Contacts of the strand formed by residues 495 - 500 (chain G) in PDB entry 1H1V


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 VAL 495 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166A  TYR*     5.3     5.6    -      -       -      +
    167A  GLU*     3.9     8.1    -      -       -      +
    412G  MET*     3.9    27.1    -      -       +      -
    453G  TYR*     5.8     0.2    -      -       -      +
    461G  GLN      3.0     9.4    +      -       -      +
    462G  ILE*     3.1    16.7    -      -       +      +
    463G  ILE*     2.7    31.4    +      -       -      -
    493G  THR      4.6     5.2    -      -       -      +
    494G  PRO*     1.3    76.7    -      -       -      +
    496G  GLN*     1.3    69.6    +      -       -      +
    497G  SER*     5.5     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 496 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148A  THR*     2.7    38.1    +      -       -      +
    149A  THR*     6.0     0.2    -      -       -      +
    167A  GLU*     2.7    44.3    +      -       +      +
    463G  ILE*     3.5     7.9    -      -       +      -
    483G  THR*     3.7    27.7    -      -       +      +
    484G  ALA*     3.6     8.5    +      -       -      +
    487G  ASP*     2.8    40.4    +      -       +      +
    495G  VAL*     1.3    83.6    -      -       -      +
    497G  SER*     1.3    63.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 497 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    462G  ILE*     4.2     9.4    -      -       -      -
    463G  ILE      2.9     8.8    +      -       -      -
    464G  TYR*     3.2    35.5    -      -       -      -
    465G  ASN*     2.9    23.5    +      -       -      +
    483G  THR*     5.5     1.0    -      -       -      +
    495G  VAL*     5.5     0.4    -      -       -      -
    496G  GLN*     1.3    78.4    -      -       -      +
    498G  ARG*     1.3    62.3    +      -       -      +
    499G  VAL*     3.6     9.5    +      -       -      +
    505G  PRO*     4.8     3.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 498 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145A  SER      5.1     3.0    +      -       -      -
    146A  GLY      3.6    20.5    +      -       -      +
    147A  ARG*     3.4    51.4    -      -       -      +
    148A  THR      5.6     0.4    -      -       -      +
    296A  ASN*     4.4     4.4    +      -       -      -
    465G  ASN*     3.7    12.1    -      -       +      +
    467G  GLN*     3.7    28.5    +      -       -      +
    497G  SER*     1.3    73.1    +      -       -      +
    499G  VAL*     1.3    65.1    +      -       -      +
    500G  VAL*     3.7    26.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 499 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    464G  TYR*     3.8     9.0    -      -       +      -
    465G  ASN      3.1     7.6    +      -       -      +
    466G  TRP*     3.3    35.0    -      -       +      +
    467G  GLN*     3.1    21.8    +      -       -      +
    497G  SER*     3.6    22.4    -      -       -      +
    498G  ARG*     1.3    81.5    -      -       -      +
    500G  VAL*     1.3    62.0    +      -       -      +
    503G  LYS      4.4     6.7    -      -       -      +
    504G  GLU*     4.5     4.3    -      -       +      -
    505G  PRO*     3.8    28.5    -      -       +      -
    508G  LEU*     3.6    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 500 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    466G  TRP*     4.6     2.2    -      -       -      -
    467G  GLN*     3.8    15.7    -      -       +      +
    498G  ARG*     3.7    34.8    -      -       -      +
    499G  VAL*     1.3    78.2    -      -       -      +
    501G  GLN*     1.3    76.5    +      -       -      +
    502G  GLY      3.2     0.5    +      -       -      -
    503G  LYS*     3.0    40.6    +      -       +      +
    504G  GLU*     4.1     2.1    +      -       -      -
----------------------------------------------------------
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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