Contacts of the strand formed by residues 2 - 14 (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 ASP 2 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  VAL*     1.3    77.5    +      -       -      +
      3A  PHE*     1.3    61.0    +      -       -      +
      4A  HIS*     3.9    20.9    +      -       +      +
     45A  LYS      3.5     0.9    -      -       -      +
     46A  LEU*     3.3     7.1    -      -       -      -
     47A  GLY      2.8    35.1    +      -       -      +
     48A  GLN*     4.2     4.3    -      -       -      -
     49A  GLU      4.6     1.3    +      -       -      -
     59A  TYR*     2.7    40.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 3 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  VAL      3.8     2.2    +      -       -      +
      2A  ASP*     1.3    72.5    -      -       -      +
      4A  HIS*     1.3    77.8    +      -       -      +
     44A  LEU*     4.5    17.0    -      -       +      -
     45A  LYS      3.4    12.6    -      -       -      -
     46A  LEU*     3.8    14.1    -      -       +      -
    427A  TRP*     3.2    54.3    -      +       -      +
      1C  VAL*     3.6    39.7    -      -       +      -
     46C  LEU*     3.9    39.3    -      -       +      -
     47C  GLY      4.6     4.7    -      -       -      -
     48C  GLN*     4.1    17.7    +      -       +      +
     60C  PHE*     4.3    12.6    -      +       -      -
     62C  THR*     5.1     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 4 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  ASP*     3.9    27.8    +      -       +      +
      3A  PHE*     1.3    79.1    +      -       -      +
      5A  GLY*     1.3    56.0    +      -       -      +
     45A  LYS*     2.7    55.9    +      -       +      +
     47A  GLY      6.1     0.4    -      -       -      -
     59A  TYR*     4.9     5.8    +      -       -      -
     61A  ASP*     6.1     0.9    -      -       -      -
    427A  TRP*     2.7    47.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 5 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  HIS*     1.3    79.5    -      -       -      +
      6A  TYR*     1.3    63.6    +      -       -      +
     43A  GLU*     3.1    14.8    -      -       -      -
     45A  LYS*     4.4    11.6    -      -       -      +
    426A  TRP*     3.3     7.4    -      -       -      +
    427A  TRP*     3.1    34.1    +      -       -      +
      3D  GLC      4.9     3.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 6 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  GLY*     1.3    75.4    -      -       -      +
      7A  ALA*     1.3    76.8    +      -       -      +
      8A  ARG*     2.9    42.5    +      -       +      +
     33A  ARG*     3.5     2.4    +      -       -      -
     41A  TYR*     3.8    20.0    -      +       -      -
     42A  ALA*     3.2     0.5    -      -       -      +
     43A  GLU*     2.7    37.8    +      -       +      +
    424A  GLU*     2.5    41.4    +      -       +      -
    425A  ILE      3.3    15.5    -      -       -      -
    426A  TRP*     3.9    16.8    -      +       +      -
    427A  TRP*     3.4     4.7    -      -       -      -
      2D  GLC      3.7    37.0    -      -       -      -
      3D  GLC      3.8    16.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 7 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  TYR*     1.3    81.2    -      -       -      +
      8A  ARG*     1.3    61.1    +      -       -      +
     41A  TYR      3.1    11.2    -      -       -      +
     42A  ALA*     3.8    12.3    -      -       +      -
    423A  MET*     4.2     8.7    -      -       +      -
    424A  GLU*     3.4     4.0    -      -       -      +
    425A  ILE*     2.9    47.8    +      -       +      +
    427A  TRP*     3.9     0.4    -      -       +      -
     60C  PHE*     4.1    20.4    -      -       +      -
     84C  ALA*     5.1     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 8 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  TYR*     2.9    37.5    +      -       -      +
      7A  ALA*     1.3    75.1    -      -       -      +
      9A  SER*     1.3    63.8    +      -       -      +
     33A  ARG*     3.7     6.3    -      -       -      +
     37A  GLU*     3.7    27.6    +      -       -      +
     39A  GLU*     2.9    39.8    +      -       -      +
     40A  THR*     3.2     5.1    -      -       -      +
     41A  TYR*     2.9    52.8    +      -       -      +
    116A  ASP*     4.4     4.2    +      -       -      -
    422A  GLN*     3.9    10.8    -      -       -      +
    423A  MET*     3.3    14.4    -      -       -      +
    424A  GLU*     4.5     3.8    -      -       +      +
      1D  BGC      4.0     7.7    +      -       -      -
      2D  GLC      3.0    27.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 9 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  ARG*     1.3    75.6    -      -       -      +
     10A  GLY*     1.3    60.6    +      -       -      +
     39A  GLU      4.6     1.1    -      -       -      -
     40A  THR*     2.8    27.3    +      -       -      +
     70A  GLN*     3.7     3.1    +      -       -      -
    422A  GLN*     3.4     5.4    -      -       -      +
    423A  MET*     2.8    39.6    +      -       -      +
     84C  ALA*     3.4    20.8    +      -       -      -
    103C  GLY*     3.5     6.4    +      -       -      -
    104C  LYS*     3.2    24.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 10 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  SER*     1.3    78.2    +      -       -      +
     11A  ILE*     1.3    62.0    +      -       -      +
     20A  GLN*     5.9     0.2    -      -       -      -
     39A  GLU      5.3     0.2    +      -       -      -
     70A  GLN*     3.2    29.9    +      -       -      +
    421A  ALA      3.2    13.2    -      -       -      -
    422A  GLN*     3.9     6.7    -      -       -      +
    103C  GLY*     4.6     8.9    -      -       -      -
    125C  PRO*     3.9    14.7    -      -       -      +
    126C  GLY      4.8     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 11 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  GLY*     1.3    75.7    -      -       -      +
     12A  GLY*     1.3    62.3    +      -       -      +
     13A  TRP*     3.8    36.3    -      -       +      -
     20A  GLN*     4.5     4.1    -      -       -      +
     70A  GLN*     5.0     2.0    -      -       -      +
    376A  PHE*     4.9     1.0    -      -       -      -
    420A  GLY*     3.3     1.4    -      -       -      -
    421A  ALA*     2.9    36.8    +      -       +      +
    125C  PRO*     4.0    15.0    -      -       +      +
    126C  GLY*     3.9    25.4    -      -       -      +
    127C  ALA*     4.0    12.1    -      -       +      +
    143C  ALA*     3.9    18.2    -      -       +      +
    144C  THR      4.0    13.7    -      -       -      +
    145C  ARG*     4.1    22.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 12 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  ILE*     1.3    78.6    -      -       -      +
     13A  TRP*     1.3    67.5    +      -       -      -
     19A  GLU*     3.7     0.2    -      -       -      -
     20A  GLN*     3.1    32.1    +      -       -      +
     70A  GLN*     5.6     1.0    -      -       -      +
    419A  PHE      3.3    10.5    -      -       -      -
    420A  GLY*     4.0     0.7    -      -       -      -
    145C  ARG*     3.0    28.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 13 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  ILE*     3.8    39.5    -      -       +      -
     12A  GLY*     1.3    73.7    -      -       -      -
     14A  THR*     1.3    62.9    +      -       -      +
     18A  GLY      3.6     4.3    -      -       -      +
     20A  GLN*     3.8     5.1    -      -       -      +
    418A  THR*     3.1     7.1    -      -       -      -
    419A  PHE*     2.8    76.3    +      +       +      -
    420A  GLY*     4.1    15.5    -      -       -      -
    421A  ALA*     4.9     0.9    -      -       +      -
    143C  ALA*     4.3    20.0    -      -       +      -
    144C  THR      5.9     0.2    -      -       -      -
    145C  ARG*     3.0    17.4    -      -       -      +
    170C  ASP*     2.7    30.8    +      -       +      -
    172C  PHE*     4.7    13.3    -      +       -      -
    197C  ASN*     3.6    14.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 14 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  TRP*     1.3    74.6    -      -       -      +
     15A  GLY*     1.3    66.5    +      -       -      +
     16A  SER*     3.7     9.9    -      -       -      +
     17A  GLY*     2.8    31.9    +      -       -      +
     18A  GLY      3.0     6.9    +      -       -      +
     19A  GLU      2.5    20.4    +      -       -      -
     21A  GLN*     3.2    32.8    +      -       -      +
    416A  GLU*     3.3    39.7    -      -       +      +
    417A  TRP      3.7     3.1    -      -       -      +
    418A  THR*     3.8     3.5    -      -       +      +
    419A  PHE*     4.6     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