Contacts of the strand formed by residues 1177 - 1186 (chain A) in PDB entry 2NZ6


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 TRP1177 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1174A  LEU*     2.9    59.3    +      -       +      +
   1175A  PRO      3.6     1.0    -      -       -      -
   1176A  GLU*     1.3   102.1    -      -       +      +
   1178A  THR*     1.3    63.7    +      -       -      +
   1179A  ILE*     4.8     3.6    -      -       +      -
   1199A  HIS      3.1    15.3    -      -       -      +
   1200A  PHE*     3.8     8.1    -      +       -      -
   1201A  THR*     3.8     3.8    +      -       -      -
   1214A  LEU*     3.6    28.7    -      -       +      -
   1217A  ASN*     4.0    20.2    -      -       +      -
   1218A  PHE*     3.7    46.2    -      +       +      -
   1221A  LEU*     3.7    33.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR1178 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1171A  GLU*     4.1     4.0    -      -       +      -
   1172A  ILE      3.3    13.7    -      -       -      +
   1173A  VAL*     3.8    32.3    -      -       +      +
   1174A  LEU      4.6     0.3    +      -       -      -
   1177A  TRP*     1.3    76.3    +      -       -      +
   1179A  ILE*     1.3    65.2    +      -       -      +
   1180A  ARG*     3.7    45.9    +      -       +      +
   1197A  GLN      3.7     0.5    -      -       -      +
   1198A  PHE*     3.6     1.9    -      -       -      -
   1199A  HIS*     2.7    42.7    +      -       -      +
   1201A  THR*     4.3    10.3    -      -       -      +
   1221A  LEU*     6.0     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1179 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1170A  SER*     4.0     1.2    +      -       -      +
   1171A  GLU*     3.5     1.4    -      -       -      -
   1172A  ILE*     2.8    54.9    +      -       +      +
   1174A  LEU*     4.4    17.7    -      -       +      -
   1177A  TRP*     4.8     4.0    -      -       +      -
   1178A  THR*     1.3    76.5    -      -       -      +
   1180A  ARG*     1.3    63.0    +      -       -      +
   1181A  ASP*     4.2     4.7    +      -       -      +
   1196A  ARG*     3.7    37.5    -      -       +      +
   1197A  GLN      3.3     4.5    -      -       -      +
   1198A  PHE*     4.3     6.7    -      -       +      -
   1221A  LEU*     4.3    32.8    -      -       +      -
   1225A  TYR*     4.7    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG1180 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1151A  GLU*     5.3     1.8    -      -       -      -
   1153A  TRP*     3.5    32.5    -      -       -      +
   1168A  MET*     3.5    20.2    -      -       +      -
   1170A  SER      3.3     7.4    -      -       -      +
   1171A  GLU*     2.9    26.7    +      -       +      -
   1173A  VAL*     5.7     1.2    -      -       -      +
   1178A  THR*     3.7    21.0    +      -       +      +
   1179A  ILE*     1.3    76.8    -      -       -      +
   1181A  ASP*     1.3    65.7    +      -       -      +
   1182A  PHE*     3.7    18.8    -      -       +      -
   1195A  LEU      4.0     0.2    -      -       -      +
   1196A  ARG*     3.4     2.8    -      -       -      +
   1197A  GLN*     2.7    64.1    +      -       -      +
   1199A  HIS*     3.2    37.4    +      -       -      +
   1201A  THR*     5.7     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP1181 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1168A  MET*     3.5     4.7    -      -       -      +
   1169A  THR*     2.7    44.1    +      -       -      +
   1170A  SER*     2.8    28.2    +      -       -      -
   1179A  ILE*     4.2     5.5    -      -       -      +
   1180A  ARG*     1.3    74.6    -      -       -      +
   1182A  PHE*     1.3    63.1    +      -       -      +
   1195A  LEU      3.3     8.1    -      -       -      +
   1196A  ARG*     2.9    44.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE1182 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1124A  TRP*     5.0     4.5    -      +       -      -
   1135A  ILE*     6.1     0.4    -      -       +      -
   1153A  TRP*     3.6    34.5    -      +       +      -
   1154A  PRO*     3.6    22.4    -      -       +      -
   1166A  VAL*     3.8    23.3    -      -       +      -
   1167A  ALA      3.1     8.3    -      -       -      +
   1168A  MET*     3.5    32.3    -      -       +      -
   1169A  THR*     4.1     5.6    +      -       -      -
   1180A  ARG*     3.7    22.9    -      -       +      -
   1181A  ASP*     1.3    74.0    -      -       -      +
   1183A  THR*     1.3    64.8    +      -       -      +
   1194A  PRO*     3.6     5.2    -      -       -      +
   1195A  LEU*     2.8    60.3    +      -       +      +
   1197A  GLN*     4.0    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR1183 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1165A  THR      3.6     1.2    +      -       -      +
   1166A  VAL*     3.5     8.0    -      -       -      +
   1167A  ALA*     2.9    41.8    +      -       -      +
   1169A  THR*     3.9    17.7    -      -       +      +
   1182A  PHE*     1.3    77.2    -      -       -      +
   1184A  VAL*     1.3    64.4    +      -       -      +
   1185A  LYS*     4.1     3.4    -      -       -      +
   1192A  SER*     3.8    17.5    -      -       -      +
   1193A  HIS      3.4     6.1    -      -       -      +
   1194A  PRO*     5.2     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL1184 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1124A  TRP*     4.3    11.7    -      -       +      +
   1127A  VAL*     4.3    15.9    -      -       +      -
   1128A  TRP*     3.3    26.8    -      -       +      -
   1132A  VAL      6.0     0.2    -      -       -      +
   1164A  ILE*     3.3    27.4    -      -       +      -
   1165A  THR      3.6     3.1    -      -       -      -
   1166A  VAL*     4.8     1.8    -      -       +      +
   1182A  PHE*     4.8     1.3    -      -       +      -
   1183A  THR*     1.3    78.3    -      -       -      +
   1185A  LYS*     1.3    58.5    +      -       -      +
   1192A  SER*     4.2     0.2    -      -       -      -
   1193A  HIS*     2.8    40.9    +      -       +      +
   1194A  PRO      5.3     0.4    -      -       -      +
   1195A  LEU*     3.3    39.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS1185 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1164A  ILE*     3.5     4.1    -      -       -      -
   1165A  THR*     2.9    52.7    +      -       +      +
   1183A  THR*     5.4     2.9    -      -       -      +
   1184A  VAL*     1.3    75.3    -      -       -      +
   1186A  ASN*     1.3    67.9    +      -       -      +
   1187A  ILE*     3.2    10.8    +      -       -      +
   1190A  SER*     3.8    34.2    +      -       -      +
   1191A  GLU      3.2    11.7    -      -       -      +
   1192A  SER*     4.0    12.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN1186 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1128A  TRP*     3.3    42.9    -      -       +      +
   1163A  ASP*     3.6    10.3    -      -       -      +
   1164A  ILE*     3.9     6.9    -      -       -      +
   1185A  LYS*     1.3    68.7    -      -       -      +
   1187A  ILE*     1.3    55.4    +      -       -      +
   1188A  GLN*     2.9    27.2    +      -       -      +
   1189A  THR*     3.1    35.1    +      -       -      +
   1190A  SER*     2.6    35.7    +      -       -      -
   1191A  GLU      2.9     8.6    +      -       -      +
----------------------------------------------------------
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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