.9    28.3    +      -       +      +
    130B  VAL*     3.6     2.3    -      -       -      -
    131B  ASP*     3.1    43.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 95 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55B  VAL      5.9     1.1    -      -       -      +
     59B  LEU*     3.7    40.2    -      -       +      +
     60B  GLN*     3.0    44.3    +      -       +      +
     63B  ILE*     4.4    14.8    -      -       +      -
     94B  LYS*     1.3    83.2    -      -       -      +
     96B  TYR*     1.3    72.3    +      -       -      +
     97B  VAL*     5.4     2.0    -      -       +      +
    128B  LEU*     4.1    14.4    -      -       +      -
    129B  PHE      3.4    10.5    -      -       -      +
    130B  VAL*     3.7    18.8    -      -       +      -
    167B  ILE*     5.0     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 96 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94B  LYS*     3.9    28.3    +      -       +      +
     95B  ILE*     1.3    82.8    -      -       -      +
     97B  VAL*     1.3    66.2    +      -       -      +
     98B  THR*     6.4     1.1    -      -       +      -
    127B  GLY      4.4     0.2    -      -       -      -
    128B  LEU*     3.7     3.3    -      -       -      -
    129B  PHE*     2.5    52.2    +      -       +      +
    131B  ASP*     3.4    37.3    +      -       -      -
    164B  LYS*     3.8    24.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 97 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55B  VAL*     4.1    22.0    -      -       +      +
     59B  LEU*     5.2     4.5    -      -       +      -
     95B  ILE*     5.4     2.5    -      -       +      +
     96B  TYR*     1.3    81.1    -      -       -      +
     98B  THR*     1.3    68.9    +      -       -      +
    126B  SER*     3.5    21.5    -      -       -      +
    127B  GLY      3.2     8.7    -      -       -      +
    128B  LEU*     3.8    17.7    -      -       +      -
    170B  LEU*     4.8     7.4    -      -       +      -
    172B  ILE*     5.0     0.9    -      -       +      -
    178B  ASN*     3.9    21.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 98 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96B  TYR*     6.4     0.9    -      -       +      -
     97B  VAL*     1.3    73.1    -      -       -      +
     99B  LYS*     1.3    65.0    +      -       -      +
    101B  MET*     3.3    21.4    -      -       +      +
    126B  SER*     3.1     9.4    -      -       -      -
    127B  GLY*     3.0    30.8    +      -       -      -
    129B  PHE*     4.2    20.9    -      -       +      -
    178B  ASN*     2.6    26.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 99 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98B  THR*     1.3    90.5    +      -       -      +
    100B  PRO*     1.3    70.2    -      -       -      +
    101B  MET*     3.4     8.0    -      -       +      +
    126B  SER*     3.5     2.1    -      -       -      -
    177B  LYS      4.0     6.1    +      -       -      -
    178B  ASN*     3.3    23.3    +      -       -      +
    179B  CYS      3.4    15.8    +      -       -      -
    180B  TYR*     3.4    38.9    -      -       +      +
    183B  GLU*     3.0    29.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 100 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99B  LYS*     1.3    86.7    -      -       +      +
    101B  MET*     1.3    59.8    +      -       -      +
    111B  ALA*     3.7     0.2    -      -       -      -
    112B  LEU*     3.5    10.7    +      -       +      +
    124B  TYR*     3.6    44.4    -      -       +      +
    125B  SER      3.3    15.9    -      -       -      +
    126B  SER*     3.6     2.5    -      -       -      -
    172B  ILE*     3.8    19.5    -      -       +      -
    178B  ASN*     3.4    22.4    -      -       -      +
    180B  TYR*     2.5    36.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with MET 101 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98B  THR*     3.3    37.5    -      -       +      +
     99B  LYS      3.4     6.7    +      -       -      +
    100B  PRO*     1.3    77.7    -      -       -      +
    102B  VAL*     1.3    70.2    +      -       -      +
    109B  THR*     3.9    19.3    -      -       +      -
    110B  HIS*     3.5    17.7    -      -       -      +
    111B  ALA*     4.7     2.2    -      -       -      +
    112B  LEU*     4.0     9.7    -      -       -      +
    123B  THR      4.7     0.7    -      -       -      +
    125B  SER*     3.2     9.4    +      -       -      +
    126B  SER*     4.4     0.4    -      -       -      +
    127B  GLY*     5.0     3.8    -      -       -      +
    129B  PHE*     5.3     8.5    -      -       +      -
    166B  PHE*     6.5     0.4    -      -       +      -
    169B  ARG*     3.4    36.7    +      -       -      +
    180B  TYR*     5.0     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 102 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101B  MET*     1.3    81.2    -      -       -      +
    103B  ASN*     1.3    61.0    +      -       -      +
    104B  GLU*     3.6    19.7    +      -       +      +
    109B  THR*     3.3    25.9    -      -       -      +
    110B  HIS*     3.0    33.2    +      -       +      +
    112B  LEU*     3.6    29.4    -      -       +      -
    120B  ARG*     4.9     1.8    -      -       -      +
    122B  LEU*     3.9    24.0    -      -       +      -
    123B  THR      4.7     3.6    -      -       -      +
    169B  ARG*     4.5     2.0    -      -       -      +
    958B  GLN*     3.8    20.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 103 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102B  VAL*     1.3    73.3    -      -       -      +
    104B  GLU*     1.3    73.6    +      -       -      +
    107B  GLY*     3.2    25.3    +      -       -      -
    108B  VAL      4.1     1.1    -      -       -      -
    109B  THR*     3.0    21.0    +      -       +      +
    169B  ARG*     4.8    15.4    +      -       -      +
    958B  GLN*     3.9    22.9    +      -       -      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il