Contacts of the strand formed by residues 128 - 140 (chain B) in PDB entry 1RVB


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 TYR 128 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73B  PRO*     3.6    13.4    -      -       +      +
     76B  THR*     2.7    43.0    +      -       +      +
     86B  LYS*     3.1    14.1    -      -       +      +
     87B  ILE      3.8     2.7    -      -       -      -
     88B  ALA*     3.5    35.0    -      -       +      -
    121B  ILE*     3.9    11.0    -      -       +      -
    122B  VAL*     3.9     0.5    -      -       -      +
    123B  TYR*     3.3    46.2    +      -       +      -
    124B  PRO      3.6    11.0    -      -       -      -
    125B  PHE*     3.1    20.1    +      -       -      +
    126B  ASP*     4.0     5.5    -      -       -      +
    127B  GLN*     1.3    80.6    -      -       -      +
    129B  ILE*     1.3    64.3    +      -       -      +
    130B  ALA      4.4     1.3    -      -       -      +
    131B  HIS*     3.7    23.5    +      +       +      +
----------------------------------------------------------
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Residues in contact with ILE 129 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84B  ASN      3.8    21.5    -      -       -      +
     85B  LYS*     3.9    32.3    -      -       +      +
     86B  LYS      2.8    14.7    +      -       -      +
     87B  ILE*     4.8     7.4    -      -       +      -
    126B  ASP      5.6     1.1    -      -       -      +
    127B  GLN      5.1     0.4    -      -       -      -
    128B  TYR*     1.3    76.9    -      -       -      +
    130B  ALA*     1.3    67.2    +      -       +      +
    131B  HIS*     5.1     2.2    -      -       -      -
    209B  GLU*     5.2     6.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 130 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86B  LYS      3.8     1.8    +      -       -      +
     87B  ILE*     3.7    14.7    -      -       +      -
     88B  ALA*     2.9    26.1    +      -       -      +
    128B  TYR*     3.6     1.3    -      -       -      +
    129B  ILE*     1.3    91.0    -      -       +      +
    131B  HIS*     1.3    71.3    +      -       -      +
    132B  TRP*     3.7    24.9    -      -       +      +
    172B  ASP*     4.8     4.7    -      -       -      +
    209B  GLU*     5.7     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 131 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72B  TYR*     2.8    32.9    +      +       -      +
     88B  ALA*     3.5     9.1    -      -       -      +
    113B  PHE*     5.4     0.4    -      -       -      -
    125B  PHE*     3.4    42.0    +      +       -      -
    128B  TYR*     3.7    36.2    +      +       +      +
    129B  ILE      5.1     1.1    -      -       -      -
    130B  ALA*     1.3    80.4    -      -       -      +
    132B  TRP*     1.3    63.6    +      -       -      +
    172B  ASP*     3.4     7.9    +      -       -      +
    173B  LYS*     2.8    45.7    +      -       +      +
    209B  GLU*     4.5    16.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 132 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3B  LEU*     4.2    12.3    -      -       +      -
      4B  ARG*     3.6    58.6    -      -       +      +
      7B  LEU*     4.0    17.0    -      -       +      -
     72B  TYR*     5.3     1.2    +      -       -      -
     87B  ILE*     4.0    41.3    -      -       +      -
     88B  ALA      2.8    11.0    +      -       -      +
     89B  ILE*     3.4    22.5    -      -       +      -
     90B  ASP*     3.1    23.6    +      -       -      +
    130B  ALA*     3.7    14.4    -      -       +      +
    131B  HIS*     1.3    84.0    -      -       -      +
    133B  ILE*     1.3    65.8    +      -       -      +
    170B  LEU*     4.0    28.9    -      -       +      -
    171B  GLN      3.4     5.2    -      -       -      +
    172B  ASP*     3.6    17.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 133 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72B  TYR*     5.8     0.4    -      -       -      +
     90B  ASP*     3.3    25.4    -      -       +      -
     92B  LYS*     3.8    28.7    -      -       +      -
    105B  PHE*     5.9     1.1    -      -       +      -
    107B  LEU*     4.1    21.3    -      -       +      -
    132B  TRP*     1.3    78.8    -      -       -      +
    134B  ILE*     1.3    69.5    +      -       -      +
    135B  GLY*     3.8     3.1    +      -       -      +
    169B  PHE*     3.5     7.5    -      -       +      +
    170B  LEU*     3.2     4.0    -      -       -      -
    171B  GLN      2.8    33.4    +      -       -      +
    173B  LYS*     3.9    39.7    -      -       +      -
    176B  ILE*     4.2    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 134 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  LEU*     4.7     2.5    -      -       +      -
     11B  LEU*     4.1    22.4    -      -       +      -
     48B  SER*     4.9     2.0    -      -       -      +
     52B  ILE*     4.0    23.1    -      -       +      -
     89B  ILE*     3.5    28.7    -      -       +      -
     90B  ASP      2.9     9.6    +      -       -      +
     91B  ILE*     3.3    12.0    -      -       +      +
     92B  LYS      2.9    24.4    +      -       -      +
    133B  ILE*     1.3    74.3    -      -       -      +
    135B  GLY*     1.3    60.2    +      -       -      +
    136B  TYR*     3.7    17.5    -      -       +      +
    168B  VAL*     3.6    26.0    -      -       +      -
    169B  PHE      3.2     5.2    -      -       -      +
    170B  LEU*     4.0    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 135 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92B  LYS      3.1     9.4    -      -       -      -
    105B  PHE*     4.2     4.5    -      -       -      -
    133B  ILE*     3.8     4.9    -      -       -      -
    134B  ILE*     1.3    75.1    -      -       -      +
    136B  TYR*     1.3    61.8    +      -       -      -
    167B  LYS      3.7     0.3    -      -       -      +
    168B  VAL*     3.1     6.4    -      -       -      +
    169B  PHE*     2.9    58.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 136 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  LEU*     4.1    14.9    -      -       -      +
     15B  ASN*     3.6    19.6    -      -       +      +
     44B  PHE*     3.8    46.0    -      +       +      -
     47B  PHE*     4.1    12.6    -      +       -      -
     48B  SER*     2.6    31.2    +      -       -      -
     51B  ILE*     5.0     0.2    -      -       -      +
     91B  ILE*     3.9    18.4    -      -       +      -
     92B  LYS      2.8     7.2    +      -       -      -
     93B  THR*     3.2     7.4    -      -       +      -
     94B  THR      3.1    24.5    +      -       -      +
    105B  PHE*     3.8     3.5    -      -       -      -
    134B  ILE*     3.7    15.7    -      -       +      -
    135B  GLY*     1.3    77.0    -      -       -      -
    137B  VAL*     1.3    60.8    +      -       -      +
    138B  TYR*     4.2     0.4    -      -       -      -
    166B  VAL*     3.9    17.7    -      -       +      -
    167B  LYS      3.2     3.6    -      -       -      -
    168B  VAL*     3.6    23.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 137 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94B  THR*     3.4    10.5    -      -       +      +
     95B  TYR      4.7     0.2    -      -       -      -
     96B  THR*     4.2    16.4    -      -       +      +
    103B  ILE*     3.5    47.1    -      -       +      -
    105B  PHE*     3.9    11.2    -      -       +      -
    136B  TYR*     1.3    77.9    -      -       -      +
    138B  TYR*     1.3    63.0    +      -       -      +
    165B  GLY      3.8     0.3    -      -       -      +
    166B  VAL*     3.3     3.9    -      -       -      -
    167B  LYS*     2.8    48.6    +      -       +      +
    169B  PHE*     4.5     3.6    -      -       +      -
    196B  TYR*     4.3    17.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 138 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  SER      5.6     0.9    -      -       -      -
     37B  THR*     3.4    36.7    +      -       -      -
     40B  LEU*     3.3    34.9    -      -       +      +
     44B  PHE*     3.7    22.7    -      +       +      -
     93B  THR*     4.3     8.3    -      -       -      -
     94B  THR      3.3    22.9    +      -       -      -
     95B  TYR*     3.1    30.1    -      -       +      +
     96B  THR*     2.9    24.2    +      -       -      -
    136B  TYR      4.8     1.3    -      -       -      -
    137B  VAL*     1.3    76.5    -      -       -      +
    139B  THR*     1.3    65.3    +      -       -      +
    140B  ARG*     4.1    13.4    +      -       +      -
    163B  TYR*     4.2    17.0    -      -       +      -
    165B  GLY      3.1    11.4    -      -       -      +
    166B  VAL*     4.3     9.2    -      -       +      -
      9D    C      4.2     1.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 139 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96B  THR*     3.1    23.3    +      -       -      +
     97B  ASN      3.6    17.5    -      -       -      +
     98B  LYS*     4.5     1.3    -      -       -      +
     99B  GLU*     4.3    21.5    -      -       +      +
    138B  TYR*     1.3    73.7    -      -       -      +
    140B  ARG*     1.3    73.3    +      -       -      +
    163B  TYR*     3.5     2.9    -      -       -      -
    164B  LYS*     2.8    45.7    +      -       +      -
    165B  GLY*     3.0    21.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 140 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67A  LYS      5.7     2.6    +      -       -      -
     69A  GLN*     3.6    27.9    +      -       -      +
     35B  SER*     4.8    14.8    +      -       -      +
     37B  THR*     5.2     0.8    -      -       -      +
     40B  LEU*     6.0     0.2    -      -       +      -
     95B  TYR*     3.1    56.9    +      -       +      +
     96B  THR      3.2    10.6    +      -       -      +
     97B  ASN*     4.4    16.7    +      -       -      +
    138B  TYR*     3.8    21.7    +      -       +      -
    139B  THR*     1.3    89.5    -      -       -      +
    141B  VAL*     1.3    70.0    +      -       -      +
    142B  ALA      4.2     0.2    +      -       -      -
    162B  PRO      4.1     9.6    -      -       -      +
    164B  LYS*     4.2     4.5    -      -       -      +
      9D    C      5.1     0.2    -      -       -      -
     10D    T      3.6    15.6    +      -       -      -
----------------------------------------------------------
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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