Contacts of the strand formed by residues 1546 - 1550 (chain A) in PDB entry 3ZQK


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 VAL1546 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1540A  LEU*     4.0    30.3    -      -       +      -
   1541A  GLN      3.7     3.6    -      -       -      +
   1542A  TYR*     4.3     4.9    -      -       +      -
   1545A  MET*     1.3    82.1    -      -       -      +
   1547A  THR*     1.3    62.9    +      -       -      +
   1548A  VAL*     4.2     1.7    +      -       +      +
   1577A  ASN      5.2     0.4    -      -       -      +
   1580A  LEU*     3.9    20.7    -      -       +      +
   1581A  ALA*     3.6    35.4    -      -       +      +
   1584A  TYR*     4.0    32.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR1547 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1540A  LEU*     3.3     4.2    -      -       -      -
   1541A  GLN      2.8    33.9    +      -       -      -
   1545A  MET*     4.0    10.7    -      -       -      +
   1546A  VAL*     1.3    74.7    +      -       -      +
   1548A  VAL*     1.3    66.4    +      -       -      +
   1549A  GLU*     3.2    29.5    +      -       -      +
   1571A  GLN*     2.7    28.4    +      -       -      +
   1507B  ASP*     4.2    10.1    -      -       +      +
   1572B  GLY*     5.8     3.2    -      -       -      -
   1573B  GLY*     5.3     6.2    +      -       -      +
   1574B  ASN*     3.9    16.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL1548 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1538A  THR*     4.6     1.8    -      -       -      +
   1539A  VAL      3.8     5.2    -      -       -      +
   1540A  LEU*     3.6    11.0    -      -       +      -
   1546A  VAL*     4.2     3.0    +      -       +      +
   1547A  THR*     1.3    72.5    -      -       -      +
   1549A  GLU*     1.3    61.4    +      -       -      +
   1550A  TYR      3.7    26.0    -      -       -      +
   1551A  PRO*     3.8    17.5    -      -       +      -
   1584A  TYR*     3.4    42.2    -      -       +      +
   1507B  ASP*     4.7     0.2    -      -       -      +
   1574B  ASN*     2.9    28.7    +      -       -      +
   4677B  NAG      3.8    27.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU1549 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1539A  VAL*     2.7    30.6    +      -       +      +
   1541A  GLN*     3.0    43.1    +      -       +      +
   1547A  THR*     3.6    24.8    -      -       -      +
   1548A  VAL*     1.3    73.3    -      -       -      +
   1550A  TYR*     1.3    59.0    +      -       -      +
   1564A  ARG*     3.3    28.2    -      -       -      +
   1565A  LEU*     4.2     9.4    -      -       +      +
   1568A  ILE*     3.4    25.0    -      -       +      +
   1569A  ARG      4.5     0.2    -      -       -      +
   1571A  GLN*     4.5     0.3    -      -       -      +
   1507B  ASP*     2.6    34.2    -      -       -      +
   4677B  NAG      4.3     3.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR1550 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1537A  VAL      3.9    11.7    -      -       -      -
   1538A  THR*     2.6    28.5    +      -       -      -
   1539A  VAL*     3.0    27.7    +      -       +      +
   1548A  VAL*     3.5     3.9    -      -       -      +
   1549A  GLU*     1.3    75.7    -      -       -      +
   1551A  PRO*     1.3    75.6    -      -       +      +
   1554A  GLU*     3.7    23.0    +      -       +      +
   1555A  ALA*     2.7    32.1    +      -       -      +
   1556A  GLN*     3.8     9.9    -      -       -      -
   1560A  ASP*     3.5    31.1    -      -       -      +
   1561A  ILE*     3.5    30.7    -      -       +      -
   1564A  ARG*     3.8    33.2    +      -       +      -
   1565A  LEU*     4.6     4.9    -      -       +      -
----------------------------------------------------------
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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