Contacts of the strand formed by residues 1144 - 1153 (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 TRP1144 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1115A  TRP*     4.3     2.5    -      +       -      -
   1132A  ALA*     3.5    32.1    -      -       +      -
   1133A  TYR      3.3     4.5    -      -       -      -
   1134A  LYS*     3.5    40.5    -      -       +      +
   1135A  PRO*     4.4     0.4    -      -       -      -
   1142A  GLY*     3.4    13.6    +      -       -      -
   1143A  GLU*     1.3    82.2    -      -       -      +
   1145A  ILE*     1.3    61.4    +      -       -      +
   1181A  LYS      3.9    18.6    -      -       -      -
   1182A  GLU      3.5    21.8    -      -       -      -
   1183A  LEU*     3.8     4.0    -      -       -      -
   1184A  LEU*     3.9    14.6    -      -       +      -
   1202A  LEU*     3.6    23.3    -      -       +      +
   1210A  THR*     3.3     5.2    -      -       -      +
   1211A  PHE*     2.7    42.5    +      -       +      -
   1250A  PRO*     3.5    33.7    -      -       +      +
   1251A  THR*     6.0     5.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE1145 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1132A  ALA*     3.4     3.2    -      -       -      -
   1133A  TYR*     2.8    57.4    +      -       +      +
   1135A  PRO*     4.1    18.6    -      -       +      -
   1143A  GLU*     5.5     2.7    -      -       +      +
   1144A  TRP*     1.3    78.4    -      -       -      +
   1146A  GLN*     1.3    64.6    +      -       -      +
   1147A  CYS*     3.4     8.5    +      -       -      -
   1163A  ASP*     3.7    18.4    -      -       -      +
   1176A  TYR*     3.9    32.1    -      -       +      +
   1209A  THR      3.9     2.2    -      -       -      -
   1210A  THR*     4.0    10.5    -      -       +      +
   1211A  PHE*     4.5     0.9    -      -       -      -
      1P  ALA*     3.6    25.4    -      -       +      +
      3P  THR*     6.3     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN1146 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1130A  GLU*     2.8    32.5    +      -       -      +
   1131A  VAL      3.4     4.5    -      -       -      -
   1145A  ILE*     1.3    72.9    -      -       -      +
   1147A  CYS*     1.3    67.3    +      -       -      +
   1163A  ASP*     3.9     8.8    -      -       -      +
   1164A  PRO*     3.8    15.7    -      -       +      +
   1186A  ILE*     3.8    20.3    -      -       +      +
   1204A  ARG*     2.7    42.1    +      -       -      +
   1209A  THR*     2.9    33.8    +      -       -      +
   1211A  PHE*     3.9    10.1    -      -       +      -
   1245A  LEU*     5.7     1.1    -      -       -      +
      1P  ALA*     5.3     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS1147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1130A  GLU*     3.4    11.8    -      -       -      +
   1131A  VAL*     2.8    41.0    +      -       +      +
   1133A  TYR*     3.9    15.9    -      -       +      -
   1145A  ILE*     3.8    18.4    -      -       -      +
   1146A  GLN*     1.3    79.8    -      -       -      +
   1148A  GLU*     1.3    59.9    +      -       -      +
   1161A  VAL*     3.8    24.0    -      -       +      -
   1162A  ARG      3.2    11.0    -      -       -      +
   1163A  ASP*     3.7    24.5    -      -       -      -
   1164A  PRO*     4.6     1.3    -      -       -      -
   1176A  TYR*     4.6     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU1148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1128A  GLY*     5.4     4.8    -      -       -      +
   1129A  SER      3.4     6.7    -      -       -      +
   1130A  GLU*     3.3    17.7    +      -       -      +
   1147A  CYS*     1.3    74.4    -      -       -      +
   1149A  VAL*     1.3    63.9    +      -       -      +
   1150A  LEU*     3.6    12.7    +      -       +      +
   1161A  VAL*     3.2     4.0    -      -       -      -
   1162A  ARG*     2.8    83.5    +      -       +      +
   1164A  PRO*     4.4    16.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1149 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1125A  ILE*     3.8    12.6    -      -       +      -
   1126A  LEU      3.3    22.0    -      -       -      +
   1127A  VAL*     3.6     2.7    -      -       -      +
   1128A  GLY*     2.9    26.3    +      -       -      -
   1129A  SER*     2.9    20.8    +      -       -      +
   1131A  VAL*     3.7    32.1    -      -       +      -
   1148A  GLU*     1.3    74.6    -      -       -      +
   1150A  LEU*     1.3    65.9    +      -       -      +
   1151A  LYS      3.7    21.1    -      -       -      +
   1152A  VAL*     3.8    14.6    -      -       +      -
   1159A  PHE*     4.5     6.1    -      -       +      -
   1160A  GLU      3.8     4.9    -      -       -      +
   1161A  VAL*     4.1     7.2    -      -       +      -
   1183A  LEU*     4.9     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU1150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1127A  VAL*     3.5    20.3    -      -       -      +
   1148A  GLU*     3.8    30.7    -      -       +      +
   1149A  VAL*     1.3    76.1    -      -       -      +
   1151A  LYS*     1.3    63.7    +      -       +      +
   1160A  GLU*     2.7    38.5    +      -       -      +
   1162A  ARG*     3.7    44.6    -      -       +      +
   1175A  VAL*     4.0    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS1151 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1127A  VAL*     4.1     3.4    -      -       -      -
   1149A  VAL*     3.7     3.7    -      -       -      +
   1150A  LEU*     1.3    84.5    -      -       +      +
   1152A  VAL*     1.3    67.6    +      -       -      +
   1153A  VAL*     4.2    18.2    -      -       +      -
   1159A  PHE*     3.3     5.1    -      -       -      -
   1160A  GLU*     2.9    70.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1152 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1109A  GLU*     3.1    33.8    -      -       +      +
   1110A  PHE      3.9     4.9    -      -       -      -
   1111A  GLY      3.8    14.4    -      -       -      +
   1125A  ILE      3.7    17.9    -      -       -      +
   1127A  VAL*     4.0    18.3    -      -       +      +
   1149A  VAL*     3.8    17.5    -      -       +      -
   1151A  LYS*     1.3    78.7    -      -       -      +
   1153A  VAL*     1.3    68.6    +      -       -      +
   1156A  GLY*     3.7    25.6    -      -       -      -
   1158A  ARG      3.7     2.7    -      -       -      +
   1159A  PHE*     3.9    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL1153 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1109A  GLU*     3.2     8.3    -      -       -      -
   1151A  LYS*     4.4    21.8    -      -       +      -
   1152A  VAL*     1.3    80.7    -      -       -      +
   1154A  ALA*     1.3    72.5    +      -       +      +
   1156A  GLY      3.2     8.7    +      -       -      -
   1157A  THR      3.3     4.2    +      -       -      -
   1158A  ARG*     2.9    47.1    +      -       +      +
   1159A  PHE*     5.3     2.0    -      -       -      -
----------------------------------------------------------
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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