Contacts of the strand formed by residues 372 - 384 (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 ALA 372 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    360A  GLN*     3.6    30.7    -      -       +      +
    361A  TRP      3.2     7.0    -      -       -      -
    362A  GLN*     4.1     4.3    -      -       +      -
    369A  SER      4.4     0.4    -      -       -      +
    370A  ARG*     4.0    18.2    -      -       -      +
    371A  PRO*     1.3    76.9    -      -       -      +
    373A  ILE*     1.3    64.4    +      -       -      +
    374A  ARG*     4.1    10.7    -      -       -      +
    423A  MET*     3.2     8.1    -      -       -      +
    424A  GLU      3.0    26.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 373 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    360A  GLN*     3.3     4.0    -      -       -      -
    361A  TRP*     2.9    41.1    +      -       +      +
    372A  ALA*     1.3    77.7    -      -       -      +
    374A  ARG*     1.3    65.7    +      -       -      +
    375A  ILE*     5.7     2.9    -      -       +      -
    421A  ALA*     5.9     1.3    -      -       +      -
    422A  GLN      3.5     3.1    -      -       -      +
    423A  MET*     4.6     4.3    -      -       +      -
     58C  PHE*     4.5    10.1    -      -       +      -
     86C  VAL*     3.9    35.4    -      -       +      +
     88C  GLY      4.1     4.9    -      -       -      +
    100C  ILE*     3.7    51.4    -      -       +      +
    101C  TRP*     4.3     4.9    -      -       -      +
    102C  ALA*     4.3    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 374 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  ARG*     5.8     3.2    -      -       -      +
     34A  LEU*     4.1    27.8    -      -       +      +
     35A  GLY      6.0     0.2    -      -       -      +
     37A  GLU*     4.5     4.6    +      -       -      -
    113A  HIS*     5.1     0.2    +      -       -      -
    321A  ARG*     4.4    10.1    -      -       -      +
    333A  LEU*     5.6     1.2    -      -       +      +
    358A  ALA*     4.6     8.3    -      -       +      -
    359A  GLN      3.3     6.3    -      -       -      +
    360A  GLN*     3.1    32.5    +      -       +      +
    370A  ARG*     3.4    21.2    -      -       -      +
    372A  ALA*     4.2     5.6    -      -       -      +
    373A  ILE*     1.3    80.6    -      -       -      +
    375A  ILE*     1.3    69.4    +      -       -      +
    376A  PHE*     4.2     7.2    -      -       +      -
    421A  ALA*     3.1     6.6    -      -       -      +
    422A  GLN*     2.8    68.0    +      -       +      +
    424A  GLU*     3.0    41.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 375 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    358A  ALA*     3.2     2.3    -      -       -      -
    359A  GLN*     2.8    54.8    +      -       +      +
    361A  TRP*     3.9    24.0    -      -       +      -
    373A  ILE*     5.7     3.1    -      -       +      -
    374A  ARG*     1.3    79.0    -      -       -      +
    376A  PHE*     1.3    60.6    +      -       -      +
    420A  GLY      3.3     7.9    -      -       -      +
    421A  ALA*     4.4    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 376 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  ILE      4.9     0.7    -      -       -      -
     20A  GLN*     3.6    28.0    -      -       -      -
     34A  LEU*     5.9     0.9    -      -       +      -
     35A  GLY*     3.6    35.9    -      -       -      +
     37A  GLU      5.8     0.2    -      -       -      -
    356A  THR*     4.3     6.5    -      -       +      -
    357A  LEU      3.2    13.5    -      -       -      +
    358A  ALA*     3.7    11.7    -      -       +      -
    374A  ARG*     4.7     7.9    -      -       +      -
    375A  ILE*     1.3    77.3    -      -       -      +
    377A  ALA*     1.3    64.6    +      -       -      +
    378A  THR*     3.9     6.3    -      -       -      -
    418A  THR*     4.3     2.9    -      -       -      -
    419A  PHE*     3.1    38.0    -      -       -      +
    420A  GLY*     2.9    46.3    +      -       -      +
    421A  ALA*     3.9    12.1    -      -       -      -
    422A  GLN*     4.3    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 377 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    355A  ILE      4.0     0.7    -      -       -      +
    356A  THR*     3.6     2.1    -      -       -      +
    357A  LEU*     3.1    35.7    +      -       +      +
    376A  PHE*     1.3    76.5    -      -       -      +
    378A  THR*     1.3    60.0    +      -       -      +
    417A  TRP*     5.1     9.0    -      -       +      -
    418A  THR      3.2     9.9    -      -       -      +
    419A  PHE*     4.0     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 378 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  PHE*     4.3    13.2    -      -       +      -
     35A  GLY*     2.7    23.5    +      -       -      +
     36A  ASN*     5.1     0.2    -      -       -      +
    354A  LYS*     3.7    22.0    -      -       +      -
    355A  ILE      3.5     2.7    -      -       -      +
    356A  THR*     2.8    29.3    +      -       -      +
    376A  PHE*     3.9     2.0    -      -       -      -
    377A  ALA*     1.3    73.3    -      -       -      +
    379A  TYR*     1.3    68.1    +      -       -      +
    417A  TRP*     2.8     9.8    -      -       -      +
    418A  THR*     2.7    52.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 379 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353A  TYR*     4.1    17.0    +      +       -      -
    354A  LYS*     3.1     4.3    -      -       -      +
    355A  ILE*     2.8    53.6    +      -       +      +
    378A  THR*     1.3    76.1    -      -       -      +
    380A  ALA*     1.3    61.2    +      -       -      +
    381A  LYS*     3.6    24.5    -      -       +      +
    415A  ASP*     2.8    45.0    +      -       +      +
    416A  GLU      3.4    13.0    -      -       -      -
    417A  TRP*     4.2    12.3    -      +       +      -
----------------------------------------------------------
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Residues in contact with ALA 380 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  PHE*     3.4    44.2    -      -       +      -
    352A  GLN*     4.6     2.9    -      -       -      -
    353A  TYR      3.5     5.8    -      -       -      +
    354A  LYS*     4.0    10.8    -      -       +      -
    379A  TYR*     1.3    78.0    -      -       -      +
    381A  LYS*     1.3    60.3    +      -       -      +
    382A  TRP*     3.5     9.2    -      -       +      -
    415A  ASP*     3.0     5.5    -      -       -      +
    416A  GLU      2.8    32.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 381 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    351A  ASN*     5.4     0.2    -      -       -      +
    352A  GLN*     3.4     2.9    -      -       -      +
    353A  TYR*     3.0    62.6    +      -       +      +
    379A  TYR*     3.6    18.3    -      -       +      +
    380A  ALA*     1.3    75.1    -      -       -      +
    382A  TRP*     1.3    89.8    +      -       -      +
    383A  ASP*     4.3     3.6    -      -       -      +
    413A  ASP*     3.1    26.0    +      -       -      -
    414A  SER      3.1    18.4    +      -       -      +
    415A  ASP*     3.4    14.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 382 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  PHE*     3.8    19.1    -      +       -      -
    351A  ASN*     3.3    14.1    -      -       -      +
    352A  GLN*     3.9     9.4    -      -       +      -
    380A  ALA*     3.5    24.9    -      -       +      -
    381A  LYS*     1.3    93.7    +      -       -      +
    383A  ASP*     1.3    61.3    +      -       -      +
    384A  GLU*     4.1     4.3    -      -       +      -
    411A  ARG*     3.2    74.5    +      -       +      +
    412A  GLY      3.3    15.0    -      -       -      -
    414A  SER*     2.9    49.5    +      -       -      +
    415A  ASP*     3.8    15.5    -      -       -      -
    416A  GLU*     3.9    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 383 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    349A  ARG      4.0     2.8    -      -       -      +
    350A  ASN*     3.7     2.4    -      -       -      -
    351A  ASN*     3.0    45.4    +      -       -      +
    381A  LYS*     4.5     3.4    -      -       -      +
    382A  TRP*     1.3    75.1    -      -       -      +
    384A  GLU*     1.3    62.3    +      -       -      +
    385A  LYS*     3.3    38.7    +      -       -      +
    412A  GLY      3.5     2.5    -      -       -      -
    413A  ASP*     3.4    25.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 384 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  ALA*     3.6     4.9    -      -       -      +
     26A  THR*     2.6    44.7    +      -       -      -
    350A  ASN*     3.0    19.5    -      -       +      +
    351A  ASN      4.7     1.3    -      -       -      +
    382A  TRP*     4.1     9.6    -      -       +      +
    383A  ASP*     1.3    77.7    +      -       -      +
    385A  LYS*     1.3    62.7    +      -       -      +
    386A  TRP      3.4     0.7    -      -       -      +
    402A  THR*     2.8    17.2    +      -       -      -
    410A  SER*     3.3    13.7    +      -       -      +
    411A  ARG*     2.7    50.0    +      -       -      +
    412A  GLY*     2.7    24.9    +      -       -      +
----------------------------------------------------------
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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