Contacts of the strand formed by residues 104 - 111 (chain A) in PDB entry 2RHM


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 THR 104 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  THR*     3.5    32.6    +      -       +      +
      4A  PRO      2.9     9.4    +      -       -      +
      5A  ALA*     3.3    21.8    +      -       -      +
      6A  LEU      3.0    17.1    +      -       -      -
    103A  PHE*     1.3    73.4    -      -       -      +
    105A  PRO*     1.3    68.8    -      -       -      +
    106A  ILE*     4.3     3.6    -      -       -      +
    188A  GLY*     5.6    10.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 105 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  LEU      3.4     8.5    -      -       -      +
      8A  ILE*     4.6     3.8    -      -       +      -
     98A  HIS*     5.7     1.3    -      -       +      -
    103A  PHE*     3.7    27.8    -      -       +      +
    104A  THR*     1.3    84.8    -      -       -      +
    106A  ILE*     1.3    64.9    +      -       -      +
    107A  GLN*     4.3     1.8    -      -       +      -
    157A  LEU*     3.7    30.1    -      -       +      +
    158A  GLY      3.6    23.3    -      -       -      +
    159A  GLY*     3.8     4.8    -      -       -      -
    160A  PRO*     3.5    16.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 106 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  ALA*     4.1     9.6    -      -       +      -
      6A  LEU      3.0     8.2    +      -       -      +
      7A  ILE*     3.2    11.8    -      -       +      +
      8A  ILE*     2.8    26.1    +      -       -      +
    104A  THR*     4.3     4.9    -      -       -      +
    105A  PRO*     1.3    79.7    -      -       -      +
    107A  GLN*     1.3    63.6    +      -       -      +
    160A  PRO*     4.0    16.2    -      -       +      -
    180A  TRP*     3.6    31.0    -      -       +      -
    181A  VAL*     4.2    20.2    -      -       +      -
    184A  HIS*     4.1    19.1    -      -       +      +
    185A  LEU*     3.5    34.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 107 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  ILE*     3.4    22.9    -      -       +      +
     10A  THR*     3.7    13.4    -      -       +      +
    105A  PRO*     4.3     1.8    -      -       +      -
    106A  ILE*     1.3    75.2    -      -       -      +
    108A  ILE*     1.3    71.5    +      -       -      +
    154A  PRO*     3.5     8.0    -      -       -      +
    155A  LEU*     2.8    55.0    +      -       -      +
    157A  LEU*     4.6     8.3    -      -       -      +
    158A  GLY      5.3     3.6    +      -       -      -
    160A  PRO      3.0    15.4    +      -       -      +
    161A  LEU*     3.4    25.3    -      -       +      +
    162A  LEU      2.9    24.7    +      -       -      -
    180A  TRP*     3.9     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  ILE*     4.9     4.5    -      -       +      -
      8A  ILE      2.8    12.1    +      -       -      +
      9A  VAL*     3.3     8.1    -      -       +      +
     10A  THR*     2.9    26.0    +      -       -      +
     20A  LEU*     3.9    20.2    -      -       +      -
     24A  LEU*     3.5    22.7    -      -       +      -
    106A  ILE*     4.3     0.4    +      -       +      -
    107A  GLN*     1.3    80.1    -      -       -      +
    109A  ARG*     1.3    65.1    +      -       -      +
    110A  CYS*     4.4     3.1    -      -       -      -
    162A  LEU*     3.3    12.3    -      -       +      +
    164A  VAL*     4.1    17.7    -      -       +      -
    177A  ILE*     3.8    14.8    -      -       +      -
    180A  TRP*     4.1    11.7    -      -       +      -
    181A  VAL*     3.5    30.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  THR*     3.4    12.6    -      -       +      -
    107A  GLN      4.2     0.4    -      -       -      -
    108A  ILE*     1.3    73.4    -      -       -      +
    110A  CYS*     1.3    66.5    +      -       -      +
    111A  VAL*     4.2     8.0    -      -       +      +
    151A  ASP*     3.7    19.2    +      -       -      +
    152A  ILE*     2.9    48.8    +      -       +      -
    153A  PRO*     4.6     0.6    -      -       -      +
    154A  PRO*     4.0    26.7    -      -       +      +
    161A  LEU*     4.3    13.9    -      -       +      +
    162A  LEU      2.8    10.2    +      -       -      +
    163A  THR*     3.1    40.8    +      -       -      +
    164A  VAL      2.8    26.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  VAL*     4.3     7.9    -      -       -      -
     10A  THR      2.8    14.8    +      -       -      +
     11A  GLY*     3.4    16.8    -      -       -      -
     12A  HIS      4.3     0.3    +      -       -      -
     15A  THR*     3.4    32.6    +      -       -      +
     16A  GLY      4.1     1.6    -      -       -      -
     17A  LYS*     3.7    26.2    -      -       -      +
     20A  LEU*     3.8    28.0    -      -       -      -
    108A  ILE*     4.4     2.2    -      -       -      -
    109A  ARG*     1.3    74.2    -      -       -      +
    111A  VAL*     1.3    68.8    +      -       -      +
    152A  ILE*     4.7     1.9    +      -       -      +
    164A  VAL*     3.4     8.5    -      -       -      +
    166A  THR*     4.9     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  THR*     4.1     8.1    -      -       -      -
    109A  ARG*     4.2    11.4    -      -       +      +
    110A  CYS*     1.3    80.6    -      -       -      +
    112A  ALA*     1.3    56.9    +      -       -      +
    151A  ASP*     3.3    45.1    -      -       +      +
    152A  ILE      5.0     0.2    -      -       -      +
    163A  THR*     3.9    25.1    -      -       +      -
    164A  VAL      3.0     7.4    +      -       -      +
    165A  ASP*     3.6    27.1    -      -       +      +
    166A  THR*     2.8    33.2    +      -       -      -
----------------------------------------------------------
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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