Contacts of the strand formed by residues 1180 - 1190 (chain A) in PDB entry 4UHW


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 HIS1180 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    434A  GLN*     3.6    18.4    +      -       -      -
    556A  LEU*     4.0     5.6    -      -       -      -
   1171A  VAL*     4.2     2.5    -      -       +      -
   1172A  GLU      3.3    13.5    -      -       -      +
   1173A  ILE*     3.9    15.3    -      -       +      -
   1178A  GLY      5.3     0.4    +      -       -      -
   1179A  ASP*     1.3    82.4    +      -       -      +
   1181A  LYS*     1.3    74.0    +      -       -      +
   1182A  ASN*     3.1    32.9    +      -       -      -
   1216A  THR*     4.3    17.4    +      -       -      +
   1217A  ILE*     4.9    10.8    -      -       +      -
   1243A  ASP*     5.9     2.0    -      -       -      -
   1279A  VAL*     4.2     3.0    -      -       -      +
   1283A  ILE*     3.7    31.7    -      -       +      +
   1306A  LEU      5.3     2.0    -      -       -      -
   1308A  PRO*     6.1     2.6    -      -       -      +
   1311A  ILE*     4.2    11.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS1181 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    434A  GLN*     4.5    13.5    +      -       -      +
    556A  LEU*     3.8    25.6    -      -       +      +
    558A  SER*     3.3    40.0    -      -       -      +
    561A  HIS*     4.7     5.1    -      -       -      -
   1171A  VAL*     3.2     6.6    -      -       -      +
   1172A  GLU*     3.0    36.7    +      -       +      +
   1180A  HIS*     1.3    76.7    -      -       -      +
   1182A  ASN*     1.3    77.4    +      -       -      +
   1183A  ILE*     3.5     8.3    +      -       +      +
   1242A  CYS*     4.0    19.9    +      -       -      +
   1244A  MET      4.7     6.9    +      -       -      -
   1246A  THR*     3.1    25.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN1182 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1170A  GLU      3.8     5.8    -      -       -      +
   1171A  VAL*     3.4     2.6    -      -       -      +
   1180A  HIS*     3.1    29.2    +      -       -      -
   1181A  LYS*     1.3    83.4    -      -       -      +
   1183A  ILE*     1.3    61.8    +      -       -      +
   1184A  ARG      3.7     0.4    -      -       -      +
   1185A  THR*     5.5     1.6    -      -       -      +
   1212A  MET*     3.1    25.0    -      -       -      +
   1216A  THR*     5.9     0.2    +      -       -      -
   1243A  ASP*     3.0    26.7    +      -       -      +
   1244A  MET      4.9     0.2    -      -       -      -
   1245A  PRO*     3.5    20.9    -      -       +      +
   1246A  THR      3.2    19.9    +      -       -      -
   1279A  VAL*     3.2    22.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE1183 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1005A  LYS*     4.0    20.9    -      -       +      +
   1170A  GLU*     2.8    39.2    +      -       +      +
   1171A  VAL*     3.4    31.0    -      -       -      +
   1172A  GLU*     3.5    15.9    -      -       +      +
   1181A  LYS*     4.1    13.7    -      -       +      +
   1182A  ASN*     1.3    74.3    -      -       -      +
   1184A  ARG*     1.3    62.1    +      -       +      +
   1246A  THR*     3.2    16.2    -      -       -      +
   1247A  GLU*     3.0    25.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG1184 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    983A  MET*     3.8    15.2    +      -       -      +
    984A  SER      3.3    19.0    +      -       -      -
    985A  SER*     5.2     2.2    +      -       -      -
    989A  ARG*     3.5    34.1    +      -       -      +
   1169A  SER*     3.4     1.0    -      -       -      -
   1170A  GLU*     2.9    28.8    +      -       -      +
   1182A  ASN*     3.7     1.0    -      -       -      -
   1183A  ILE*     1.3    88.9    -      -       +      +
   1185A  THR*     1.3    71.4    +      -       -      +
   1186A  ASP*     3.3    32.5    +      -       -      +
   1245A  PRO*     4.4     1.8    -      -       -      -
   1247A  GLU*     3.4    35.7    +      -       +      +
   1249A  HIS*     3.6    27.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR1185 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1167A  ALA*     5.2     0.4    -      -       +      -
   1168A  CYS      3.2     7.6    -      -       -      +
   1169A  SER*     2.6    22.8    +      -       -      +
   1182A  ASN*     5.5     1.2    -      -       -      +
   1184A  ARG*     1.3    74.7    +      -       -      +
   1186A  ASP*     1.3    68.1    +      -       -      +
   1187A  ILE*     3.9    19.3    -      -       +      -
   1208A  PHE*     3.5    36.4    -      -       +      -
   1245A  PRO*     4.0    18.3    -      -       -      +
   1247A  GLU      3.1     6.1    +      -       -      -
   1248A  LEU*     3.4     8.9    -      -       +      +
   1249A  HIS*     3.0    25.1    +      -       -      +
   1278A  SER*     4.8     0.9    -      -       -      +
   1279A  VAL*     4.7     2.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP1186 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    980A  CYS*     3.6     5.4    -      -       -      -
    983A  MET*     3.7    15.7    -      -       +      +
    984A  SER*     3.5    26.3    -      -       -      -
    989A  ARG*     3.2    25.1    +      -       -      -
   1167A  ALA*     3.2     4.5    -      -       -      -
   1168A  CYS*     2.8    36.4    +      -       +      +
   1184A  ARG*     3.3    29.2    +      -       -      +
   1185A  THR*     1.3    77.0    -      -       -      +
   1187A  ILE*     1.3    62.2    +      -       -      +
   1249A  HIS*     3.4    21.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1187 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    983A  MET*     3.6     2.6    -      -       -      +
   1166A  ALA      3.6     4.0    -      -       -      +
   1167A  ALA*     4.1     8.5    -      -       +      -
   1185A  THR*     3.9    14.6    -      -       +      -
   1186A  ASP*     1.3    79.2    -      -       -      +
   1188A  VAL*     1.3    65.9    +      -       -      +
   1189A  MET*     3.7    30.5    -      -       +      -
   1204A  ILE*     4.0    17.0    -      -       +      -
   1205A  GLU*     5.9     0.4    -      -       -      -
   1208A  PHE*     3.9    36.3    -      -       +      -
   1248A  LEU*     4.6     4.9    -      -       +      -
   1249A  HIS      2.9    13.4    +      -       -      +
   1250A  ILE*     3.3    18.4    -      -       +      -
   1251A  ALA      2.8    26.7    +      -       -      +
   1275A  LEU*     3.9    11.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL1188 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    976A  CYS*     4.0    25.5    -      -       -      +
    979A  GLU*     3.6    31.9    -      -       +      +
    980A  CYS*     3.8    28.2    -      -       +      +
    983A  MET*     3.8    18.4    -      -       +      -
   1165A  GLY*     3.3     2.9    -      -       -      -
   1166A  ALA      3.0    32.4    +      -       -      +
   1187A  ILE*     1.3    77.5    -      -       -      +
   1189A  MET*     1.3    67.0    +      -       -      +
   1251A  ALA*     3.4    14.1    -      -       +      +
   1253A  LEU*     4.4    12.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET1189 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    976A  CYS*     4.3     0.7    -      -       -      -
   1012A  LEU*     3.9    23.8    -      -       +      -
   1163A  VAL*     4.3    10.3    -      -       +      -
   1164A  TYR      3.7     8.5    -      -       -      +
   1165A  GLY*     4.2     2.0    -      -       -      -
   1187A  ILE*     3.7     6.3    -      -       +      -
   1188A  VAL*     1.3    77.6    -      -       -      +
   1190A  ASP*     1.3    63.9    +      -       -      +
   1191A  VAL*     3.5    14.5    +      -       +      +
   1204A  ILE*     3.6    50.7    -      -       +      -
   1251A  ALA      3.0    12.8    +      -       -      +
   1252A  LEU*     3.4     8.6    -      -       +      -
   1253A  LEU*     3.1    22.1    +      -       -      -
   1268A  LEU*     5.5     2.5    -      -       +      -
   1271A  SER*     4.8     3.8    -      -       -      -
   1272A  GLY*     4.6     8.3    -      -       -      +
   1275A  LEU*     3.4    30.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP1190 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    972A  ASN*     2.8    36.8    +      -       +      +
    976A  CYS*     3.8     9.6    -      -       -      -
   1163A  VAL*     3.6    22.9    -      -       -      +
   1164A  TYR*     2.8    31.2    +      -       +      +
   1189A  MET*     1.3    69.0    -      -       -      +
   1191A  VAL*     1.3    59.8    +      -       -      +
   1192A  GLY*     3.1    18.7    +      -       -      -
   1253A  LEU*     4.0    18.6    -      -       +      +
   1254A  PRO      5.5     0.3    -      -       -      +
   1255A  PRO*     5.6     2.1    -      -       -      +
   1256A  SER      5.8     0.5    +      -       -      -
   1266A  LYS*     3.0    28.5    +      -       -      +
----------------------------------------------------------
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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