Contacts of the strand formed by residues 992 - 999 (chain A) in PDB entry 3I7N


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 LEU 992 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    930A  VAL*     4.3     7.0    -      -       +      +
    931A  LEU      5.7     0.2    -      -       -      -
    932A  LEU*     4.2    19.7    -      -       +      +
    946A  ALA*     4.2     6.3    -      -       +      +
    947A  ARG*     3.0    19.0    +      -       -      +
    948A  ASP*     3.1    58.4    -      -       +      +
    949A  PHE      5.0     0.9    +      -       -      -
    965A  PHE*     3.9    34.3    -      -       +      -
    977A  CYS*     3.8    11.2    -      -       +      -
    978A  GLN      2.8    25.1    -      -       -      +
    979A  LYS*     3.9     4.3    -      -       -      +
    991A  HIS*     1.3    75.4    -      -       -      +
    993A  GLN*     1.3    66.6    +      -       -      +
    994A  GLU*     3.9     1.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 993 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    977A  CYS*     3.2     3.4    -      -       -      -
    978A  GLN      2.9    29.4    +      -       -      +
    980A  ASP*     2.8    41.0    +      -       -      +
    988A  GLU*     6.0     0.2    -      -       -      +
    991A  HIS*     3.6    26.1    +      -       -      +
    992A  LEU*     1.3    78.9    +      -       -      +
    994A  GLU*     1.3    61.1    +      -       -      +
    995A  VAL*     3.0    23.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 994 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    948A  ASP*     2.4    34.1    -      -       -      +
    950A  ASN*     3.3    23.8    -      -       -      +
    952A  ASN*     3.2    24.4    +      -       -      -
    975A  PHE*     3.9     9.7    -      -       -      +
    976A  VAL      3.2     9.4    -      -       -      +
    977A  CYS*     4.5     0.7    -      -       -      +
    992A  LEU      5.1     0.2    -      -       -      +
    993A  GLN*     1.3    70.1    -      -       -      +
    995A  VAL*     1.3    60.2    +      -       -      +
    996A  GLY      3.2     6.1    +      -       -      +
    997A  LEU*     3.2    35.9    -      -       +      +
   1076A  PHE*     4.6     5.7    -      -       -      -
   1081A  LYS*     4.8     6.6    +      -       -      -
   1086A  THR*     5.1     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 995 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  MET*     4.5    12.1    +      -       +      +
      2A  SER*     3.1    46.8    +      -       -      +
    976A  VAL*     2.9    22.6    +      -       +      +
    978A  GLN*     3.2    42.0    -      -       +      +
    993A  GLN*     3.0    19.0    +      -       +      +
    994A  GLU*     1.3    72.2    -      -       -      +
    996A  GLY*     1.3    55.1    +      -       -      +
   1086A  THR*     3.7     9.6    +      -       -      -
   1087A  GLY*     4.5     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 996 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  SER*     4.5     2.2    -      -       -      -
    975A  PHE*     3.1     8.0    -      -       -      +
    976A  VAL*     2.9    28.2    +      -       -      +
    994A  GLU      3.2     2.8    +      -       -      -
    995A  VAL*     1.3    81.3    -      -       -      +
    997A  LEU*     1.3    65.7    +      -       -      +
   1086A  THR*     3.2    16.5    +      -       -      -
   1087A  GLY*     4.6     0.4    -      -       -      -
   1088A  PHE*     3.7    15.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 997 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    974A  LEU      3.5     6.3    -      -       -      -
    975A  PHE*     4.1     2.5    -      -       +      -
    994A  GLU*     3.2    40.4    -      -       +      +
    996A  GLY*     1.3    84.8    -      -       -      +
    998A  PHE*     1.3    66.9    +      -       -      +
   1076A  PHE*     3.4    39.0    -      -       +      -
   1081A  LYS*     5.2     6.3    -      -       -      +
   1083A  GLU*     4.2    21.1    -      -       +      -
   1084A  PRO      4.2    10.1    -      -       -      +
   1085A  ALA*     3.3     4.8    -      -       -      +
   1086A  THR*     3.0    37.9    +      -       +      +
   1088A  PHE*     3.8     0.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 998 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  VAL*     3.7    25.8    -      -       +      -
    973A  ASN*     3.5     2.9    -      -       -      -
    974A  LEU*     2.8    40.9    +      -       +      +
    997A  LEU*     1.3    79.0    -      -       -      +
    999A  HIS*     1.3    77.7    +      -       -      +
   1000A  LEU*     3.8    12.8    -      -       +      -
   1055A  GLN*     5.6     0.7    -      -       -      -
   1074A  ARG*     3.2    54.7    -      -       +      -
   1076A  PHE*     4.0     6.6    -      -       -      +
   1085A  ALA*     4.1     7.9    -      -       +      -
   1088A  PHE*     3.4    40.6    -      +       +      -
   1090A  ASP*     4.1    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 999 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  LYS*     4.6     5.9    -      -       -      +
     83A  LYS*     3.6    24.8    +      -       +      +
    971A  ALA      3.5    19.1    -      -       -      -
    972A  PHE*     3.5    13.8    +      +       +      +
    973A  ASN*     2.7    22.9    +      -       -      +
    998A  PHE*     1.3    73.5    -      -       -      +
   1000A  LEU*     1.3    49.4    +      -       -      +
   1001A  GLY*     3.8    14.4    -      -       -      -
   1073A  TRP*     3.5    42.9    -      +       -      +
   1074A  ARG*     2.6    45.6    +      -       -      -
   1075A  SER      3.4    18.3    +      -       -      +
   1076A  PHE      4.2     1.6    -      -       -      +
   1077A  HIS*     4.5     9.0    +      +       +      -
----------------------------------------------------------
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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