Contacts of the strand formed by residues 185 - 197 (chain A) in PDB entry 2MPR


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 GLY 185 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180A  GLN*     3.2    14.8    +      -       -      +
    181A  THR*     3.3     8.9    +      -       -      -
    182A  ASN*     2.9    29.3    +      -       -      +
    183A  PRO      3.1     1.6    -      -       -      -
    184A  ASP*     1.3    79.8    -      -       -      +
    186A  VAL*     1.3    61.9    +      -       -      -
    219A  HIS*     3.6     2.7    -      -       -      -
    220A  THR      3.3     6.3    -      -       -      -
    221A  GLN*     3.4    14.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 186 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178A  GLY*     3.4    34.5    -      -       -      +
    179A  LEU      3.2     6.3    -      -       -      +
    180A  GLN*     3.3    29.4    -      -       +      +
    181A  THR*     4.4     0.2    -      -       -      -
    184A  ASP      5.3     1.8    -      -       -      -
    185A  GLY*     1.3    76.5    -      -       -      +
    187A  LEU*     1.3    64.9    +      -       -      +
    188A  GLU*     6.0     0.4    -      -       +      -
    218A  GLU      3.8     0.5    -      -       -      +
    219A  HIS*     3.3     9.0    +      -       -      -
    220A  THR*     2.8    42.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 187 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177A  ALA      4.0     0.2    -      -       -      -
    178A  GLY      3.5     4.7    +      -       -      -
    179A  LEU*     2.7    50.3    +      -       +      +
    181A  THR*     3.7    27.6    -      -       +      +
    186A  VAL*     1.3    77.8    -      -       -      +
    188A  GLU*     1.3    65.4    +      -       -      +
    189A  LEU*     3.9    25.6    -      -       +      -
    217A  ALA*     4.7     5.8    -      -       +      -
    218A  GLU      3.5    24.2    -      -       -      +
    219A  HIS*     4.2    12.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 188 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  GLN*     4.1     9.2    -      -       -      +
    110A  HIS*     3.1    26.3    +      -       -      -
    120A  TRP*     3.8    21.9    -      -       +      -
    175A  ARG*     4.0    18.7    +      -       -      +
    176A  LEU      3.2    12.1    -      -       -      +
    177A  ALA*     3.9    22.7    -      -       +      +
    178A  GLY      5.0     0.4    -      -       -      +
    186A  VAL*     6.0     0.7    -      -       +      -
    187A  LEU*     1.3    75.7    -      -       -      +
    189A  LEU*     1.3    71.6    +      -       -      +
    216A  THR*     3.9     1.2    -      -       -      +
    217A  ALA*     3.4     4.7    -      -       -      -
    218A  GLU*     2.9    43.2    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 189 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  TRP*     4.4     0.4    -      -       -      -
    175A  ARG*     3.3     4.0    -      -       -      +
    176A  LEU*     2.8    45.2    +      -       +      +
    179A  LEU*     3.6    27.8    -      -       +      -
    187A  LEU*     3.9    19.3    -      -       +      -
    188A  GLU*     1.3    85.2    -      -       -      +
    190A  GLY*     1.3    58.8    +      -       -      +
    191A  VAL*     6.5     0.2    -      -       +      -
    216A  THR      3.4     3.8    -      -       -      +
    217A  ALA*     3.9    20.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 190 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  TRP*     3.7    24.4    -      -       -      -
    174A  VAL      3.2    10.8    -      -       -      -
    175A  ARG*     4.0     0.2    -      -       -      -
    189A  LEU*     1.3    76.2    -      -       -      +
    191A  VAL*     1.3    65.2    +      -       -      +
    192A  ASP*     5.3     0.4    -      -       -      -
    215A  PHE*     3.5     4.3    -      -       -      +
    216A  THR*     2.9    35.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 191 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  TRP*     4.9     0.6    -      -       -      -
    172A  PHE      3.8     1.6    -      -       -      +
    173A  ASP*     3.6     3.8    -      -       -      +
    174A  VAL*     2.9    40.0    +      -       +      +
    189A  LEU*     6.5     0.4    -      -       +      -
    190A  GLY*     1.3    77.8    -      -       -      +
    192A  ASP*     1.3    67.6    +      -       -      +
    193A  TYR*     4.9     0.9    -      -       +      +
    213A  TRP*     3.7    34.1    -      -       +      -
    214A  MET      3.5     3.8    -      -       -      -
    215A  PHE*     4.0    22.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 192 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  TRP*     3.1    29.7    +      -       -      -
    122A  ILE*     4.0     4.0    -      -       -      +
    171A  VAL*     3.6    13.0    -      -       +      +
    172A  PHE      3.5     2.0    -      -       -      -
    173A  ASP*     2.5    34.9    -      -       -      +
    190A  GLY      5.3     0.3    -      -       -      -
    191A  VAL*     1.3    78.6    +      -       -      +
    193A  TYR*     1.3    59.0    +      -       -      +
    213A  TRP*     3.3     7.8    -      -       -      -
    214A  MET*     2.9    42.6    +      -       +      +
    216A  THR*     5.1     1.0    +      -       -      -
    239A  MET*     3.5    20.5    -      -       +      +
    245A  GLY*     4.3     8.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 193 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171A  VAL*     4.4     0.9    -      -       -      -
    172A  PHE*     3.0    57.3    +      +       +      +
    191A  VAL*     4.3     0.8    -      -       +      +
    192A  ASP*     1.3    75.0    -      -       -      +
    194A  GLY*     1.3    58.8    +      -       -      +
    195A  ARG*     3.8    30.0    -      -       +      +
    210A  LYS*     5.6     0.5    -      -       -      -
    211A  ASP*     2.7    41.0    +      -       +      +
    212A  GLY      3.3    17.3    -      -       -      -
    213A  TRP*     3.4    49.1    -      +       +      -
    239A  MET*     4.6     1.1    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 194 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170A  ASP      3.0    11.2    -      -       -      -
    171A  VAL*     4.2     2.7    -      -       -      -
    193A  TYR*     1.3    77.2    -      -       -      +
    195A  ARG*     1.3    63.0    +      -       -      -
    211A  ASP*     3.2     5.5    -      -       -      +
    212A  GLY      3.1    33.4    +      -       -      +
    239A  MET*     4.1     7.7    -      -       -      +
    247A  ALA*     3.8    21.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 195 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169A  ASN*     4.1     4.7    -      -       -      -
    170A  ASP*     2.9    56.1    +      -       -      +
    172A  PHE*     3.4    30.6    -      -       +      -
    193A  TYR*     3.8    21.5    -      -       +      +
    194A  GLY*     1.3    77.0    -      -       -      +
    196A  ALA*     1.3    68.3    +      -       -      +
    197A  ASN*     3.2    31.3    +      -       -      +
    210A  LYS*     3.2    17.7    -      -       -      +
    211A  ASP*     3.6    15.9    -      -       +      +
    247A  ALA*     3.9     3.7    -      -       -      +
     13B  TRP*     4.8     3.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167A  THR*     3.7    22.4    -      -       +      -
    168A  ALA      3.3     7.0    -      -       -      -
    169A  ASN*     3.6    15.6    +      -       -      +
    195A  ARG*     1.3    75.1    +      -       -      +
    197A  ASN*     1.3    59.7    +      -       -      +
    198A  THR*     3.9     2.1    +      -       +      +
    204A  LEU*     4.2    20.0    -      -       +      -
    210A  LYS*     2.9    38.9    +      -       -      +
    249A  GLY*     4.1    10.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145A  ARG*     5.0     0.4    -      -       -      +
    167A  THR*     4.5     0.6    -      -       -      +
    168A  ALA*     2.7    30.8    +      -       +      +
    170A  ASP*     3.0    23.6    +      -       -      +
    195A  ARG*     3.2    26.5    +      -       -      +
    196A  ALA*     1.3    70.5    -      -       -      +
    198A  THR*     1.3    60.6    +      -       -      +
    199A  THR      3.9     0.3    +      -       -      -
    210A  LYS*     5.5     0.2    -      -       -      +
     13B  TRP*     3.6    17.8    -      -       -      -
     17B  GLY*     3.8     4.2    -      -       -      -
     18B  GLY*     2.7    47.8    +      -       -      +
     19B  GLU*     4.2     1.9    -      -       -      +
----------------------------------------------------------
 Back to top of page


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