Contacts of the strand formed by residues 1097 - 1102 (chain C) in PDB entry 6KQG


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 LEU1097 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1092C  LEU*     2.9    38.5    +      -       +      +
   1093C  GLN*     3.4     9.2    +      -       -      +
   1095C  LEU*     3.8    10.1    -      -       +      +
   1096C  ALA*     1.3    88.4    -      -       -      +
   1098C  ASP*     1.3    63.0    +      -       -      +
   1099C  VAL*     3.7     2.8    +      -       -      -
     10D  ILE*     4.3    25.1    -      -       +      -
     11D  ALA      3.7     5.8    -      -       -      +
     12D  LEU*     4.1    14.1    -      -       +      -
     21D  TRP*     4.1     2.7    -      -       -      -
    101D  HIS*     5.5     0.4    -      -       -      +
    103D  TRP*     3.5    33.7    -      -       +      -
    104D  PHE*     4.5     8.5    -      -       +      -
   1447D  LEU*     4.6     4.7    -      -       +      +
   1448D  THR*     5.7     0.2    -      -       -      -
   1451D  ALA*     3.6    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP1098 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1093C  GLN*     4.3     5.6    +      -       -      -
   1096C  ALA      4.3     0.4    +      -       -      -
   1097C  LEU*     1.3    71.4    -      -       -      +
   1099C  VAL*     1.3    64.9    +      -       -      +
   1100C  GLN*     2.5    41.3    +      -       -      +
      9D  ARG*     3.7     2.9    +      -       -      +
     10D  ILE*     3.2     4.7    -      -       -      -
     11D  ALA*     2.8    47.6    +      -       +      +
     12D  LEU      4.6     4.3    -      -       -      +
     13D  ALA*     4.3     5.8    -      -       +      +
     17D  LYS*     3.4    16.5    +      -       +      -
     21D  TRP*     3.3    32.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL1099 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1085C  PHE*     5.0     5.8    -      -       +      -
   1088C  LEU*     6.0     0.4    -      -       +      -
   1089C  VAL*     4.0    40.3    -      -       +      +
   1092C  LEU*     3.5    39.3    -      -       +      -
   1093C  GLN*     5.1     5.4    +      -       -      +
   1097C  LEU      3.7     2.3    +      -       -      +
   1098C  ASP*     1.3    79.7    +      -       -      +
   1100C  GLN*     1.3    63.2    +      -       -      +
   1101C  THR*     4.0     2.1    +      -       +      +
      8D  VAL*     4.0    22.0    -      -       +      -
      9D  ARG      3.3     2.9    -      -       -      +
     10D  ILE*     3.8    21.8    -      -       +      -
   1434D  TRP*     4.4     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN1100 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1098C  ASP*     2.5    39.3    +      -       -      +
   1099C  VAL*     1.3    73.2    -      -       -      +
   1101C  THR*     1.3    63.1    +      -       -      +
   1102C  LEU*     3.5    14.2    +      -       +      +
   1108C  PRO*     4.2    19.5    -      -       -      +
   1109C  VAL      5.6     0.9    -      -       -      +
      8D  VAL*     3.3     5.7    -      -       -      -
      9D  ARG*     2.7    77.0    +      -       +      +
     11D  ALA*     6.5     0.4    -      -       +      -
     17D  LYS*     3.8    13.3    -      -       -      +
     21D  TRP*     5.9     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR1101 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1085C  PHE*     4.1    20.4    -      -       +      -
   1089C  VAL*     5.9     0.9    -      -       +      -
   1099C  VAL*     4.0     4.2    +      -       +      +
   1100C  GLN*     1.3    72.1    +      -       -      +
   1102C  LEU*     1.3    55.1    +      -       -      +
   1108C  PRO*     3.6     4.5    -      -       -      +
   1109C  VAL*     2.8    58.2    +      -       -      +
   1111C  ILE*     3.6    26.9    +      -       +      +
      5D  VAL*     3.9    22.9    -      -       +      -
      7D  LYS      3.7     3.8    -      -       -      -
      8D  VAL*     4.1    18.6    -      -       +      -
   1468D  LEU*     4.8     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU1102 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1100C  GLN*     3.5    18.6    +      -       +      +
   1101C  THR*     1.3    76.8    -      -       -      +
   1103C  ASP*     1.3    59.2    +      -       -      +
   1106C  ASP*     4.1    18.6    -      -       +      +
   1107C  ASN      3.8     3.8    -      -       -      -
   1108C  PRO*     3.7    33.9    -      -       +      -
   1109C  VAL*     4.2     3.8    -      -       -      -
      5D  VAL*     3.6     3.1    -      -       -      -
      6D  ARG      2.7    29.5    +      -       -      -
      7D  LYS*     2.9    24.5    +      -       +      +
      9D  ARG*     3.7    39.9    -      -       +      +
   1456D  LYS*     3.9    23.1    -      -       +      -
----------------------------------------------------------
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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