Contacts of the strand formed by residues 700 - 703 (chain D) in PDB entry 4OIN


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 700 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    642D  CYS*     4.1    16.2    -      -       -      -
    644D  LEU*     4.4     6.7    -      -       +      -
    653D  PHE*     3.8    31.2    -      -       +      -
    699D  VAL*     1.3    78.7    -      -       -      +
    701D  LEU*     1.3    64.2    +      -       -      +
    702D  LEU*     3.7     2.7    +      -       +      -
    715D  ALA*     3.4     2.1    -      -       -      -
    716D  PHE*     2.9    34.8    +      -       -      +
    718D  PRO*     4.0    17.9    -      -       +      +
    747D  VAL*     3.7    27.8    -      -       +      -
    748D  HIS      3.6    10.3    -      -       -      +
    749D  VAL*     4.2     9.6    -      -       +      -
    750D  PRO*     4.3     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 701 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1032C  PHE*     5.5     1.3    -      -       +      -
   1040C  LEU*     4.6     3.4    -      -       +      -
   1048C  THR*     3.7    30.1    -      -       +      -
   1052C  MET*     4.2    16.4    -      -       +      -
    700D  VAL*     1.3    70.3    -      -       -      +
    702D  LEU*     1.3    62.9    +      -       -      +
    703D  ASN      4.0     0.2    +      -       -      -
    713D  ILE*     4.0    14.4    -      -       +      -
    714D  GLN      3.5     2.5    -      -       -      +
    715D  ALA*     3.8    23.1    -      -       +      -
    746D  ALA      3.5     1.0    -      -       -      +
    747D  VAL*     3.3     5.9    -      -       -      -
    748D  HIS*     2.9    50.4    +      -       +      +
    750D  PRO*     4.1     9.0    -      -       +      -
    759D  ALA*     4.0    15.5    -      -       +      -
    763D  MET*     3.7    28.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 702 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    642D  CYS*     3.7    35.4    -      -       +      -
    644D  LEU*     5.5     0.7    -      -       +      -
    700D  VAL*     3.7     2.2    +      -       +      +
    701D  LEU*     1.3    73.3    -      -       -      +
    703D  ASN*     1.3    59.7    +      -       -      +
    713D  ILE*     3.2     4.6    -      -       -      -
    714D  GLN      2.9    32.4    +      -       -      -
    716D  PHE*     3.9    20.0    -      -       +      -
    726D  ILE*     4.0    24.2    -      -       +      -
    728D  LEU*     3.8    22.9    -      -       +      -
    736D  PHE*     3.8     6.3    -      -       +      -
    745D  MET*     4.5    12.1    -      -       +      -
    746D  ALA      3.4     7.4    -      -       -      +
    747D  VAL*     3.8    32.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 703 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1031C  ARG      5.4     1.4    -      -       -      +
   1036C  GLU*     3.5    21.6    -      -       -      +
    702D  LEU*     1.3    76.8    -      -       -      +
    704D  ARG*     1.3    69.4    +      -       -      +
    705D  ALA*     4.8     2.6    +      -       -      +
    707D  THR*     3.0    23.8    +      -       -      -
    712D  GLY      2.8    23.9    +      -       -      +
    713D  ILE*     3.4    21.6    -      -       +      +
    736D  PHE*     4.5     0.2    -      -       -      -
    745D  MET*     3.4     8.5    -      -       -      +
    746D  ALA*     2.9    44.1    +      -       +      +
    748D  HIS*     4.6    15.1    +      -       +      -
----------------------------------------------------------
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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