Contacts of the strand formed by residues 1073 - 1080 (chain I) in PDB entry 6XAV


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 LYS1073 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    565I  GLU*     5.1     4.9    +      -       -      -
    678I  ARG*     4.7    15.0    -      -       -      +
    681I  MET*     4.9    14.3    -      -       +      +
    685I  MET*     3.7    27.4    -      -       +      -
    814I  ASP*     3.8    22.0    -      -       -      +
    816I  ILE*     5.2     1.7    -      -       -      +
   1065I  LYS*     3.8    18.2    -      -       -      +
   1066I  MET      3.6     0.4    -      -       -      -
   1067I  ALA*     3.6     8.5    -      -       +      -
   1071I  GLY      3.8     3.8    +      -       -      +
   1072I  ASN*     1.3    76.0    -      -       -      +
   1074I  GLY*     1.3    59.8    +      -       -      +
    462J  ASP*     3.3    34.1    +      -       +      -
     18R    A      2.4    41.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY1074 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    814I  ASP      3.2    16.4    -      -       -      -
    816I  ILE*     4.4     8.1    -      -       -      -
   1065I  LYS*     3.5     8.4    -      -       -      +
   1066I  MET      2.7    41.5    +      -       -      -
   1073I  LYS*     1.3    78.5    -      -       -      +
   1075I  VAL*     1.3    56.7    +      -       -      -
    461J  PHE      4.0     7.4    -      -       -      -
    462J  ASP*     4.4     4.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL1075 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    814I  ASP      4.0     1.2    +      -       -      -
    815I  SER*     3.3    14.7    -      -       -      +
    816I  ILE*     3.1    22.0    +      -       -      -
   1063I  GLY*     3.5    37.7    -      -       -      +
   1064I  ASP      3.6     6.1    -      -       -      +
   1065I  LYS*     4.5     2.9    -      -       +      +
   1074I  GLY*     1.3    75.4    -      -       -      +
   1076I  ILE*     1.3    72.8    +      -       -      +
   1077I  SER      3.5     0.3    +      -       -      -
    354J  VAL*     4.2    12.1    -      -       +      -
    355J  ILE      4.2    16.2    -      -       -      +
    356J  THR*     5.1     2.2    -      -       +      -
    461J  PHE*     3.3    26.4    +      -       +      +
    462J  ASP      5.1     0.2    -      -       -      -
    463J  GLY*     4.9     9.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1076 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    816I  ILE*     3.7     7.6    -      -       +      +
    818I  VAL*     4.0    23.6    -      -       +      -
   1060I  ILE*     3.8    35.0    -      -       +      -
   1061I  GLN      4.3     5.6    -      -       -      +
   1062I  PRO*     3.5    19.9    -      -       +      +
   1063I  GLY      3.1    20.8    +      -       -      -
   1064I  ASP*     3.2    23.5    +      -       +      +
   1066I  MET*     3.9    26.0    -      -       +      -
   1075I  VAL*     1.3    76.2    -      -       -      +
   1077I  SER*     1.3    60.4    +      -       -      +
   1078I  LYS      4.1     9.2    -      -       -      +
   1079I  ILE*     4.1    15.3    -      -       +      -
    356J  THR*     3.8     5.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER1077 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    810I  TYR*     2.8    33.9    +      -       -      +
    815I  SER*     3.7    22.2    -      -       -      -
    816I  ILE      3.4     8.4    +      -       -      -
    817I  LEU*     5.0     0.9    -      -       -      -
   1062I  PRO*     4.0    11.1    -      -       -      +
   1075I  VAL      3.5     0.2    +      -       -      -
   1076I  ILE*     1.3    76.6    -      -       -      +
   1078I  LYS*     1.3    65.2    +      -       -      +
    356J  THR*     4.2    22.6    +      -       -      +
    357J  VAL*     4.6     8.5    -      -       -      -
    358J  GLY      5.5     0.9    -      -       -      -
    448J  GLN*     5.5     5.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS1078 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    807I  TRP*     5.1     3.8    -      -       +      -
    810I  TYR*     3.5    48.3    +      -       +      -
    816I  ILE      4.5     0.2    +      -       -      -
    817I  LEU*     3.6    15.8    -      -       +      +
    818I  VAL      3.4    23.4    +      -       -      +
   1062I  PRO*     4.4     5.4    -      -       -      -
   1076I  ILE*     3.9     4.0    -      -       -      +
   1077I  SER*     1.3    83.5    +      -       -      +
   1079I  ILE*     1.3    78.9    +      -       -      +
   1080I  ASN*     3.5    20.4    +      -       -      +
   1081I  PRO*     4.9     4.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1079 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33H  ARG*     5.6     8.2    +      -       -      +
    818I  VAL*     3.4    11.4    -      -       +      +
    819I  SER      4.2     1.1    -      -       -      +
    820I  GLU*     4.2    21.3    -      -       +      -
    823I  VAL*     3.9    26.0    -      -       +      -
   1060I  ILE*     4.1    25.4    -      -       +      -
   1062I  PRO*     4.1    22.4    -      -       +      +
   1076I  ILE*     4.1    18.4    -      -       +      -
   1078I  LYS*     1.3    84.4    +      -       -      +
   1080I  ASN*     1.3    62.7    +      -       -      +
   1081I  PRO*     3.7     6.8    -      -       -      +
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Residues in contact with ASN1080 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    807I  TRP*     3.8    19.0    -      -       -      -
    817I  LEU*     3.7    24.6    -      -       +      +
    818I  VAL      2.8    13.3    +      -       -      +
    819I  SER*     3.2     1.7    -      -       -      -
    820I  GLU*     2.8    27.0    +      -       -      +
   1078I  LYS*     3.5    12.7    +      -       -      +
   1079I  ILE*     1.3    73.1    -      -       -      +
   1081I  PRO*     1.3    78.6    +      -       -      +
   1084I  ASP*     3.3    40.0    +      -       -      +
   1085I  MET*     3.4    22.1    -      -       +      +
----------------------------------------------------------
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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