Contacts of the strand formed by residues 578 - 583 (chain A) 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 ILE 578 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    577A  GLY*     1.3    79.2    -      -       -      +
    579A  ARG*     1.3    67.5    +      -       -      +
    580A  ILE*     4.0    23.1    -      -       +      -
    601A  LEU*     3.6    10.3    -      -       +      +
    602A  ASN*     3.3     2.6    +      -       -      -
    603A  LEU*     2.7    49.5    +      -       +      +
    627A  THR*     3.9    24.5    -      -       +      +
    630A  ILE*     5.4     3.6    -      -       +      -
    631A  ALA*     5.1     2.7    -      -       +      -
    645A  VAL*     5.2     3.8    -      -       +      -
    646A  GLU      3.4     8.3    -      -       -      +
    647A  ILE*     4.2    19.1    -      -       +      -
    650A  ILE*     4.5    11.2    -      -       +      -
    689A  LEU*     4.3    17.7    -      -       +      -
    722A  LEU*     4.0    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 579 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    573A  ILE*     4.2    23.3    -      -       +      +
    577A  GLY      5.5     0.7    -      -       -      -
    578A  ILE*     1.3    79.7    -      -       -      +
    580A  ILE*     1.3    64.5    +      -       -      +
    581A  THR      4.0     0.2    +      -       -      -
    601A  LEU      3.2     6.5    -      -       -      +
    602A  ASN*     3.3    27.1    -      -       -      +
    603A  LEU      4.6     4.9    +      -       -      +
    604A  SER*     5.7     7.1    -      -       -      -
    644A  LYS*     3.7     2.1    -      -       -      +
    645A  VAL*     3.4     5.7    -      -       -      -
    646A  GLU*     2.8    78.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 580 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    578A  ILE*     4.0    16.4    -      -       +      -
    579A  ARG*     1.3    75.5    -      -       -      +
    581A  THR*     1.3    62.5    +      -       -      +
    583A  GLY*     3.4    33.7    -      -       -      +
    599A  ASN      4.5     1.3    -      -       -      +
    600A  PRO*     3.2    10.5    -      -       -      +
    601A  LEU*     2.9    56.5    +      -       +      +
    623A  TYR*     6.4     0.7    -      -       +      -
    626A  GLN*     5.6     3.8    -      -       +      +
    627A  THR*     4.5    12.1    -      -       +      +
    630A  ILE*     3.9    23.1    -      -       +      -
    642A  ALA*     3.8    14.4    -      -       +      -
    644A  LYS      3.5     3.4    -      -       -      +
    645A  VAL*     4.0     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 581 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    579A  ARG      4.0     1.0    +      -       -      -
    580A  ILE*     1.3    71.4    +      -       -      +
    582A  GLU*     1.3    75.7    +      -       +      +
    583A  GLY      3.5     0.4    +      -       -      -
    600A  PRO*     4.9     2.7    -      -       +      -
    642A  ALA*     3.8     0.7    -      -       -      +
    643A  GLN*     3.1    43.9    +      -       -      +
    644A  LYS*     2.9    37.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 582 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    580A  ILE      3.9     0.8    +      -       -      -
    581A  THR*     1.3    88.1    -      -       +      +
    583A  GLY*     1.3    64.7    +      -       -      +
    584A  ARG*     3.9     7.4    +      -       -      -
    598A  ALA*     3.5    39.2    -      -       +      +
    599A  ASN*     3.8    11.9    +      -       -      -
    600A  PRO*     4.4     3.9    -      -       -      +
    642A  ALA*     3.4    13.4    -      -       -      -
    643A  GLN*     3.6    25.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 583 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    580A  ILE*     3.4    24.2    -      -       -      +
    582A  GLU*     1.3    77.2    -      -       -      +
    584A  ARG*     1.3    58.8    +      -       -      -
    598A  ALA*     3.3     6.1    -      -       -      -
    599A  ASN      3.0    24.5    +      -       -      -
    626A  GLN*     2.9    20.2    +      -       -      -
    630A  ILE*     4.2     3.8    -      -       -      -
    641A  PRO      3.7     8.3    -      -       -      -
    642A  ALA*     3.7     0.7    -      -       -      -
----------------------------------------------------------
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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