Contacts of the strand formed by residues 580 - 587 (chain A) in PDB entry 1MWH


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 GLN 580 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323A  SER*     3.8     8.5    +      -       -      -
    574A  ALA      3.7     5.0    -      -       -      +
    578A  PRO      4.7     0.2    -      -       -      +
    579A  ASN*     1.3    81.0    -      -       -      +
    581A  SER*     1.3    60.2    +      -       -      +
    582A  ILE*     5.8     0.7    -      -       +      -
    739A  ILE*     3.7     1.7    -      -       -      +
    740A  ILE*     2.7    46.5    +      -       +      +
    747A  LYS*     3.1    40.7    -      -       +      +
    748A  VAL*     3.1    28.6    +      -       -      +
    753A  ILE*     3.7    13.0    -      -       +      +
    775A  TYR*     2.9    37.2    +      -       +      -
----------------------------------------------------------
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Residues in contact with SER 581 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    574A  ALA*     3.7    21.9    +      -       -      -
    575A  SER*     4.5     1.8    +      -       -      +
    580A  GLN*     1.3    77.2    -      -       -      +
    582A  ILE*     1.3    67.9    +      -       -      +
    583A  ASN      4.1     0.6    +      -       -      -
    737A  LEU*     3.7    20.0    -      -       -      -
    738A  MET      3.1    10.3    -      -       -      -
    739A  ILE*     4.7     0.2    -      -       -      -
    774A  ALA      4.6     1.0    -      -       -      +
    775A  TYR*     4.5     7.6    -      -       -      -
    776A  ASP      5.3     0.3    +      -       -      -
    777A  GLY*     5.3     1.7    +      -       -      -
    778A  THR      3.5    18.7    +      -       -      +
    779A  ALA*     3.3    24.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 582 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    580A  GLN*     5.9     0.7    -      -       +      -
    581A  SER*     1.3    75.1    -      -       -      +
    583A  ASN*     1.3    60.7    +      -       -      +
    584A  ILE*     3.3     9.7    +      -       +      -
    737A  LEU*     3.8     1.7    -      -       -      -
    738A  MET*     2.9    54.8    +      -       +      +
    740A  ILE*     4.5     9.2    -      -       +      -
    753A  ILE*     3.5    24.7    -      -       +      -
    757A  LEU*     3.3    32.1    -      -       +      -
    773A  ILE*     3.5    19.7    -      -       +      -
    774A  ALA      3.5     8.5    -      -       -      +
    775A  TYR*     3.3    36.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 583 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    283A  HIS*     5.8     0.6    -      -       -      -
    582A  ILE*     1.3    70.5    -      -       -      +
    584A  ILE*     1.3    59.7    +      -       -      +
    585A  ASP*     4.5     4.2    -      -       -      +
    736A  GLY      3.8     6.1    -      -       -      -
    737A  LEU*     3.5     8.7    -      -       -      +
    772A  ASP      3.5     5.7    -      -       -      +
    773A  ILE*     3.5     0.2    -      -       -      -
    774A  ALA*     2.9    49.2    +      -       +      +
    776A  ASP*     4.0    10.5    +      -       -      -
    778A  THR*     3.1    25.4    +      -       -      +
    779A  ALA*     3.3     7.3    -      -       -      -
    780A  GLU*     2.6    57.6    +      -       +      +
   1500A   MN      4.6     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 584 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    582A  ILE*     3.3    21.7    +      -       +      +
    583A  ASN*     1.3    72.8    -      -       -      +
    585A  ASP*     1.3    74.7    +      -       -      +
    586A  ILE*     5.8     0.2    -      -       +      -
    699A  MET*     3.6    26.2    -      -       +      -
    729A  TYR*     4.0    15.8    +      -       +      +
    734A  ASP      4.1     0.2    -      -       -      +
    736A  GLY*     2.7    33.9    +      -       -      +
    738A  MET*     3.7    29.6    -      -       +      -
    757A  LEU*     4.9     0.7    -      -       +      -
    760A  ILE*     4.3    10.8    -      -       +      -
    771A  TYR*     3.6    32.1    -      -       +      -
    772A  ASP      3.9     1.6    -      -       -      -
    773A  ILE*     4.1    13.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 585 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    583A  ASN*     4.5     4.0    -      -       -      +
    584A  ILE*     1.3    89.2    -      -       -      +
    586A  ILE*     1.3    64.6    +      -       -      +
    734A  ASP*     3.3     8.5    -      -       -      +
    735A  ASP*     2.3    12.4    -      -       -      +
    771A  TYR*     3.2     9.2    -      -       -      -
    772A  ASP*     2.5    54.6    +      -       +      +
    780A  GLU*     3.7     2.1    -      -       -      +
   1500A   MN      2.2    36.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 586 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    584A  ILE*     5.8     0.7    -      -       +      -
    585A  ASP*     1.3    79.6    -      -       -      +
    587A  SER*     1.3    68.7    +      -       -      +
    588A  ALA      4.1     0.5    +      -       -      -
    589A  CYS*     4.3    16.0    -      -       +      +
    592A  SER*     5.4     0.4    -      -       -      +
    691A  HIS      5.6     0.7    -      -       -      +
    695A  ASN*     3.5    32.3    -      -       +      +
    729A  TYR*     5.9     0.2    -      -       -      +
    733A  GLY      4.8     0.7    -      -       -      +
    734A  ASP*     3.0    38.6    +      -       +      +
    769A  TRP*     3.4    62.6    -      -       +      -
    770A  LYS      3.7     6.5    -      -       -      +
    771A  TYR*     3.8    18.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 587 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    585A  ASP      4.1     0.8    -      -       -      -
    586A  ILE*     1.3    74.6    -      -       -      +
    588A  ALA*     1.3    74.7    +      -       -      +
    589A  CYS      3.2     2.6    +      -       -      -
    592A  SER*     4.0     5.5    +      -       -      -
    770A  LYS*     3.1    38.7    +      -       -      +
    772A  ASP*     4.4    18.7    -      -       -      +
----------------------------------------------------------
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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