Contacts of the helix formed by residues 117 - 128 (chain A) in PDB entry 2P7I


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 ASP 117 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  ILE*     3.6     9.8    -      -       -      +
    116A  ASP*     1.3    79.8    -      -       +      +
    118A  PRO*     1.3    65.0    -      -       -      +
    119A  VAL*     3.7     7.8    +      -       -      +
    120A  ALA*     3.2    35.7    +      -       +      +
    121A  LEU      3.5     8.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  LEU*     3.6    28.1    -      -       +      +
    115A  ILE*     3.5    14.6    -      -       +      +
    116A  ASP      3.4     7.9    -      -       -      +
    117A  ASP*     1.3    89.7    -      -       -      +
    119A  VAL*     1.3    63.9    +      -       +      +
    121A  LEU*     3.2     3.8    +      -       -      +
    122A  LEU*     3.0    27.7    +      -       -      +
    174A  CYS*     6.1     3.1    -      -       +      -
    176A  TYR*     3.2    28.3    -      -       -      +
    184A  ASP*     3.7    10.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  ASP*     3.3     6.8    +      -       -      +
    118A  PRO*     1.3    79.1    -      -       +      +
    120A  ALA*     1.3    58.7    +      -       -      +
    122A  LEU*     3.4     6.2    +      -       -      -
    123A  LYS*     2.8    32.2    +      -       +      +
    184A  ASP*     3.8    41.1    -      -       -      +
    187A  ARG*     4.0    22.9    -      -       +      +
    188A  ALA*     3.7    22.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 120 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  ASP*     3.2    37.1    +      -       +      +
    119A  VAL*     1.3    74.7    -      -       -      +
    121A  LEU*     1.3    63.0    +      -       -      +
    123A  LYS*     3.5     8.1    +      -       -      +
    124A  ARG*     3.1    27.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 121 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  LEU*     4.9     2.0    -      -       +      -
     94A  PHE*     3.8    41.1    -      -       +      -
    108A  LEU*     4.1    28.3    -      -       +      -
    112A  LEU*     4.2     2.9    -      -       +      -
    115A  ILE*     3.8    34.3    -      -       +      -
    117A  ASP      3.5     7.5    +      -       -      +
    118A  PRO      3.2     8.3    +      -       -      +
    120A  ALA*     1.3    75.4    -      -       -      +
    122A  LEU*     1.3    66.4    +      -       -      +
    124A  ARG*     3.3    10.0    +      -       +      +
    125A  ILE*     3.1    29.0    +      -       +      +
    129A  TRP*     4.2    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 122 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  LEU*     4.0    26.7    -      -       +      -
    112A  LEU*     3.8    24.9    -      -       +      -
    118A  PRO      3.0    18.6    +      -       -      +
    119A  VAL      3.8     0.2    -      -       -      +
    121A  LEU*     1.3    77.3    -      -       -      +
    123A  LYS*     1.3    57.3    +      -       -      +
    125A  ILE*     3.3    14.6    +      -       +      +
    126A  ASN*     2.9    27.4    +      -       -      +
    136A  LEU*     4.2    16.4    -      -       +      -
    138A  LEU*     4.2    11.7    -      -       +      -
    184A  ASP*     3.8    10.8    -      -       +      +
    185A  ALA*     3.8    30.5    -      -       -      +
    188A  ALA*     3.4    16.6    -      -       +      +
    190A  LEU*     4.0     7.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 123 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119A  VAL*     2.8    21.9    +      -       +      +
    120A  ALA*     3.7     9.0    -      -       -      +
    121A  LEU      3.2     0.2    -      -       -      -
    122A  LEU*     1.3    73.3    -      -       -      +
    124A  ARG*     1.3    59.9    +      -       -      +
    127A  ASP*     2.8    52.7    +      -       -      +
    187A  ARG      5.8     1.1    -      -       -      +
    188A  ALA*     3.5    28.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 124 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  PHE      2.9    26.9    +      -       -      -
     95A  GLU*     3.3    22.4    +      -       -      +
     96A  ASP      4.5     0.2    -      -       -      -
     97A  ALA      3.4    22.2    +      -       -      -
     98A  GLN*     5.0     6.1    +      -       -      +
    120A  ALA      3.1    19.0    +      -       -      +
    121A  LEU*     3.5    12.1    -      -       +      +
    123A  LYS*     1.3    71.6    -      -       -      +
    125A  ILE*     1.3    61.2    +      -       -      +
    127A  ASP*     4.9     0.2    -      -       -      -
    128A  ASP*     2.9    52.1    +      -       -      +
    129A  TRP*     3.3    43.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 125 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  LEU*     3.7    31.4    -      -       +      -
    106A  ILE*     3.9    19.3    -      -       +      -
    108A  LEU*     4.0    23.3    -      -       +      -
    121A  LEU*     3.1    17.5    +      -       +      +
    122A  LEU*     3.4    19.3    -      -       +      +
    124A  ARG*     1.3    77.0    -      -       -      +
    126A  ASN*     1.3    63.4    +      -       -      +
    129A  TRP*     3.4    15.0    +      -       +      -
    130A  LEU*     3.0    40.5    +      -       +      +
    136A  LEU*     4.1    26.7    -      -       +      -
    190A  LEU*     4.6     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 126 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122A  LEU      2.9    16.9    +      -       -      +
    123A  LYS      3.3     4.2    +      -       -      +
    124A  ARG      3.2     0.2    -      -       -      -
    125A  ILE*     1.3    79.2    -      -       -      +
    127A  ASP*     1.3    81.6    +      -       -      +
    130A  LEU*     4.4     5.9    -      -       -      +
    188A  ALA      3.9     9.2    +      -       -      +
    189A  GLY*     3.3    22.7    +      -       -      +
    190A  LEU*     3.5    18.4    -      -       +      +
    245A  LYS*     3.3    32.0    -      -       -      +
    246A  GLY      2.9    35.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 127 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  ARG*     5.1     2.8    +      -       -      -
    123A  LYS*     2.8    57.0    +      -       -      +
    126A  ASN*     1.3    97.2    +      -       -      +
    128A  ASP*     1.3    72.6    +      -       -      +
    130A  LEU      5.8     0.7    -      -       -      -
    188A  ALA      4.5     0.9    -      -       -      +
    245A  LYS*     4.8    10.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 128 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  ARG*     2.8    38.1    +      -       -      +
    124A  ARG*     2.9    41.1    +      -       -      +
    127A  ASP*     1.3    91.3    -      -       -      +
    129A  TRP*     1.3    76.0    +      -       +      +
    130A  LEU      3.8     1.6    -      -       -      -
----------------------------------------------------------
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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