Contacts of the strand formed by residues 609 - 613 (chain B) in PDB entry 1OH7


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 MET 609 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    607B  ARG*     3.6     0.9    -      -       -      +
    608B  ARG*     1.3    82.2    -      -       +      +
    610B  LEU*     1.3    68.4    +      -       -      +
    611B  ILE*     4.1    19.7    -      -       +      -
    712B  ALA*     3.5    38.8    -      -       -      +
    715B  LEU*     3.4    33.4    -      -       +      -
    716B  ALA*     3.9    14.1    -      -       +      +
    721B  ALA      5.7     0.2    -      -       -      +
    723B  THR*     3.2    26.2    -      -       +      +
    725B  PHE*     4.4     5.6    -      -       +      -
    741B  GLY      3.2     3.7    +      -       -      +
    742B  VAL*     3.4    19.4    -      -       +      -
    743B  ALA      2.9    26.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 610 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    601B  LEU*     3.4    33.7    -      -       +      -
    602B  ASN      5.0     1.1    -      -       -      +
    603B  LEU*     3.7    12.8    -      -       +      -
    607B  ARG*     3.5    39.3    -      -       +      +
    609B  MET*     1.3    78.3    -      -       -      +
    611B  ILE*     1.3    62.5    +      -       -      +
    612B  ILE*     3.5     3.0    +      -       +      +
    623B  TYR*     4.5     4.5    -      -       +      +
    723B  THR      2.9     8.9    +      -       -      -
    724B  LEU*     3.5    17.0    -      -       +      -
    725B  PHE*     2.9    26.2    +      -       -      -
    743B  ALA*     3.5    11.2    -      -       +      +
    745B  VAL*     3.7    29.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 611 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    609B  MET*     3.9    21.0    +      -       +      -
    610B  LEU*     1.3    71.4    -      -       -      +
    612B  ILE*     1.3    60.3    +      -       -      +
    613B  THR*     3.7     9.5    +      -       +      +
    712B  ALA*     4.4     0.4    -      -       +      -
    725B  PHE*     3.5    18.8    -      -       +      +
    727B  THR*     3.7    26.5    -      -       +      -
    732B  LEU*     4.0    24.9    -      -       +      +
    735B  LEU*     3.8    23.6    -      -       +      -
    742B  VAL*     3.6    18.8    -      -       +      -
    743B  ALA      2.8    10.0    +      -       -      +
    744B  ASN*     3.7    18.3    -      -       -      +
    745B  VAL      3.0    26.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 612 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    610B  LEU*     3.5    10.3    -      -       +      +
    611B  ILE*     1.3    75.1    -      -       -      +
    613B  THR*     1.3    64.5    +      -       -      +
    620B  LYS*     2.9    41.6    +      -       +      +
    623B  TYR*     4.2    23.8    -      -       +      -
    624B  MET*     4.5     9.9    -      -       +      -
    724B  LEU*     3.9    38.4    -      -       +      -
    725B  PHE      2.9    11.3    +      -       -      +
    726B  ALA*     3.5     8.9    -      -       -      +
    727B  THR      3.1    13.8    +      -       -      -
    745B  VAL*     3.6    18.6    -      -       +      +
    746B  HIS*     4.6     3.8    -      -       -      -
    747B  LEU*     4.5     7.4    -      -       +      -
    762B  VAL*     5.5     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 613 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    611B  ILE*     4.2     4.7    -      -       +      +
    612B  ILE*     1.3    77.8    -      -       -      +
    614B  GLY*     1.3    62.9    +      -       -      +
    620B  LYS*     3.5     5.6    -      -       -      -
    727B  THR*     3.6    28.5    -      -       +      +
    728B  HIS      5.3     2.2    -      -       -      -
    729B  TYR      4.4     4.5    -      -       -      +
    730B  PHE*     4.9     3.8    -      -       -      -
    733B  THR*     3.4    27.1    -      -       +      +
    744B  ASN*     5.5     0.3    +      -       -      -
    745B  VAL      3.1    12.9    +      -       -      +
    746B  HIS*     3.1     4.0    -      -       -      -
    747B  LEU      3.0    22.9    +      -       -      -
    766B  ALA*     3.8     4.3    -      -       -      -
    767B  ALA*     3.0    30.4    +      -       -      -
----------------------------------------------------------
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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