Contacts of the strand formed by residues 962 - 966 (chain B) in PDB entry 1OFD


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 GLN 962 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    898B  LYS*     3.4    34.1    -      -       +      +
    941B  ALA      3.0     5.0    +      -       -      +
    942B  ILE*     3.4    14.7    -      -       +      +
    943B  LYS      3.0    23.3    +      -       -      -
    960B  GLY*     4.0     1.2    -      -       -      -
    961B  LYS*     1.3    83.9    -      -       +      +
    963B  LEU*     1.3    70.9    +      -       -      +
   1029B  ALA*     4.2     1.3    -      -       -      -
   1030B  GLN*     3.3    37.8    +      -       +      +
   1032B  SER*     5.4     2.1    +      -       -      +
   1055B  ILE*     3.4    16.4    -      -       +      +
   1103B  ARG*     3.2    27.5    +      -       -      +
   1124B  GLU*     5.1     2.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 963 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    942B  ILE*     4.7     0.7    -      -       -      -
    943B  LYS*     3.3    22.9    -      -       +      +
    945B  ILE*     3.9     9.9    -      -       +      -
    957B  LEU*     3.6    45.3    -      -       +      +
    960B  GLY*     4.5     4.3    -      -       -      -
    962B  GLN*     1.3    83.2    -      -       -      +
    964B  GLU*     1.3    62.1    +      -       -      +
   1022B  LEU*     4.1    37.2    -      -       +      +
   1025B  ILE*     5.1     0.7    -      -       +      -
   1026B  ASN*     4.4     4.9    -      -       +      -
   1029B  ALA*     4.1    19.7    -      -       +      -
   1030B  GLN      2.9     8.6    +      -       -      +
   1031B  VAL*     3.3    11.2    -      -       +      +
   1032B  SER*     2.8    26.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 964 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    900B  ASN*     3.0    24.3    +      -       -      -
    942B  ILE*     3.7    14.7    -      -       +      +
    943B  LYS      2.9    10.7    +      -       -      +
    944B  GLN*     3.2    24.1    +      -       +      +
    945B  ILE*     2.7    35.2    +      -       -      +
    963B  LEU*     1.3    72.6    -      -       -      +
    965B  ILE*     1.3    70.9    +      -       -      +
    966B  LYS      3.6     0.9    +      -       -      -
   1032B  SER*     3.1    26.2    +      -       -      +
   1034B  LYS*     3.7    26.4    +      -       +      +
   1057B  GLN*     4.0    14.7    +      -       -      +
   1103B  ARG*     3.7    14.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 965 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    945B  ILE*     3.5     5.8    -      -       +      +
    964B  GLU*     1.3    71.7    -      -       -      +
    966B  LYS*     1.3    60.7    +      -       -      +
    967B  MET*     3.4    26.6    +      -       +      -
   1006B  HIS*     4.0     7.6    -      -       +      -
   1009B  ILE*     3.9     5.2    -      -       +      -
   1015B  LEU*     3.9     9.9    -      -       +      -
   1018B  LEU*     3.7    34.1    -      -       +      -
   1019B  ILE*     3.7    30.1    -      -       +      -
   1022B  LEU*     3.7    28.5    -      -       +      -
   1031B  VAL*     4.0     6.5    -      -       +      -
   1032B  SER      2.8    14.2    +      -       -      +
   1033B  VAL*     3.5     7.7    -      -       +      +
   1034B  LYS      2.9    26.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 966 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    903B  GLU*     2.6    31.9    +      -       -      +
    944B  GLN*     3.7    21.8    -      -       +      +
    945B  ILE      3.0    12.9    +      -       -      +
    946B  ALA*     4.0    14.6    -      -       +      -
    947B  SER      4.8     0.5    +      -       -      -
    964B  GLU*     3.6     2.2    +      -       -      -
    965B  ILE*     1.3    69.1    -      -       -      +
    967B  MET*     1.3    60.7    +      -       -      +
    968B  ALA*     4.2     7.4    -      -       -      +
    969B  GLN*     3.3    35.5    +      -       -      +
    972B  LYS*     5.3     0.2    -      -       -      +
    975B  GLU      5.2     4.5    +      -       -      -
    976B  GLY*     4.9     1.4    -      -       -      -
    977B  GLY      4.0    12.5    -      -       -      +
   1006B  HIS*     2.7    22.2    +      -       -      -
   1034B  LYS*     4.1    14.1    -      -       +      -
   3508B  FMN      3.3    30.1    -      -       +      +
----------------------------------------------------------
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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