Contacts of the strand formed by residues 1030 - 1036 (chain A) 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 GLN1030 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    961A  LYS      3.6     5.5    +      -       -      -
    962A  GLN*     3.4    28.4    +      -       +      +
    963A  LEU      3.0    25.3    +      -       -      +
   1028A  GLU      3.7     0.6    +      -       -      -
   1029A  ALA*     1.3    73.0    -      -       -      +
   1031A  VAL*     1.3    61.8    +      -       -      +
   1054A  ASP*     3.4    29.5    +      -       +      +
   1055A  ILE*     3.9    17.0    -      -       +      +
   1101A  LEU*     5.9     2.8    -      -       -      +
   1237A  HIS*     5.3     5.5    -      -       -      +
   1238A  GLU      3.7     8.5    +      -       -      -
   1239A  PRO*     2.6    33.3    +      -       -      +
   1240A  VAL*     3.4     9.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1031 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    963A  LEU*     3.3    11.0    -      -       +      +
    965A  ILE*     3.9    22.7    -      -       +      -
   1019A  ILE*     4.0    19.7    -      -       +      +
   1022A  LEU*     3.9    29.6    -      -       +      -
   1023A  HIS*     3.6    28.7    -      -       +      +
   1029A  ALA      4.1     3.1    -      -       -      +
   1030A  GLN*     1.3    75.2    -      -       -      +
   1032A  SER*     1.3    72.8    +      -       -      +
   1033A  VAL*     5.0     0.2    -      -       +      -
   1053A  ALA*     3.9     1.6    -      -       -      -
   1054A  ASP*     2.8    38.8    +      -       -      +
   1055A  ILE*     3.1     6.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER1032 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    942A  ILE*     5.3     0.5    -      -       -      +
    962A  GLN*     5.3     1.9    +      -       -      +
    963A  LEU      2.7    11.9    +      -       -      +
    964A  GLU*     3.0    35.7    +      -       -      +
    965A  ILE*     2.8    30.2    +      -       -      +
   1030A  GLN      4.0     0.8    +      -       -      -
   1031A  VAL*     1.3    76.9    -      -       -      +
   1033A  VAL*     1.3    63.4    +      -       -      +
   1055A  ILE*     3.2    37.0    -      -       -      -
   1057A  GLN      5.2     1.6    -      -       -      -
   1103A  ARG*     3.9     6.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL1033 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    502A  VAL*     4.4     3.1    -      -       +      -
    965A  ILE*     3.5     9.0    -      -       +      +
    967A  MET*     3.8    25.6    -      -       +      -
   1015A  LEU*     4.2    11.4    -      -       +      -
   1019A  ILE*     4.1    14.6    -      -       +      -
   1031A  VAL*     5.0     0.4    -      -       +      -
   1032A  SER*     1.3    78.8    -      -       -      +
   1034A  LYS*     1.3    61.7    +      -       -      +
   1035A  LEU*     3.7    16.2    +      -       +      -
   1048A  VAL*     3.6    37.7    -      -       +      -
   1053A  ALA*     4.0    10.5    -      -       +      -
   1055A  ILE      3.0     5.6    +      -       -      +
   1056A  ILE*     3.5     7.5    -      -       +      +
   1057A  GLN*     2.9    25.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS1034 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    874A  GLY      4.8     1.6    -      -       -      +
    944A  GLN*     4.3     3.6    -      -       -      +
    964A  GLU*     3.7    27.6    +      -       -      +
    965A  ILE      2.9    13.9    +      -       -      +
    966A  LYS*     4.1     6.3    -      -       +      -
    967A  MET*     3.0    29.3    +      -       -      +
    968A  ALA      3.5    20.1    +      -       -      +
    969A  GLN*     4.4     5.6    -      -       -      +
   1032A  SER      4.2     0.4    -      -       -      -
   1033A  VAL*     1.3    71.1    -      -       -      +
   1035A  LEU*     1.3    60.8    +      -       -      +
   1057A  GLN*     3.5    24.7    -      -       +      +
   1059A  SER*     3.4    25.1    -      -       -      +
   3508A  FMN      2.8    65.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU1035 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    501A  GLN*     3.4    19.5    -      -       -      +
    502A  VAL*     3.8    28.3    -      -       +      -
    967A  MET*     4.2     4.0    -      -       +      -
    968A  ALA*     4.4     0.9    -      -       -      -
   1033A  VAL*     3.9    17.9    -      -       +      +
   1034A  LYS*     1.3    76.8    -      -       -      +
   1036A  VAL*     1.3    65.1    +      -       -      +
   1041A  ILE*     3.8    28.5    -      -       +      -
   1044A  ILE*     4.1    15.5    -      -       +      -
   1045A  ALA*     4.5     9.4    -      -       +      -
   1048A  VAL*     4.6     5.2    -      -       +      -
   1056A  ILE*     3.7    22.7    -      -       +      -
   1057A  GLN      2.8    10.5    +      -       -      +
   1059A  SER*     2.9    29.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL1036 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    499A  PHE*     3.5    26.0    -      -       +      -
    501A  GLN*     2.9    32.7    +      -       -      -
    968A  ALA*     3.5    20.4    -      -       +      +
    969A  GLN      3.3    32.8    -      -       -      +
    970A  GLY*     3.5    13.7    -      -       -      +
    973A  PRO*     4.0    10.1    -      -       +      -
   1035A  LEU*     1.3    74.8    -      -       -      +
   1037A  ALA*     1.3    74.3    +      -       -      +
   1038A  GLU      3.3     0.3    +      -       -      -
   1041A  ILE*     3.5     6.2    -      -       -      +
   1059A  SER*     3.4    12.3    -      -       -      +
   1061A  HIS      5.0     1.8    -      -       -      +
   1077A  GLY*     4.3     6.7    -      -       -      -
   1078A  SER      4.9     0.9    -      -       -      +
----------------------------------------------------------
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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