Contacts of the strand formed by residues 455 - 460 (chain A) in PDB entry 4MZ7


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 LYS 455 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    453A  LEU*     3.6    13.5    -      -       +      +
    454A  PHE*     1.3    73.2    -      -       -      +
    456A  TYR*     1.3    62.7    +      -       -      +
    457A  VAL*     3.4     0.5    +      -       -      +
    553A  TYR*     3.0     6.5    -      -       -      -
    554A  CYS*     2.7    44.4    +      -       +      +
    556A  LYS      5.0     0.2    -      -       -      +
    557A  VAL*     3.7    42.0    -      -       +      +
    562A  LEU*     3.8    34.3    -      -       +      -
    801B  DGT      3.4    34.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 456 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    377A  LYS*     3.5    42.4    -      -       +      +
    378A  VAL*     6.0     1.6    -      -       +      -
    454A  PHE      3.7     3.4    +      -       -      -
    455A  LYS*     1.3    71.9    -      -       -      +
    457A  VAL*     1.3    63.6    +      -       -      +
    458A  GLY*     3.5    28.3    -      -       -      -
    459A  GLU*     3.2    29.6    +      -       -      +
    551A  ARG*     4.0    15.9    -      -       +      -
    552A  VAL      4.1     2.9    -      -       -      -
    553A  TYR*     3.6    28.2    -      +       +      -
    562A  LEU*     4.2     8.8    -      -       -      +
    566A  ARG*     4.6     8.3    +      -       -      -
    583A  ASP*     5.7     4.5    -      -       -      -
    703A  DGT      5.9     0.2    -      -       -      -
    801B  DGT      5.1    10.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 457 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    455A  LYS      3.8     1.1    -      -       -      +
    456A  TYR*     1.3    79.9    -      -       -      +
    458A  GLY*     1.3    56.5    +      -       -      +
    552A  VAL*     2.8    23.7    +      -       +      +
    553A  TYR      3.8     3.1    -      -       -      -
    554A  CYS*     3.6    27.1    -      -       +      +
    562A  LEU*     4.3     7.0    -      -       +      -
    565A  ALA*     3.6    40.4    -      -       +      +
    566A  ARG*     3.7    25.7    +      -       +      +
    569A  PHE*     3.7    17.1    -      -       +      -
    583A  ASP*     4.6     5.7    -      -       -      +
    587A  ILE*     4.2    16.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 458 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    456A  TYR*     3.5    21.9    -      -       -      -
    457A  VAL*     1.3    81.4    -      -       -      +
    459A  GLU*     1.3    60.6    +      -       -      -
    550A  ILE      3.9     0.3    -      -       -      +
    551A  ARG*     3.4     3.3    -      -       -      -
    552A  VAL      2.9    29.2    +      -       -      -
    569A  PHE*     3.6    15.7    -      -       -      -
    581A  PRO*     5.8     0.2    -      -       -      -
    583A  ASP*     5.5     5.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 459 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    371A  ARG*     4.5     8.0    +      -       -      -
    456A  TYR*     3.2    19.4    +      -       +      +
    458A  GLY*     1.3    72.1    -      -       -      +
    460A  THR*     1.3    72.3    +      -       -      +
    461A  GLN*     5.7     0.9    -      -       +      -
    549A  LEU*     3.3    28.9    -      -       +      +
    550A  ILE      3.2    11.4    -      -       -      +
    551A  ARG*     2.8    35.6    +      -       +      +
    569A  PHE*     3.6     7.8    -      -       -      -
    581A  PRO*     3.9    19.4    -      -       -      +
    582A  GLN*     5.0     7.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 460 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    459A  GLU*     1.3    79.0    -      -       -      +
    461A  GLN*     1.3    74.0    +      -       -      +
    549A  LEU*     3.8     0.5    -      -       -      -
    550A  ILE*     2.9    52.6    +      -       +      +
    569A  PHE*     4.2     6.3    -      -       +      -
    572A  TRP*     4.5     1.6    -      -       +      -
    573A  CYS*     3.6    25.8    -      -       -      -
    578A  PHE*     3.2    28.1    -      -       +      +
    579A  THR*     2.7    29.5    +      -       -      -
    581A  PRO*     5.0     0.2    -      -       -      -
----------------------------------------------------------
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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