Contacts of the strand formed by residues 58 - 65 (chain A) in PDB entry 1ZRC


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 GLU 58 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  LEU*     3.5    19.1    -      -       +      +
     51A  ILE      3.6     5.4    -      -       -      +
     52A  LYS*     3.1    25.1    +      -       +      +
     56A  GLY      3.3    12.8    -      -       -      +
     57A  LYS*     1.3    74.2    -      -       -      +
     59A  MET*     1.3    61.6    +      -       -      +
     60A  ILE*     6.0     0.4    -      -       +      -
     87A  ARG*     3.0    35.3    +      -       -      -
    174A  GLN*     3.3    51.7    +      -       +      +
    136B  PHE*     4.2     2.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 59 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  LEU*     3.2     4.4    -      -       -      +
     51A  ILE*     2.9    38.7    +      -       +      +
     58A  GLU*     1.3    74.1    -      -       -      +
     60A  ILE*     1.3    81.0    +      -       -      +
     61A  LEU*     3.6     3.0    +      -       -      -
    130A  LYS*     6.4     2.0    -      -       +      -
    134A  LEU*     4.2    12.3    -      -       +      -
    174A  GLN*     3.5     7.9    -      -       -      +
    175A  ILE      3.6    20.9    -      -       -      +
    177A  GLY*     4.5    10.3    -      -       -      +
    131B  VAL*     3.8    27.1    -      -       +      +
    135B  ALA*     3.7    34.3    -      -       +      -
    136B  PHE*     3.2    23.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 60 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  ALA*     5.2     6.5    -      -       +      -
     49A  VAL      3.9     4.5    -      -       -      +
     50A  LEU*     4.1    16.6    -      -       +      -
     58A  GLU      5.8     0.2    -      -       -      -
     59A  MET*     1.3    85.7    -      -       -      +
     61A  LEU*     1.3    63.1    +      -       -      +
     62A  SER*     3.6    24.5    -      -       -      +
     63A  TYR*     4.0    18.8    -      -       +      +
    130A  LYS*     3.8    11.6    +      -       -      +
    171A  GLU*     3.6    33.9    -      -       +      +
    174A  GLN*     2.5    35.4    +      -       +      +
    175A  ILE*     3.9    25.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 61 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  VAL*     2.9    21.7    +      -       +      +
     51A  ILE*     4.0    37.7    -      -       +      -
     59A  MET*     3.6     2.1    +      -       -      +
     60A  ILE*     1.3    75.6    -      -       -      +
     62A  SER*     1.3    66.3    +      -       -      +
     83A  SER      5.7     0.4    -      -       -      +
    126A  VAL*     5.9     0.2    -      -       -      +
    127A  THR*     4.9     5.8    +      -       +      -
    130A  LYS*     3.1    28.2    +      -       +      +
    210A  CMP      3.6    38.7    +      -       +      +
    128B  SER*     3.7    18.6    -      -       -      +
    131B  VAL*     3.8    39.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 62 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  ALA*     3.6     2.9    -      -       -      -
     49A  VAL*     2.9    29.6    +      -       -      +
     60A  ILE*     3.4    11.4    -      -       -      +
     61A  LEU*     1.3    86.1    -      -       -      +
     63A  TYR*     1.3    85.1    +      -       -      +
     64A  LEU*     4.0     8.0    -      -       -      +
    123A  ARG*     6.0     0.3    -      -       -      +
    126A  VAL*     6.0     3.2    -      -       -      +
    130A  LYS*     4.7     5.8    -      -       -      +
    210A  CMP      4.0    23.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 63 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  VAL      3.3     9.0    -      -       -      +
     48A  ALA*     4.0    13.5    -      -       +      -
     60A  ILE*     4.0    10.3    -      -       +      +
     62A  SER*     1.3    92.2    +      -       -      +
     64A  LEU*     1.3    66.2    +      -       -      +
     65A  ASN*     4.4     4.9    +      -       -      +
     68A  ASP*     4.8     0.3    -      -       -      +
     89A  LYS*     3.5    38.6    -      -       +      +
    150A  LEU*     3.5    26.7    -      -       +      -
    153A  GLN*     3.6    38.8    +      -       +      +
    155A  ASP*     6.0     0.2    -      -       -      -
    167A  ILE*     3.9     6.4    -      -       -      +
    171A  GLU*     2.5    31.0    +      -       -      -
    175A  ILE*     3.8    21.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 64 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  ILE*     4.0     4.4    -      -       +      +
     47A  VAL*     2.8    42.1    +      -       +      +
     49A  VAL*     3.6    29.4    -      -       +      -
     62A  SER*     4.0     7.9    -      -       -      +
     63A  TYR*     1.3    82.7    -      -       -      +
     65A  ASN*     1.3    70.1    +      -       -      +
     68A  ASP*     3.6    15.3    -      -       +      +
     69A  PHE      3.7    20.2    -      -       -      +
     70A  ILE*     4.2    15.3    -      -       +      -
    123A  ARG*     3.6    30.3    -      -       +      +
    210A  CMP      4.1    11.2    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 65 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  ILE*     3.7     9.3    -      -       -      +
     45A  GLY      3.8     9.4    -      -       -      +
     46A  SER*     3.1    23.4    -      -       -      -
     63A  TYR*     4.4     2.9    +      -       -      +
     64A  LEU*     1.3    81.1    +      -       -      +
     66A  GLN*     1.3    63.8    +      -       +      +
     67A  GLY      3.1     0.2    +      -       -      -
     68A  ASP*     2.6    48.0    +      -       -      +
     89A  LYS*     4.5     4.0    +      -       -      -
    153A  GLN*     3.7    23.4    +      -       -      +
    154A  PRO*     3.9    28.3    -      -       +      +
    155A  ASP*     5.1     0.5    -      -       -      +
----------------------------------------------------------
 Back to top of page


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