Contacts of the strand formed by residues 120 - 129 (chain B) in PDB entry 6H25


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 GLN 120 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54B  GLY      3.1    16.5    -      -       -      +
     55B  PRO*     3.5     1.4    -      -       -      +
     56B  HIS*     3.3    51.8    +      -       +      +
     58B  ILE*     4.0    32.9    -      -       +      +
     59B  ARG*     4.5     2.3    +      -       -      +
     64B  ARG*     6.1     0.8    -      -       -      +
     71B  LEU*     3.5    21.1    -      -       +      +
     73B  ASN*     4.0    25.2    -      -       +      +
    118B  ARG      4.3     0.4    +      -       -      -
    119B  SER*     1.3    71.9    -      -       -      +
    121B  ILE*     1.3    67.9    +      -       -      +
    122B  ASP*     5.0     4.6    -      -       -      +
    124B  TYR*     5.7     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 121 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52B  VAL*     4.3     6.5    -      -       +      -
     54B  GLY      4.1     3.4    -      -       -      -
     55B  PRO*     4.0    22.0    -      -       +      -
     70B  ALA*     4.7    17.3    -      -       +      -
     71B  LEU      2.9    11.6    +      -       -      +
     72B  VAL*     3.4    12.4    -      -       +      +
     73B  ASN*     2.9    24.6    +      -       -      +
    111B  ILE*     4.9    15.5    -      -       +      -
    112B  LEU      6.1     0.7    -      -       -      +
    113B  THR*     6.3     0.2    -      -       -      -
    116B  HIS*     5.2     7.0    -      -       +      +
    119B  SER*     5.3     0.4    -      -       -      -
    120B  GLN*     1.3    79.2    -      -       -      +
    122B  ASP*     1.3    69.9    +      -       -      +
    123B  ILE*     4.5    12.3    -      -       +      -
    146B  VAL*     5.8     0.7    -      -       +      -
    151B  ILE*     3.7    45.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 122 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52B  VAL*     3.3    23.7    -      -       -      +
     53B  TYR*     3.1    38.9    +      -       -      +
     54B  GLY      3.6     6.6    +      -       -      +
     56B  HIS*     3.9    18.4    -      -       +      -
     73B  ASN*     3.3    13.7    -      -       +      +
    120B  GLN*     4.1     6.0    -      -       -      +
    121B  ILE*     1.3    72.1    -      -       -      +
    123B  ILE*     1.3    61.7    +      -       -      +
    124B  TYR*     3.2    34.8    -      -       +      +
     91E  PRO*     4.0     6.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 123 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50B  ALA*     5.7     1.1    -      -       +      -
     51B  VAL      3.9     4.3    -      -       -      +
     52B  VAL*     4.6     5.4    -      -       +      -
     72B  VAL*     4.4     7.0    -      -       +      -
     73B  ASN      2.8     9.3    +      -       -      +
     74B  CYS*     3.4    22.7    -      -       +      +
     75B  GLN      3.3    23.4    +      -       -      +
    103B  LEU*     5.4     3.1    -      -       +      -
    107B  PHE*     3.8    40.4    -      -       +      -
    111B  ILE*     5.5     2.5    -      -       +      -
    121B  ILE*     4.5    10.8    -      -       +      -
    122B  ASP*     1.3    77.2    -      -       -      +
    124B  TYR*     1.3    62.6    +      -       -      +
    125B  VAL*     4.1    11.1    +      -       +      +
    142B  ALA*     3.8    27.1    -      -       +      +
    145B  ALA*     6.1     1.1    -      -       +      -
    146B  VAL*     4.2    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 124 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49B  LEU      4.1     0.2    -      -       -      +
     50B  ALA*     3.4     2.8    -      -       -      +
     51B  VAL*     2.9    49.1    +      -       +      +
     53B  TYR*     4.0    15.9    -      +       -      -
     73B  ASN*     5.0    12.8    +      -       -      -
     74B  CYS      6.0     0.2    -      -       -      -
     75B  GLN*     3.3    37.2    -      -       +      +
    120B  GLN*     5.7     1.0    +      -       -      -
    122B  ASP*     3.2    39.5    +      -       +      +
    123B  ILE*     1.3    75.9    -      -       -      +
    125B  VAL*     1.3    60.0    +      -       -      +
    126B  GLN      4.3     0.2    -      -       -      -
     87E  ALA*     3.6    42.6    -      -       +      +
     88E  SER*     4.8     6.7    -      -       -      +
     91E  PRO*     4.0    13.0    -      -       +      +
     94E  GLU*     3.7    18.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 125 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48B  ALA*     5.3     0.9    -      -       +      -
     49B  LEU      3.5    11.0    -      -       -      +
     50B  ALA*     4.3     6.5    -      -       +      -
     75B  GLN      3.5    12.0    +      -       -      +
     76B  TYR*     4.0     9.4    -      -       +      -
     77B  SER*     3.4    25.3    +      -       -      +
    103B  LEU*     5.1     9.9    -      -       +      -
    123B  ILE*     4.2    18.6    -      -       +      +
    124B  TYR*     1.3    79.0    -      -       -      +
    126B  GLN*     1.3    66.6    +      -       -      +
    127B  VAL*     4.8     0.4    -      -       +      -
    138B  CYS*     3.7    50.7    -      -       +      +
    141B  ALA*     5.3     1.3    -      -       +      -
    142B  ALA*     4.3     7.6    -      -       +      -
     88E  SER*     5.6     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 126 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48B  ALA*     3.9     0.2    -      -       -      -
     49B  LEU*     2.8    44.7    +      -       +      +
     77B  SER*     3.4    19.0    +      -       -      +
     78B  SER      5.9     0.2    -      -       -      -
     79B  ALA*     4.9     3.2    -      -       -      +
    124B  TYR      4.3     0.2    -      -       -      -
    125B  VAL*     1.3    74.1    -      -       -      +
    127B  VAL*     1.3    68.0    +      -       -      +
    128B  LEU*     3.9    10.3    -      -       +      +
     84E  ASP*     5.5     0.6    +      -       -      -
     86E  SER*     3.5    14.7    +      -       -      -
     88E  SER*     2.8    28.5    +      -       -      +
    140E  LEU*     2.1    59.3    -      -       +      +
    142E  LEU*     4.5     8.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 127 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46B  THR*     5.3     3.4    -      -       +      -
     47B  LYS      3.7    15.5    -      -       -      +
     48B  ALA*     4.8     4.3    -      -       +      -
     76B  TYR*     4.1    11.7    -      -       +      +
     77B  SER      3.4     5.5    +      -       -      -
     78B  SER*     4.4    12.1    +      -       -      +
     79B  ALA*     3.1    27.4    +      -       -      +
     82B  SER*     4.9     1.5    -      -       -      +
    125B  VAL*     4.8     0.9    -      -       +      -
    126B  GLN*     1.3    76.6    -      -       -      +
    128B  LEU*     1.3    63.1    +      -       -      +
    129B  GLN      3.8     9.9    -      -       -      +
    130B  ALA*     4.2    22.7    -      -       +      +
    134B  THR*     4.0    14.1    -      -       +      -
    137B  ALA*     6.2     0.4    -      -       +      -
    138B  CYS*     3.4    33.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 128 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40B  TYR*     5.4     2.2    -      -       +      -
     47B  LYS*     3.3    25.2    +      -       +      +
     48B  ALA      5.2     0.7    -      -       -      -
     49B  LEU*     3.9    25.8    -      -       +      +
     79B  ALA*     4.5     8.0    -      -       -      +
     81B  PHE*     4.0    22.9    -      -       +      +
     82B  SER*     4.6     5.6    -      -       -      -
    126B  GLN*     3.9    27.4    -      -       +      +
    127B  VAL*     1.3    76.9    -      -       -      +
    129B  GLN*     1.3    61.4    +      -       +      +
     41E  VAL*     5.8     2.5    -      -       +      -
     42E  VAL*     4.2    13.4    -      -       +      +
     59E  LEU*     4.0    31.0    -      -       +      -
    140E  LEU*     5.2     8.7    -      -       +      -
    142E  LEU*     5.3     4.9    -      -       +      -
    289E  PHE*     5.0    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 129 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  ASN*     3.3    25.1    +      -       +      +
     46B  THR*     3.0     9.5    -      -       -      +
     47B  LYS*     2.9    51.7    +      -       +      +
     82B  SER*     4.5     4.9    -      -       -      -
    127B  VAL*     3.7     3.4    -      -       -      +
    128B  LEU*     1.3    81.7    -      -       +      +
    130B  ALA*     1.3    63.0    +      -       -      +
    131B  ASP*     5.8     0.7    -      -       +      -
     42E  VAL*     4.0     6.7    -      -       +      +
     43E  SER*     3.3    47.7    +      -       -      +
     44E  ASN*     3.4    27.7    +      -       +      +
     20J  VAL*     5.4     3.2    +      -       -      +
----------------------------------------------------------
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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