Contacts of the strand formed by residues 742 - 747 (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 VAL 742 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    607B  ARG*     6.1     0.2    -      -       -      -
    609B  MET*     3.4    14.4    -      -       +      +
    611B  ILE*     3.6    34.1    -      -       +      -
    716B  ALA*     3.8    27.1    -      -       +      -
    735B  LEU*     4.2     6.1    -      -       +      -
    736B  PRO*     3.3    36.2    -      -       +      +
    739B  MET*     3.8    28.2    +      -       +      +
    740B  GLU      3.3     4.1    -      -       -      +
    741B  GLY*     1.3    82.9    -      -       -      +
    743B  ALA*     1.3    64.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 743 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    607B  ARG*     3.3    38.8    -      -       +      +
    609B  MET      2.9     9.3    +      -       -      +
    610B  LEU*     3.5     9.7    -      -       +      -
    611B  ILE*     2.8    31.0    +      -       -      +
    736B  PRO*     3.9    10.1    -      -       -      -
    741B  GLY      4.1     0.2    +      -       -      -
    742B  VAL*     1.3    75.5    -      -       -      +
    744B  ASN*     1.3    61.9    +      -       -      +
    745B  VAL      4.0     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 744 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    607B  ARG*     5.7     0.2    +      -       -      -
    611B  ILE*     3.7    17.9    -      -       -      +
    613B  THR*     5.5     0.3    -      -       -      +
    733B  THR*     2.8    53.4    +      -       -      +
    736B  PRO*     3.7    13.9    -      -       +      +
    737B  GLU*     5.0     2.8    +      -       -      -
    743B  ALA*     1.3    75.9    -      -       -      +
    745B  VAL*     1.3    60.0    +      -       -      +
    764B  ASP*     3.4     2.6    -      -       -      +
    765B  GLY*     2.6    48.0    +      -       -      +
    766B  ALA*     3.6    10.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 745 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    607B  ARG*     4.2    20.6    -      -       -      +
    610B  LEU*     3.7    36.6    -      -       +      -
    611B  ILE      3.0    19.4    +      -       -      +
    612B  ILE*     3.9    12.8    -      -       +      -
    613B  THR*     3.1    14.4    +      -       -      -
    623B  TYR*     5.3     0.2    -      -       +      -
    743B  ALA      3.9     0.2    +      -       -      -
    744B  ASN*     1.3    78.3    -      -       -      +
    746B  HIS*     1.3    63.9    +      -       -      +
    762B  VAL*     3.7    22.4    -      -       +      -
    763B  GLN      3.2    15.3    -      -       -      +
    764B  ASP*     4.0    10.3    -      -       -      +
    765B  GLY      3.2     5.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 746 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    612B  ILE*     4.6     2.7    -      -       -      -
    613B  THR*     3.1    25.4    -      -       -      +
    745B  VAL*     1.3    76.5    -      -       -      +
    747B  LEU*     1.3    77.3    +      -       -      +
    748B  ASP*     3.9     9.7    -      -       +      +
    761B  SER      3.6     0.9    -      -       -      +
    762B  VAL*     3.6     7.4    -      -       -      +
    763B  GLN*     3.0    51.6    +      -       +      +
    764B  ASP      3.6    15.3    -      -       -      -
    765B  GLY      2.6    20.3    +      -       -      +
    766B  ALA      2.7    20.8    +      -       -      -
    767B  ALA*     3.8    11.4    -      -       +      +
    768B  SER*     4.9     5.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 747 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    612B  ILE*     4.5     6.5    -      -       +      -
    613B  THR      3.0     6.6    +      -       -      +
    614B  GLY*     3.5     6.8    -      -       -      -
    615B  PRO*     3.3    33.8    -      -       +      +
    616B  ASN      5.6     0.4    -      -       -      +
    619B  GLY*     4.0    15.5    -      -       -      +
    620B  LYS*     3.2    46.9    -      -       +      +
    623B  TYR*     5.9     0.4    -      -       +      -
    746B  HIS*     1.3    81.5    -      -       -      +
    748B  ASP*     1.3    63.0    +      -       -      +
    759B  MET      3.2    24.9    -      -       -      +
    760B  HIS*     3.9    20.9    -      -       -      +
    761B  SER      3.9     8.7    -      -       -      +
    762B  VAL*     5.0     9.4    -      -       +      +
    767B  ALA*     4.6     2.4    -      -       -      +
----------------------------------------------------------
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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