Contacts of the helix formed by residues 1071 - 1083 (chain A) in PDB entry 1RPM


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 THR1071 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1069A  HIS*     3.0    20.2    +      -       -      +
   1070A  ALA*     1.3    76.2    -      -       -      +
   1072A  GLY*     1.3    57.9    +      -       -      +
   1074A  LEU*     3.3     5.0    +      -       -      +
   1075A  GLY*     2.9    25.5    +      -       -      -
   1153A  GLU*     2.7    29.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY1072 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1034A  GLU*     3.5    32.0    +      -       -      -
   1035A  TYR*     5.0     4.5    -      -       -      -
   1058A  PHE*     3.7     8.9    -      -       -      -
   1069A  HIS*     4.2     4.2    +      -       -      +
   1070A  ALA      3.3     0.8    -      -       -      -
   1071A  THR*     1.3    79.0    -      -       -      +
   1073A  LEU*     1.3    56.6    +      -       -      +
   1075A  GLY*     3.2     2.7    +      -       -      -
   1076A  PHE*     2.9    26.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU1073 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    997A  VAL*     4.8     5.4    -      -       +      -
   1034A  GLU*     4.4     0.2    +      -       -      -
   1058A  PHE*     3.7    35.5    -      -       +      -
   1061A  TRP*     3.7    16.2    -      -       +      -
   1067A  PRO*     5.4     1.5    -      -       +      +
   1069A  HIS      5.1     0.6    +      -       -      -
   1070A  ALA*     3.2     8.3    +      -       +      +
   1072A  GLY*     1.3    71.6    -      -       -      +
   1074A  LEU*     1.3    61.0    +      -       +      +
   1076A  PHE*     3.3    25.0    -      -       +      +
   1077A  VAL*     2.9    39.0    +      -       +      +
   1104A  CYS*     5.1     2.7    -      -       +      -
   1105A  PHE*     5.1    10.3    -      -       +      +
   1108A  ILE*     3.7    21.8    -      -       +      -
   1146A  PHE*     3.2    39.0    -      -       +      -
   1150A  ALA*     5.6     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU1074 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1070A  ALA*     2.9    16.8    +      -       +      +
   1071A  THR*     3.4     9.2    -      -       -      +
   1073A  LEU*     1.3    73.9    -      -       +      +
   1075A  GLY*     1.3    65.9    +      -       -      +
   1077A  VAL*     3.3     5.2    +      -       -      +
   1078A  ARG*     3.2    26.6    +      -       -      +
   1108A  ILE*     4.2    21.8    -      -       +      -
   1112A  LEU*     4.6     7.7    -      -       +      +
   1150A  ALA*     3.2    35.7    -      -       +      +
   1153A  GLU*     3.6    27.4    -      -       +      +
   1154A  ALA*     3.6    29.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY1075 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1035A  TYR*     4.8     7.1    +      -       -      -
   1071A  THR      2.9    14.3    +      -       -      -
   1072A  GLY*     3.2     4.0    +      -       -      -
   1074A  LEU*     1.3    78.4    -      -       -      +
   1076A  PHE*     1.3    60.6    +      -       -      +
   1078A  ARG*     3.4     6.2    +      -       -      +
   1079A  GLN*     3.2    20.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE1076 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    995A  ILE*     3.8    23.3    -      -       +      -
    996A  MET      4.4     0.2    -      -       -      -
    997A  VAL*     4.3     3.4    -      -       +      -
   1035A  TYR*     3.7    37.1    -      +       +      -
   1056A  PHE*     3.2    52.7    -      +       +      -
   1057A  HIS      4.0     1.6    -      -       -      -
   1058A  PHE*     3.6    34.1    -      +       +      -
   1072A  GLY      2.9    14.3    +      -       -      +
   1073A  LEU*     3.3    22.9    -      -       +      +
   1075A  GLY*     1.3    75.7    -      -       -      +
   1077A  VAL*     1.3    64.3    +      -       -      +
   1079A  GLN*     3.2     5.3    +      -       -      +
   1080A  VAL*     3.0    27.4    +      -       +      +
   1105A  PHE*     4.1    15.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with VAL1077 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1073A  LEU*     2.9    37.5    +      -       +      +
   1074A  LEU*     3.3     7.6    +      -       -      +
   1076A  PHE*     1.3    75.4    -      -       -      +
   1078A  ARG*     1.3    57.4    +      -       -      +
   1080A  VAL*     3.1     4.9    +      -       -      +
   1081A  LYS*     2.9    35.2    +      -       +      +
   1105A  PHE*     4.3    26.5    -      -       +      -
   1108A  ILE*     4.2    20.0    -      -       +      -
   1109A  ASP*     3.6    32.3    -      -       +      +
   1112A  LEU*     4.1    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG1078 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1074A  LEU      3.2    11.5    +      -       -      +
   1075A  GLY*     3.8     9.0    -      -       -      +
   1076A  PHE      3.4     0.2    -      -       -      -
   1077A  VAL*     1.3    76.4    -      -       +      +
   1079A  GLN*     1.3    59.9    +      -       -      +
   1081A  LYS*     3.4    41.9    -      -       +      +
   1082A  SER*     2.9    46.8    +      -       -      +
   1112A  LEU*     5.5     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN1079 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1030A  GLU*     4.3    10.7    +      -       -      -
   1032A  LEU*     4.5     2.8    -      -       -      +
   1035A  TYR*     2.7    32.9    +      -       +      +
   1037A  ILE*     3.6    25.7    -      -       +      +
   1056A  PHE*     4.1     8.1    -      -       +      -
   1075A  GLY      3.2    12.4    +      -       -      +
   1076A  PHE      3.2    11.1    +      -       -      +
   1078A  ARG*     1.3    72.4    -      -       -      +
   1080A  VAL*     1.3    62.0    +      -       -      +
   1082A  SER*     3.0     7.5    +      -       -      -
   1083A  LYS*     2.9    61.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1080 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    995A  ILE*     4.1    28.0    -      -       +      -
   1056A  PHE*     3.6    40.2    -      -       +      -
   1076A  PHE*     3.0    20.4    +      -       +      +
   1077A  VAL      3.5     6.3    -      -       -      +
   1079A  GLN*     1.3    77.4    -      -       -      +
   1081A  LYS*     1.3    58.6    +      -       +      +
   1084A  SER*     2.6    48.1    +      -       -      +
   1091A  LEU*     4.2     9.4    -      -       +      -
   1105A  PHE*     4.1    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS1081 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1077A  VAL*     2.9    23.1    +      -       +      +
   1078A  ARG*     3.4    36.1    -      -       -      +
   1080A  VAL*     1.3    77.4    -      -       +      +
   1082A  SER*     1.3    64.0    +      -       -      +
   1084A  SER*     3.8    14.6    +      -       -      +
   1109A  ASP*     2.5    59.7    +      -       -      +
   1112A  LEU*     3.7    26.1    -      -       +      +
   1113A  ASP*     3.5    18.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER1082 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1078A  ARG*     2.9    37.0    +      -       -      +
   1079A  GLN*     3.0    18.2    +      -       -      -
   1081A  LYS*     1.3    80.7    -      -       -      +
   1083A  LYS*     1.3    69.8    +      -       -      +
   1084A  SER      4.6     2.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS1083 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1030A  GLU*     3.4    17.6    +      -       -      -
   1037A  ILE*     3.3    32.9    -      -       +      +
   1054A  ARG*     2.8    50.3    +      -       -      +
   1056A  PHE*     3.8    13.5    -      -       +      -
   1079A  GLN*     2.9    40.0    +      -       -      +
   1082A  SER*     1.3    83.0    +      -       -      +
   1084A  SER*     1.3    62.6    +      -       -      +
   1085A  PRO*     3.4     5.0    -      -       -      +
   1028B  GLU*     4.1     4.6    -      -       -      +
   1030B  GLU*     6.2     0.2    -      -       -      +
   1083B  LYS*     5.6    13.5    -      -       -      +
----------------------------------------------------------
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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