Contacts of the strand formed by residues 79 - 91 (chain B) in PDB entry 2X5Q


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 79 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57B  VAL*     4.0    17.5    -      -       +      -
     58B  LEU      3.1    14.6    -      -       -      +
     59B  THR*     3.9    11.2    -      -       +      -
     61B  TYR      3.2     9.0    +      -       -      -
     76B  PRO      5.7     0.9    -      -       -      -
     77B  CYS      3.7    12.3    -      -       -      -
     78B  ASP*     1.3    74.4    -      -       -      +
     80B  VAL*     1.3    58.8    +      -       -      +
     81B  LYS*     3.4    25.3    +      -       +      -
    142B  PHE*     3.5    14.6    -      -       -      -
    186B  ASN*     2.9    42.0    +      -       -      -
    187B  TYR*     4.1     2.9    -      -       -      -
    188B  TYR*     2.8    51.3    +      +       -      +
----------------------------------------------------------
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Residues in contact with VAL 80 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  PHE*     3.6     5.7    -      -       +      -
     14B  PRO*     4.0    15.7    -      -       +      -
     15B  ILE      5.2     0.9    -      -       -      +
     16B  THR*     5.3     1.1    -      -       +      -
     58B  LEU*     2.9    35.5    +      -       +      +
     61B  TYR      3.7     3.4    -      -       -      +
     62B  ALA*     3.6    10.5    -      -       -      -
     63B  ILE*     3.6    35.2    -      -       +      +
     70B  LEU*     3.9    26.2    -      -       +      -
     79B  TYR*     1.3    80.1    -      -       -      +
     81B  LYS*     1.3    74.8    +      -       -      +
    187B  TYR*     4.0    13.9    -      -       +      -
    188B  TYR      3.9     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 81 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  PHE*     3.7     2.5    -      -       -      -
     14B  PRO*     3.9     0.7    -      -       -      +
     15B  ILE      3.3    21.0    +      -       -      +
     55B  ILE*     4.2     2.9    -      -       +      -
     56B  LEU      3.3     5.2    -      -       -      +
     57B  VAL*     4.1    27.1    -      -       +      -
     79B  TYR*     3.4    23.1    +      -       +      -
     80B  VAL*     1.3    84.1    -      -       -      +
     82B  GLY*     1.3    59.6    +      -       -      +
    108B  ILE*     4.9     5.9    -      -       +      +
    183B  GLU      5.1     0.6    +      -       -      -
    184B  ILE*     2.8    38.4    +      -       +      +
    185B  PHE*     3.8    19.9    -      -       +      -
    186B  ASN*     3.1    38.2    +      -       -      +
    187B  TYR*     4.4     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 82 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  PHE*     3.4    13.6    -      -       -      -
     13B  LEU      3.3    13.2    -      -       -      -
     15B  ILE*     4.3     0.9    -      -       -      -
     55B  ILE*     3.3     7.8    -      -       -      +
     56B  LEU*     2.9    34.1    +      -       -      -
     81B  LYS*     1.3    78.1    -      -       -      +
     83B  ILE*     1.3    65.9    +      -       -      -
    185B  PHE*     3.7     7.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 83 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  VAL      3.4     1.6    -      -       -      +
     12B  PHE*     3.6     2.5    -      -       -      -
     13B  LEU*     2.8    53.0    +      -       +      +
     15B  ILE*     4.6     7.2    -      -       +      -
     45B  SER*     3.3    19.7    -      -       -      +
     52B  LEU*     4.5    14.6    -      -       +      -
     55B  ILE*     4.8     2.7    -      -       +      -
     82B  GLY*     1.3    78.3    -      -       -      +
     84B  LEU*     1.3    61.4    +      -       -      +
     85B  ILE*     3.7    22.4    -      -       +      -
    157B  VAL*     5.7     0.2    -      -       +      -
    158B  LEU*     4.2    16.6    -      -       +      -
    161B  ILE*     4.0    20.4    -      -       +      -
    162B  TYR*     4.1     7.9    -      -       +      +
    185B  PHE*     3.9    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 84 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  GLN*     3.3     8.5    -      -       +      +
     11B  VAL      3.4     2.9    -      -       -      +
     12B  PHE*     3.9    17.7    -      -       +      -
     44B  VAL*     3.3    34.8    +      -       +      -
     45B  SER*     2.8    30.5    +      -       -      -
     54B  ASN      5.2     2.7    -      -       -      +
     56B  LEU*     4.1    31.0    -      -       +      -
     82B  GLY      4.3     0.2    +      -       -      -
     83B  ILE*     1.3    73.8    -      -       -      +
     85B  ILE*     1.3    64.5    +      -       -      +
    105B  LEU*     4.8     9.4    -      -       +      -
    107B  ILE*     4.9     5.2    -      -       +      -
    117B  ILE*     4.7    15.5    -      -       +      -
    119B  PHE*     3.8    37.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 85 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  GLN*     3.1     9.2    +      -       -      -
     11B  VAL*     2.8    48.7    +      -       +      +
     13B  LEU*     3.7    31.4    -      -       +      -
     35B  ILE*     4.4     2.9    -      -       +      -
     37B  TYR*     3.5    31.2    -      -       +      -
     43B  HIS*     3.4    17.0    -      -       +      +
     83B  ILE*     3.7    16.2    -      -       +      -
     84B  LEU*     1.3    79.5    -      -       -      +
     86B  SER*     1.3    61.7    +      -       -      +
     87B  GLY      3.4     0.2    +      -       -      -
    161B  ILE*     4.1    11.2    -      -       +      -
    162B  TYR*     3.4    21.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 86 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  GLU*     3.0    33.4    +      -       -      +
      9B  GLU      3.6    10.9    +      -       -      -
     10B  GLN*     3.5     7.6    +      -       -      +
     37B  TYR*     3.5     6.2    -      -       -      +
     38B  ASN*     2.9    37.1    +      -       -      -
     41B  GLY*     3.7     9.6    -      -       -      -
     42B  GLN      3.6    12.3    -      -       -      -
     43B  HIS*     2.9    18.3    +      -       -      -
     85B  ILE*     1.3    70.1    -      -       -      +
     87B  GLY*     1.3    57.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 87 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  GLU*     3.8    11.4    +      -       -      +
     10B  GLN      4.6     0.2    -      -       -      -
     11B  VAL*     3.3    19.1    -      -       -      +
     36B  GLU*     3.0    14.8    -      -       -      -
     37B  TYR*     4.0     2.0    -      -       -      -
     38B  ASN*     3.4    18.7    +      -       -      +
     85B  ILE      3.4     3.4    +      -       -      -
     86B  SER*     1.3    75.0    +      -       -      +
     88B  LYS*     1.3    68.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 88 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  VAL*     3.8     8.9    -      -       -      +
     35B  ILE*     3.4     4.0    -      -       -      -
     36B  GLU*     2.8    50.7    +      -       +      +
     38B  ASN*     5.8     2.9    -      -       -      +
     87B  GLY*     1.3    77.6    -      -       -      +
     89B  ILE*     1.3    64.4    +      -       -      +
     90B  LEU*     3.2     8.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 89 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  VAL*     3.9    15.0    -      -       +      +
     33B  VAL*     4.7     2.0    -      -       +      -
     34B  SER      3.8     5.8    -      -       -      +
     35B  ILE*     4.4    13.0    -      -       +      -
     88B  LYS*     1.3    71.5    -      -       -      +
     90B  LEU*     1.3    61.6    +      -       -      +
     91B  LYS      3.3    22.7    -      -       -      +
     92B  GLY*     3.7    20.3    -      -       -      +
     93B  ASN      4.2     2.0    -      -       -      +
     94B  HIS*     3.5    36.3    +      -       +      +
    120B  SER*     4.0    14.8    -      -       -      +
    121B  LEU      3.6    26.9    -      -       -      -
    122B  PRO*     3.6    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 90 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  GLN*     3.4    38.8    -      -       +      +
     34B  SER      2.9    11.9    +      -       -      +
     35B  ILE      4.6     0.2    -      -       -      -
     36B  GLU*     3.4    46.4    -      -       +      +
     88B  LYS*     3.2    10.9    +      -       +      +
     89B  ILE*     1.3    73.5    -      -       -      +
     91B  LYS*     1.3    60.7    +      -       +      +
     92B  GLY      5.3     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 91 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30B  GLY      5.4     0.4    -      -       -      -
     31B  SER      3.1    27.9    +      -       -      -
     32B  SER*     3.4    14.3    -      -       -      +
     33B  VAL*     3.2    18.1    -      -       -      +
     34B  SER*     3.2    30.5    +      -       -      +
     89B  ILE*     3.3    11.9    -      -       -      +
     90B  LEU*     1.3    81.0    -      -       +      +
     92B  GLY*     1.3    64.1    +      -       -      +
----------------------------------------------------------
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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