Contacts of the strand formed by residues 94 - 109 (chain B) in PDB entry 3UR9


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 LEU 94 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  PRO*     3.6    44.9    -      -       +      +
      4A  THR*     4.3     6.1    -      -       -      +
      7A  SER*     3.7    12.4    +      -       -      -
     67A  ASP*     5.0     0.6    +      -       -      -
    201A   CL      4.1    17.9    -      -       +      -
      6B  TRP*     3.8    33.0    -      -       +      -
     87B  ILE      3.7     2.2    -      -       -      -
     88B  LYS*     3.8    26.7    -      -       +      -
     92B  GLY      3.4    11.4    +      -       -      +
     93B  GLU*     1.3    83.6    -      -       -      +
     95B  LEU*     1.3    61.5    +      -       -      +
     96B  PRO*     3.7     7.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 95 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  TRP*     4.0     0.4    -      -       -      -
     85B  VAL      3.5     0.7    -      -       -      +
     87B  ILE*     2.8    39.2    +      -       +      +
     89B  ARG*     3.6    39.0    -      -       +      +
     93B  GLU*     3.9    22.7    -      -       +      +
     94B  LEU*     1.3    75.4    -      -       -      +
     96B  PRO*     1.3    68.1    -      -       +      +
     97B  LEU*     3.2    29.8    +      -       +      +
    132B  LEU*     4.0    31.4    -      -       +      -
    133B  GLY      4.0     7.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 96 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      0B  MET*     6.5     0.7    -      -       -      -
      1B  ALA*     6.2     0.4    -      -       +      -
      6B  TRP*     3.8    25.3    -      -       +      -
     84B  SER*     3.5    16.6    -      -       -      +
     85B  VAL      3.3     8.7    -      -       -      +
     86B  LEU*     4.4     1.3    -      -       +      -
     94B  LEU*     3.7     8.5    -      -       +      +
     95B  LEU*     1.3    88.0    -      -       +      +
     97B  LEU*     1.3    65.2    +      -       -      +
     98B  ALA      4.1     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 97 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84B  SER*     3.4     4.0    -      -       -      -
     85B  VAL*     2.8    42.4    +      -       +      +
     87B  ILE*     3.1    33.0    -      -       +      -
     95B  LEU*     3.7    26.5    -      -       +      +
     96B  PRO*     1.3    76.6    -      -       -      +
     98B  ALA*     1.3    62.9    +      -       -      +
     99B  VAL      3.7     0.7    +      -       -      -
    121B  LEU*     4.0    22.2    -      -       +      -
    132B  LEU*     3.9    25.6    -      -       +      +
    133B  GLY*     4.0    13.7    -      -       -      +
    134B  THR*     3.6    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 98 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82B  VAL*     4.5     6.3    -      -       +      -
     83B  CYS      3.4     8.5    -      -       -      +
     84B  SER*     4.6     2.0    -      -       -      +
     96B  PRO      4.1     2.2    +      -       -      -
     97B  LEU*     1.3    72.0    -      -       -      +
     99B  VAL*     1.3    60.9    +      -       -      +
    121B  LEU*     3.6     6.2    -      -       -      +
    122B  LEU*     2.9    47.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 99 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82B  VAL*     3.4     1.6    -      -       -      -
     83B  CYS*     2.9    46.7    +      -       +      +
     85B  VAL*     3.9    21.3    -      -       +      -
     98B  ALA*     1.3    76.2    -      -       -      +
    100B  ARG*     1.3    63.2    +      -       -      +
    101B  MET*     3.6    18.5    +      -       -      -
    119B  GLY*     3.6    28.9    -      -       -      -
    120B  MET      3.4    15.0    -      -       -      +
    121B  LEU*     4.1     9.2    -      -       +      +
    122B  LEU*     3.9     5.3    -      -       -      +
    143B  TYR*     4.3     1.1    -      -       +      -
    167B  VAL*     3.7    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 100 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80B  GLY*     4.0    26.7    -      -       -      +
     81B  THR      3.7     3.4    -      -       -      -
     82B  VAL*     4.5     9.9    -      -       +      +
     99B  VAL*     1.3    70.8    -      -       -      +
    101B  MET*     1.3    64.8    +      -       -      +
    102B  GLY*     4.8     0.2    -      -       -      -
    119B  GLY*     4.2     0.4    -      -       -      -
    120B  MET*     2.9    41.4    +      -       +      +
    122B  LEU*     3.9    26.8    -      -       +      +
----------------------------------------------------------
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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
----------------------------------------------------------
     77B  CYS*     3.5    27.1    -      -       -      -
     78B  PRO      4.7     1.8    -      -       -      +
     79B  GLU*     4.4     0.2    -      -       -      +
     80B  GLY*     2.9    26.0    +      -       -      -
     81B  THR      3.0    22.4    +      -       -      +
     83B  CYS*     3.8     9.6    -      -       -      -
     99B  VAL*     3.7    32.1    -      -       -      +
    100B  ARG*     1.3    76.0    -      -       -      +
    102B  GLY*     1.3    60.4    +      -       -      +
    117B  GLN*     3.7    28.7    -      -       +      +
    118B  SER      3.6    16.8    -      -       -      +
    119B  GLY*     4.1     1.1    -      -       -      -
    143B  TYR*     3.9    14.6    -      -       +      -
    154B  CYS*     6.0     0.9    -      -       -      -
    169B  CYS*     3.8    24.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 102 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79B  GLU*     3.2    19.2    -      -       -      +
    100B  ARG      3.7     1.6    +      -       -      -
    101B  MET*     1.3    72.0    -      -       -      +
    103B  ALA*     1.3    61.9    +      -       -      -
    117B  GLN*     2.8    23.9    +      -       -      -
    118B  SER*     2.7    22.8    +      -       -      -
    119B  GLY*     4.1     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 103 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79B  GLU*     3.8    27.0    +      -       -      +
    102B  GLY*     1.3    72.8    -      -       -      -
    104B  ILE*     1.3    68.6    +      -       -      +
    105B  ALA*     3.8     4.9    +      -       +      +
    107B  MET*     4.6     2.9    -      -       -      +
    116B  GLY      4.1     0.2    -      -       -      +
    117B  GLN*     3.6     1.9    -      -       -      -
    118B  SER*     3.4    26.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 104 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75B  GLU*     3.7    30.1    -      -       +      +
     76B  GLY*     4.2     3.8    -      -       -      -
     77B  CYS      4.6     6.7    -      -       -      +
    102B  GLY      4.0     0.2    +      -       -      -
    103B  ALA*     1.3    79.2    -      -       -      +
    105B  ALA*     1.3    65.9    +      -       -      +
    115B  HIS*     3.8    29.4    -      -       +      +
    116B  GLY      3.2    11.2    -      -       -      +
    117B  GLN*     3.6    30.5    -      -       +      +
    171B  VAL*     4.4     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 105 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103B  ALA*     3.8     4.4    +      -       +      +
    104B  ILE*     1.3    78.6    -      -       -      +
    106B  SER*     1.3    70.1    +      -       -      +
    107B  MET*     3.5    17.1    -      -       +      +
    114B  VAL      3.6     0.2    -      -       -      +
    115B  HIS*     4.8     5.8    -      -       -      -
    116B  GLY      2.8    31.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 106 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105B  ALA*     1.3    77.4    -      -       -      +
    107B  MET*     1.3    64.3    +      -       -      +
    113B  LEU*     4.5    17.9    -      -       -      +
    114B  VAL      3.4     7.1    +      -       -      -
    115B  HIS*     4.5    11.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 107 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103B  ALA      4.6     1.8    -      -       -      +
    105B  ALA*     3.5    29.2    -      -       +      +
    106B  SER*     1.3    79.5    -      -       -      +
    108B  ARG*     1.3    60.0    +      -       -      +
    109B  ILE*     3.9    18.6    -      -       +      -
    112B  ARG      3.4     1.0    -      -       -      +
    113B  LEU*     3.4     8.0    -      -       -      +
    114B  VAL*     2.7    42.2    +      -       +      +
    116B  GLY*     3.6    23.3    -      -       -      +
    117B  GLN      4.0     2.5    -      -       -      +
    118B  SER*     4.1    19.5    -      -       -      +
    168B  VAL*     3.8    30.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 108 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107B  MET*     1.3    73.3    -      -       -      +
    109B  ILE*     1.3    62.9    +      -       -      +
    110B  GLN      4.2     0.7    +      -       -      -
    111B  GLY*     3.4    34.9    +      -       -      +
    112B  ARG*     3.4     4.3    -      -       -      +
    113B  LEU*     3.5    41.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 109 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107B  MET*     4.0    29.8    -      -       +      -
    108B  ARG*     1.3    78.8    -      -       -      +
    110B  GLN*     1.3    73.9    +      -       +      +
    112B  ARG*     2.9    24.1    +      -       -      +
    114B  VAL*     4.0    19.1    -      -       +      -
    159B  ALA*     3.8    21.3    -      -       +      -
    168B  VAL*     4.5     9.4    -      -       +      -
    203B  K36      3.8    49.5    -      -       +      +
----------------------------------------------------------
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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