Contacts of the strand formed by residues 798 - 804 (chain C) in PDB entry 7C97


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 798 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    692C  THR*     3.3    18.1    +      -       -      +
    694C  ARG*     3.7    22.2    +      -       -      +
    695C  ALA*     4.0     3.2    -      -       -      +
    696C  ASP*     3.3    21.1    -      -       -      +
    797C  GLY*     1.3    78.0    -      -       -      -
    799C  ASN*     1.3    54.9    +      -       -      +
    800C  MET*     4.2     4.0    -      -       +      -
    827C  ARG*     3.2    62.5    +      -       +      +
    828C  PHE*     4.0    21.2    -      -       +      -
   1231C  TYR*     3.5     1.1    -      -       -      -
   1232C  MET*     2.6    42.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 799 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    696C  ASP*     3.0    21.3    +      -       -      +
    697C  LYS      4.3     5.5    +      -       -      -
    699C  LEU*     3.1    49.7    -      -       +      +
    798C  GLN*     1.3    76.5    +      -       -      +
    800C  MET*     1.3    60.4    +      -       -      +
    827C  ARG*     4.1    13.6    +      -       -      -
   1122C  LYS*     5.7     2.6    -      -       -      +
   1229C  TYR*     4.4    17.8    -      -       -      +
   1230C  MET      4.4     1.3    -      -       -      -
   1231C  TYR*     3.7    30.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 800 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    798C  GLN*     4.5     4.7    -      -       +      -
    799C  ASN*     1.3    74.1    -      -       -      +
    801C  ARG*     1.3    66.9    +      -       -      +
    802C  VAL*     3.1     7.3    +      -       -      +
    822C  VAL*     3.4    24.9    -      -       +      -
    827C  ARG*     3.8    28.9    -      -       +      +
    828C  PHE*     3.3    40.6    -      -       +      -
   1095C  ASP*     4.3    11.0    -      -       +      +
   1096C  ILE*     3.6    31.2    -      -       +      -
   1229C  TYR*     4.3     6.1    -      -       -      -
   1230C  MET      3.6    24.9    +      -       -      +
   1232C  MET*     4.4    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 801 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    800C  MET*     1.3    70.1    -      -       -      +
    802C  VAL*     1.3    60.5    +      -       -      +
   1088C  ASP*     4.6    13.7    +      -       -      +
   1092C  THR*     4.3    22.8    +      -       -      -
   1093C  PRO      3.5    24.2    -      -       -      -
   1094C  VAL*     3.7    16.0    -      -       +      +
   1095C  ASP*     2.9    39.0    +      -       -      +
   1096C  ILE      3.3     5.2    +      -       -      -
   1119C  MET*     3.3    30.1    -      -       -      +
   1210C  ILE*     4.9     2.2    -      -       -      +
   1227C  VAL*     4.0    26.9    -      -       +      +
   1228C  GLY      3.3    14.6    -      -       -      +
   1229C  TYR*     3.7    34.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 802 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    800C  MET      3.1    10.4    +      -       -      +
    801C  ARG*     1.3    73.5    -      -       -      +
    803C  ALA*     1.3    62.3    +      -       -      +
    804C  PHE*     3.8    19.7    -      -       +      -
   1096C  ILE*     3.3    38.8    -      -       +      -
   1098C  LEU*     3.7    29.4    -      -       +      -
   1115C  THR*     4.6     4.7    -      -       +      +
   1227C  VAL*     3.3     4.7    -      -       -      +
   1228C  GLY      2.9    30.8    +      -       -      +
   1230C  MET*     4.3    18.6    -      -       +      +
   1232C  MET*     4.5     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 803 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    802C  VAL*     1.3    76.6    -      -       -      +
    804C  PHE*     1.3    64.4    +      -       -      +
    805C  MET*     3.6     9.3    +      -       +      -
   1086C  PRO*     6.5     0.2    -      -       +      -
   1094C  VAL*     4.1    16.8    -      -       +      -
   1096C  ILE      3.3    10.0    +      -       -      +
   1097C  VAL*     3.5     6.9    -      -       +      +
   1098C  LEU      3.0    23.2    +      -       -      -
   1212C  LEU*     4.3     9.9    -      -       +      -
   1225C  VAL*     5.0     0.2    -      -       +      -
   1226C  THR      3.3    15.3    -      -       -      +
   1227C  VAL*     3.6    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 804 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    802C  VAL*     3.8    14.8    -      -       +      -
    803C  ALA*     1.3    72.4    -      -       -      +
    805C  MET*     1.3    59.5    +      -       -      +
   1098C  LEU*     3.8    32.1    -      -       +      -
   1099C  ASN      4.2    17.9    -      -       -      -
   1100C  PRO*     4.3    15.5    -      -       +      -
   1103C  VAL*     4.9     3.6    -      -       +      -
   1111C  GLN*     4.0    28.3    -      -       +      -
   1112C  ILE*     4.8    13.0    -      -       +      -
   1115C  THR*     3.6    31.2    -      -       +      -
   1225C  VAL*     3.0    20.0    -      -       -      +
   1226C  THR*     3.5    24.4    +      -       +      -
   1230C  MET*     4.8     0.9    -      -       -      -
    638D  SER*     3.0    21.0    -      -       -      +
    639D  VAL*     4.8    12.3    -      -       +      +
----------------------------------------------------------
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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