Contacts of the strand formed by residues 601 - 606 (chain C) in PDB entry 4OIR


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 GLY 601 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    599C  GLU      3.8     0.4    +      -       -      -
    600C  ASP*     1.3    76.8    -      -       -      +
    602C  GLU*     1.3    60.1    +      -       -      -
    613C  VAL*     5.2     0.9    -      -       -      -
    614C  ARG      3.4    11.2    -      -       -      -
    615C  TYR*     4.0     8.1    -      -       -      -
    616C  GLU*     4.5     8.5    -      -       -      +
    648C  ARG*     3.8     3.3    -      -       -      +
    649C  VAL*     2.8    40.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 602 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    601C  GLY*     1.3    75.2    -      -       -      +
    603C  VAL*     1.3    67.8    +      -       -      +
    604C  ALA*     3.5     1.1    +      -       -      -
    613C  VAL*     3.8     2.3    -      -       -      +
    614C  ARG*     2.8    41.2    +      -       +      +
    646C  GLY*     3.4    34.9    -      -       -      +
    647C  GLN      3.7     3.8    -      -       -      +
    648C  ARG*     4.7     9.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 603 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    602C  GLU*     1.3    73.7    -      -       -      +
    604C  ALA*     1.3    63.3    +      -       -      +
    605C  LYS      3.7    21.5    -      -       -      +
    606C  VAL*     3.7    18.4    -      -       +      -
    611C  ILE*     4.2     6.1    -      -       +      -
    612C  VAL      3.8     6.3    -      -       -      +
    613C  VAL*     4.2    11.7    -      -       +      -
    643C  VAL*     4.0    19.1    -      -       +      -
    644C  VAL      3.9    11.9    -      -       -      +
    645C  VAL*     4.3     0.2    -      -       -      +
    646C  GLY*     2.8    30.5    +      -       -      -
    647C  GLN      3.2    18.8    +      -       -      +
    649C  VAL*     3.9    22.9    -      -       +      -
    655C  LEU*     4.3     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 604 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133A  GLU*     4.7     0.3    -      -       -      +
    602C  GLU*     3.5     5.3    +      -       -      +
    603C  VAL*     1.3    72.3    -      -       -      +
    605C  LYS*     1.3    66.4    +      -       +      +
    612C  VAL*     2.8    29.2    +      -       +      +
    614C  ARG*     4.6    13.5    -      -       +      +
    620C  LEU*     4.8    11.7    -      -       +      -
    645C  VAL*     3.5    21.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 605 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133A  GLU*     3.1    16.2    -      -       +      +
    603C  VAL*     3.6     2.8    -      -       -      +
    604C  ALA*     1.3    87.5    -      -       +      +
    606C  VAL*     1.3    68.5    +      -       -      +
    610C  ARG*     3.3    32.5    -      -       -      +
    611C  ILE*     3.4     3.5    -      -       -      -
    612C  VAL*     2.9    53.4    +      -       +      +
    620C  LEU*     6.5     0.9    -      -       -      -
    645C  VAL*     4.7     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 606 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  GLY      4.5     2.6    -      -       -      +
     72A  LYS*     3.7    31.9    -      -       +      +
    131A  THR*     6.3     0.4    -      -       +      -
    133A  GLU*     2.4    40.8    +      -       -      +
    603C  VAL*     3.7     9.0    -      -       +      -
    605C  LYS*     1.3    75.3    -      -       -      +
    607C  ASP*     1.3    61.8    +      -       -      +
    610C  ARG      3.9     1.8    -      -       -      -
    611C  ILE*     4.7     2.7    -      -       +      +
    641C  PRO*     4.1    12.8    -      -       +      -
    643C  VAL*     3.6    45.8    -      -       +      +
    644C  VAL*     3.7    12.8    -      -       +      -
    645C  VAL*     3.9    11.1    -      -       +      +
----------------------------------------------------------
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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