Contacts of the strand formed by residues 1142 - 1147 (chain B) in PDB entry 3PT6


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 LEU1142 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1140B  PRO      5.2     1.6    -      -       -      +
   1141B  LYS*     1.3    77.5    -      -       -      +
   1143B  ARG*     1.3    64.5    +      -       -      +
   1144B  THR*     3.0     5.9    +      -       -      -
   1163B  ILE*     2.8    19.6    +      -       +      +
   1164B  SER*     3.3     3.1    -      -       -      -
   1165B  GLU*     3.0    22.5    +      -       -      -
   1221B  GLU*     3.6    22.2    -      -       +      +
   1222B  MET*     4.2    31.2    -      -       +      -
   1264B  ARG*     3.5    30.5    -      -       -      +
   1265B  PHE*     3.7    30.3    -      -       +      -
   1594B  ILE*     4.7     5.2    -      -       +      -
   1598B  LEU*     4.0    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG1143 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1141B  LYS      3.9     1.5    +      -       -      +
   1142B  LEU*     1.3    67.2    -      -       -      +
   1144B  THR*     1.3    58.4    +      -       -      +
   1165B  GLU*     3.7    13.5    -      -       +      +
   1167B  LEU*     3.9    22.2    -      -       +      -
   1168B  TRP*     4.0    10.8    -      -       +      -
   1218B  GLY      3.0    20.4    +      -       -      -
   1219B  ASP*     2.6    34.7    +      -       -      +
   1220B  VAL*     3.8     1.2    -      -       -      -
   1221B  GLU*     2.8    61.5    +      -       -      +
   1222B  MET      3.0     6.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR1144 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1142B  LEU      3.0     4.4    +      -       -      -
   1143B  ARG*     1.3    73.5    -      -       -      +
   1145B  LEU*     1.3    65.3    +      -       -      +
   1146B  ASP*     4.3     1.8    -      -       +      +
   1155B  SER*     5.4     0.4    -      -       -      +
   1158B  PHE*     5.2     1.6    -      -       +      -
   1164B  SER*     2.8    37.6    -      -       -      +
   1165B  GLU      3.1     5.5    +      -       -      -
   1166B  THR*     3.4    21.0    -      -       +      +
   1167B  LEU      3.1    22.2    +      -       -      -
   1168B  TRP*     3.4     9.9    +      -       -      -
   1222B  MET*     3.4    21.2    -      -       +      +
   1224B  CYS*     3.6    31.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU1145 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1143B  ARG      4.1     0.4    +      -       -      -
   1144B  THR*     1.3    76.2    -      -       -      +
   1146B  ASP*     1.3    71.5    +      -       -      +
   1147B  VAL*     4.0     6.3    -      -       +      -
   1168B  TRP*     3.7    32.7    -      -       +      +
   1169B  ALA      4.1     1.6    -      -       -      +
   1170B  ILE*     4.3    13.2    -      -       +      -
   1215B  PRO*     4.6    10.5    -      -       +      -
   1220B  VAL*     3.8    29.8    -      -       +      +
   1222B  MET      2.8    10.8    +      -       -      +
   1223B  LEU*     3.5    20.7    -      -       +      +
   1224B  CYS      3.3    21.8    +      -       -      -
   1257B  TYR*     4.0    24.9    -      -       +      -
   1261B  TYR*     4.5     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP1146 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1144B  THR*     4.0     1.3    -      -       +      -
   1145B  LEU*     1.3    74.2    -      -       -      +
   1147B  VAL*     1.3    67.2    +      -       -      +
   1148B  PHE      3.9     0.5    -      -       -      +
   1149B  SER*     3.0    35.6    -      -       -      +
   1152B  GLY*     5.5     0.5    -      -       -      -
   1154B  LEU*     4.3     8.4    -      -       -      +
   1155B  SER*     2.6    35.9    +      -       -      +
   1166B  THR*     4.0    12.8    -      -       +      -
   1168B  TRP      3.0    10.0    +      -       -      +
   1169B  ALA*     3.2     3.9    -      -       +      -
   1170B  ILE      3.0    22.3    +      -       -      -
   1180B  PHE*     4.7     0.4    -      -       +      -
   1224B  CYS*     3.4    22.9    -      -       -      +
   1225B  GLY*     4.7     0.3    -      -       -      -
   1603B  SAH      5.5     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL1147 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1145B  LEU*     4.0    13.7    -      -       +      -
   1146B  ASP*     1.3    74.3    -      -       -      +
   1148B  PHE*     1.3   104.5    +      -       +      +
   1149B  SER      3.2     1.3    -      -       -      -
   1170B  ILE*     4.1    14.4    -      -       +      -
   1194B  CYS*     4.4    16.6    -      -       +      -
   1223B  LEU*     3.6    29.6    -      -       +      -
   1224B  CYS      3.1     3.8    +      -       -      -
   1225B  GLY*     3.0    21.0    -      -       -      -
   1254B  PHE*     3.9    15.3    -      -       +      -
   1257B  TYR*     4.7    12.8    -      -       +      -
----------------------------------------------------------
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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