Contacts of the strand formed by residues 1130 - 1133 (chain A) in PDB entry 3MP6


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 GLU1130 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1128A  GLY      3.7     5.4    +      -       -      +
   1129A  SER*     1.3    76.6    -      -       -      +
   1131A  VAL*     1.3    63.7    +      -       -      +
   1146A  GLN*     2.8    37.1    +      -       -      +
   1147A  CYS      3.4     9.4    -      -       -      +
   1148A  GLU*     3.3    24.8    +      -       -      +
   1164A  PRO*     5.8     4.3    -      -       -      +
   1185A  LEU*     3.8     2.8    -      -       -      +
   1186A  ILE*     3.0    48.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1131 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1125A  ILE*     4.1    15.3    -      -       +      -
   1129A  SER*     4.6     2.0    -      -       -      -
   1130A  GLU*     1.3    80.4    -      -       -      +
   1132A  ALA*     1.3    67.7    +      -       -      +
   1133A  TYR*     4.8     1.3    -      -       +      +
   1145A  ILE      3.6     0.2    -      -       -      +
   1146A  GLN*     3.4     4.9    -      -       -      -
   1147A  CYS*     2.8    53.0    +      -       +      +
   1149A  VAL*     3.7    29.2    -      -       +      -
   1161A  VAL*     4.1    11.7    -      -       +      -
   1183A  LEU*     4.1    14.4    -      -       +      -
   1184A  LEU      3.1    15.9    -      -       -      +
   1185A  LEU*     4.2     7.0    -      -       -      -
   1186A  ILE*     3.6     9.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA1132 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1131A  VAL*     1.3    72.0    -      -       -      +
   1133A  TYR*     1.3    61.2    +      -       -      +
   1144A  TRP*     3.5    21.1    -      -       +      -
   1145A  ILE      3.4     5.4    -      -       -      -
   1183A  LEU*     3.1     6.6    -      -       -      +
   1184A  LEU*     2.9    34.0    +      -       +      +
   1186A  ILE*     4.1     2.2    -      -       -      +
   1202A  LEU*     5.6     0.2    -      -       +      -
   1211A  PHE*     3.8    21.1    -      -       +      -
   1247A  LEU*     3.6    27.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR1133 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1131A  VAL*     4.8     2.9    -      -       +      -
   1132A  ALA*     1.3    75.6    -      -       -      +
   1134A  LYS*     1.3    78.2    +      -       -      +
   1135A  PRO*     3.2    24.8    -      -       +      +
   1136A  ARG*     4.2    13.7    +      -       -      +
   1144A  TRP*     3.3     4.7    -      -       -      -
   1145A  ILE*     2.8    47.6    +      -       +      +
   1147A  CYS*     3.9    13.0    -      -       +      -
   1161A  VAL*     4.1    10.3    -      -       +      -
   1176A  TYR*     3.4    53.9    -      +       +      +
   1177A  LYS      4.4     4.9    +      -       -      -
   1178A  CYS*     3.5    34.1    -      -       +      -
   1182A  GLU*     3.3    17.2    +      -       +      -
   1183A  LEU*     5.0     1.3    -      -       +      -
----------------------------------------------------------
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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