Contacts of the helix formed by residues 377 - 388 (chain B) in PDB entry 2VIG


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 PRO 377 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    289B  CYS*     4.0    20.4    -      -       +      -
    375B  GLU      4.8     0.4    -      -       -      +
    376B  MET*     1.3    93.7    -      -       +      +
    378B  ALA*     1.3    63.0    +      -       -      +
    379B  GLU      3.4     0.9    -      -       -      -
    380B  ARG*     3.3    33.3    +      -       +      +
    381B  HIS*     3.1    40.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 378 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    289B  CYS*     4.4     6.9    -      -       -      -
    360B  SER*     4.7     1.9    -      -       -      +
    363B  ALA*     4.4     6.7    -      -       +      -
    364B  ILE*     3.9    28.8    -      -       +      +
    367B  LEU*     3.8    27.1    -      -       +      -
    371B  GLY*     4.3     4.3    -      -       -      +
    376B  MET*     3.3     2.4    -      -       +      -
    377B  PRO*     1.3    79.5    -      -       -      +
    379B  GLU*     1.3    63.1    +      -       -      +
    381B  HIS*     3.1    23.2    +      -       -      +
    382B  TYR*     3.1    13.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 379 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  LEU*     3.3    35.7    -      -       +      +
    234A  ARG*     5.5     1.4    +      -       -      -
     61B  ASP*     4.7     0.3    -      -       -      +
    364B  ILE*     4.0     8.1    -      -       -      -
    371B  GLY      3.4    18.5    +      -       -      +
    372B  TYR      4.6     2.5    -      -       -      +
    373B  VAL      3.7    25.8    -      -       -      +
    374B  THR*     3.6    26.5    -      -       -      +
    376B  MET      4.3     4.2    +      -       -      +
    378B  ALA*     1.3    78.5    -      -       -      +
    380B  ARG*     1.3    66.5    +      -       -      +
    382B  TYR*     3.5     2.6    +      -       -      +
    383B  ARG*     2.9    65.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 380 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54B  PHE*     6.3     1.0    -      -       -      -
     57B  ALA*     3.5    37.0    +      -       -      +
     58B  ALA*     4.3    10.4    -      -       -      +
     61B  ASP*     3.6    34.1    -      -       -      +
    107B  ARG      6.0     0.2    +      -       -      -
    108B  GLY      4.8     4.0    +      -       -      -
    109B  CYS*     5.2     5.5    -      -       -      +
    110B  ALA      5.3     1.4    -      -       -      +
    376B  MET      5.5     0.2    -      -       -      +
    377B  PRO*     3.3    35.4    +      -       +      +
    378B  ALA      3.2     0.4    -      -       -      -
    379B  GLU*     1.3    83.1    -      -       -      +
    381B  HIS*     1.3    77.9    +      -       -      +
    383B  ARG*     3.4    22.3    +      -       -      +
    384B  ASP*     3.0    45.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 381 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54B  PHE*     6.4     0.4    -      +       -      -
    107B  ARG      5.4     1.6    -      -       -      -
    282B  ILE*     3.6    12.1    -      -       +      +
    285B  THR*     3.3    36.4    +      -       +      +
    286B  ALA*     3.8    35.0    -      -       +      -
    289B  CYS*     4.8     3.9    -      -       +      +
    360B  SER*     3.8     5.8    -      -       -      -
    377B  PRO*     3.1    43.3    +      -       +      +
    378B  ALA*     3.1    11.7    +      -       +      +
    380B  ARG*     1.3   102.1    +      -       -      +
    382B  TYR*     1.3    56.9    +      -       -      +
    384B  ASP*     4.5     4.4    +      -       -      +
    385B  ALA*     2.9    34.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 382 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  LEU*     4.1    13.2    -      -       +      -
    357A  THR*     3.9     7.4    +      -       -      +
    382A  TYR*     3.2    56.3    +      +       -      -
    383A  ARG*     5.9     0.7    -      -       +      -
    386A  ARG*     3.7    26.0    -      -       +      +
    357B  THR*     4.2     5.3    +      -       +      -
    360B  SER*     3.3    23.0    -      -       -      +
    361B  HIS*     3.4    47.4    -      +       +      -
    364B  ILE*     3.5    28.0    -      -       +      -
    378B  ALA      3.1     5.3    +      -       -      +
    379B  GLU      3.6     5.6    -      -       -      +
    380B  ARG      3.2     0.2    -      -       -      -
    381B  HIS*     1.3    77.6    -      -       -      +
    383B  ARG*     1.3    62.8    +      -       +      +
    385B  ALA*     3.8     2.6    +      -       -      +
    386B  ARG*     3.5    20.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 383 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  LEU*     3.7    21.5    -      -       +      -
    234A  ARG*     5.6     1.9    -      -       -      +
    372A  TYR*     2.8    31.5    +      -       -      -
    382A  TYR*     5.8     1.3    -      -       +      -
    383A  ARG*     4.4     2.9    -      -       +      +
     61B  ASP*     2.9    41.2    +      -       -      -
    231B  LEU*     3.0    56.1    +      -       +      +
    232B  GLY*     4.1     2.6    -      -       -      -
    234B  ARG*     3.1    24.6    -      -       -      +
    374B  THR*     5.7     0.2    -      -       -      +
    379B  GLU*     2.9    45.6    +      -       -      +
    380B  ARG*     3.4    16.7    -      -       -      +
    381B  HIS      3.3     0.2    -      -       -      -
    382B  TYR*     1.3    79.5    -      -       +      +
    384B  ASP*     1.3    56.8    +      -       -      +
    386B  ARG*     3.6     7.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 384 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    372A  TYR*     3.9     4.0    -      -       -      -
     61B  ASP*     4.6     3.6    -      -       -      +
    110B  ALA*     3.5    33.6    +      -       +      +
    111B  SER*     5.9     0.2    -      -       -      -
    232B  GLY*     3.6     4.0    -      -       -      -
    233B  ILE*     2.8    27.6    +      -       +      +
    282B  ILE*     3.9    12.8    -      -       +      +
    380B  ARG*     3.0    44.8    +      -       -      +
    381B  HIS*     3.9     6.8    +      -       -      +
    383B  ARG*     1.3    72.3    -      -       -      +
    385B  ALA*     1.3    63.4    -      -       -      +
    386B  ARG      3.1     2.2    +      -       -      -
    387B  ILE*     3.2    25.1    -      -       -      +
    388B  THR*     4.1     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 385 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282B  ILE*     3.9    14.5    -      -       +      +
    356B  ALA*     3.5    37.9    -      -       +      +
    357B  THR*     3.9     9.5    +      -       -      +
    360B  SER*     3.7     7.2    -      -       -      +
    381B  HIS      2.9    18.7    +      -       -      +
    382B  TYR      3.8     2.5    -      -       -      +
    384B  ASP*     1.3    75.7    -      -       -      +
    386B  ARG*     1.3    62.7    +      -       -      +
    388B  THR*     2.7    28.3    +      -       -      -
    389B  GLU*     4.0     1.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 386 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    361A  HIS*     2.9    45.1    +      -       -      -
    364A  ILE*     3.5    21.4    -      -       +      +
    365A  GLN*     2.9    42.4    +      -       -      +
    372A  TYR*     4.0     7.2    -      -       +      -
    382A  TYR*     3.6    31.0    -      -       +      +
    231B  LEU*     4.1    13.9    -      -       +      -
    357B  THR*     3.9     5.2    -      -       -      -
    382B  TYR      3.5    10.4    +      -       -      +
    383B  ARG      3.7    12.3    -      -       -      +
    384B  ASP      3.1     1.4    -      -       -      -
    385B  ALA*     1.3    78.7    -      -       -      +
    387B  ILE*     1.3    62.9    +      -       -      +
    388B  THR      3.4     0.5    +      -       -      -
    389B  GLU*     3.5    23.9    +      -       -      +
    390B  ILE*     3.7    10.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 387 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    372A  TYR*     3.4    34.0    -      -       +      +
    233B  ILE*     3.9    19.5    -      -       +      -
    278B  GLN*     5.0     0.2    -      -       -      +
    384B  ASP      3.2    17.3    +      -       -      +
    386B  ARG*     1.3    77.5    -      -       -      +
    388B  THR*     1.3    63.5    +      -       +      +
    390B  ILE*     2.8    30.7    +      -       +      -
    391B  TYR*     3.1    55.2    +      -       +      +
    501B  FAD      3.5    40.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 388 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    275B  ILE*     4.1     9.2    -      -       +      -
    278B  GLN*     3.6    24.5    -      -       -      +
    279B  ALA*     4.0    15.6    -      -       +      +
    282B  ILE*     4.1    14.8    -      -       +      -
    349B  LYS*     2.6    34.9    +      -       -      -
    353B  SER*     3.3    29.3    +      -       -      -
    356B  ALA*     4.3     1.7    -      -       -      +
    384B  ASP      4.1     5.2    -      -       -      +
    385B  ALA      2.7    20.8    +      -       -      +
    387B  ILE*     1.3    84.2    -      -       +      +
    389B  GLU*     1.3    50.2    +      -       -      +
    390B  ILE      3.2     1.1    -      -       -      -
    391B  TYR*     3.9     8.1    -      -       +      -
----------------------------------------------------------
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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