Contacts of the strand formed by residues 32 - 36 (chain A) in PDB entry 1ZMC


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 THR 32 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  VAL*     3.4    10.1    -      -       +      +
     11A  VAL*     4.4     4.5    -      -       +      -
     22A  ALA*     3.6    42.0    -      -       +      +
     25A  ALA*     3.5    13.1    -      -       +      +
     26A  ALA*     3.4    19.4    +      -       -      +
     30A  PHE*     2.9    18.8    +      -       -      +
     31A  LYS*     1.3    76.1    -      -       -      +
     33A  VAL*     1.3    73.9    +      -       -      +
    111A  LYS      4.1     5.9    +      -       -      +
    112A  VAL*     3.8     7.3    -      -       +      -
    113A  VAL*     3.0    25.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 33 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  ILE*     4.0    18.6    -      -       +      -
      7A  ALA*     3.9    16.6    -      -       +      -
      9A  VAL      2.7    13.3    +      -       -      +
     10A  THR*     3.2    13.4    -      -       +      +
     11A  VAL*     2.6    35.7    +      -       -      +
     31A  LYS*     6.1     1.1    -      -       +      -
     32A  THR*     1.3    82.7    -      -       -      +
     34A  CYS*     1.3    58.0    +      -       -      +
     35A  ILE*     4.1     4.0    -      -       +      -
    113A  VAL*     3.4    23.1    -      -       +      +
    115A  VAL*     4.1    11.2    -      -       +      -
    139A  ILE*     3.6    32.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 34 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  VAL*     3.3    10.1    -      -       +      -
     13A  GLY      3.6    25.1    -      -       -      -
     14A  SER*     3.9    13.5    -      -       -      -
     18A  GLY      4.7     1.1    -      -       -      -
     22A  ALA*     4.0     9.6    -      -       +      -
     33A  VAL*     1.3    73.7    -      -       -      +
     35A  ILE*     1.3    59.9    +      -       -      +
     41A  LEU*     5.3     0.9    -      -       -      -
    107A  PHE*     3.7    39.7    -      -       +      -
    112A  VAL*     4.0     8.8    -      -       +      +
    113A  VAL      2.9     8.5    +      -       -      +
    114A  HIS*     3.4     5.9    -      -       -      -
    115A  VAL      2.8    29.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  THR*     3.6     8.7    -      -       +      -
     11A  VAL      2.9     9.2    +      -       -      +
     12A  ILE*     4.4    10.1    -      -       +      -
     13A  GLY*     2.9    31.0    +      -       -      -
     33A  VAL*     4.1     3.1    -      -       +      -
     34A  CYS*     1.3    77.4    -      -       -      +
     36A  GLU*     1.3    64.7    +      -       -      +
    115A  VAL*     3.1    17.3    -      -       +      +
    117A  GLY      3.3    20.4    -      -       -      +
    119A  GLY*     4.2     5.4    -      -       -      +
    127A  VAL*     3.5    25.6    -      -       +      -
    129A  ALA*     4.1    18.2    -      -       +      -
    139A  ILE*     3.4    33.7    -      -       +      -
    480A  FAD      3.9     9.2    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 36 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  SER*     2.4    52.3    +      -       -      +
     34A  CYS      4.3     0.2    +      -       -      -
     35A  ILE*     1.3    75.5    -      -       -      +
     37A  LYS*     1.3    75.4    +      -       -      +
     38A  ASN*     3.1    14.8    +      -       -      +
     40A  THR      3.5    20.0    -      -       -      +
     41A  LEU*     4.1    13.0    -      -       +      -
    114A  HIS*     4.1     6.5    -      -       +      +
    115A  VAL      3.1     6.5    +      -       -      -
    116A  ASN*     3.4    12.0    +      -       -      -
    117A  GLY      3.0    21.3    +      -       -      -
    480A  FAD      2.9    41.0    +      -       -      -
----------------------------------------------------------
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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