Contacts of the strand formed by residues 360 - 364 (chain B) in PDB entry 5ZR1


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 CYS 360 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    330B  ALA*     4.1    15.5    -      -       -      +
    331B  ILE*     3.9    20.0    -      -       +      -
    335B  SER*     5.1     2.0    -      -       -      +
    358B  ILE      4.3     6.3    -      -       -      +
    359B  PRO*     1.3    72.0    -      -       -      +
    361B  LEU*     1.3    60.5    +      -       -      +
    362B  ILE*     3.1    21.7    +      -       -      +
    421B  ILE*     3.4    12.6    -      -       +      -
    423B  VAL*     3.7    28.0    -      -       -      -
     24C  THR*     4.5     0.6    -      -       -      +
     25C  VAL*     3.0    37.3    +      -       +      +
     27C  PRO*     4.7     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 361 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    359B  PRO      3.8     3.6    +      -       -      -
    360B  CYS*     1.3    69.2    -      -       -      +
    362B  ILE*     1.3    67.1    +      -       -      +
    363B  LEU*     4.8     5.1    -      -       +      +
    375B  VAL*     4.6     9.6    -      -       +      +
    378B  GLU*     3.6    23.6    -      -       +      -
    379B  ILE*     3.7    32.1    -      -       +      -
    382B  LEU*     4.3    13.5    -      -       +      -
    420B  LEU*     4.8     5.6    -      -       +      +
    421B  ILE      3.2     7.0    +      -       -      +
    422B  LEU*     3.2    17.0    -      -       +      +
    423B  VAL      3.0    20.6    +      -       -      -
     22C  HIS*     3.9    12.1    -      -       +      -
     23C  TYR      3.3    21.5    -      -       -      +
     24C  THR*     3.4    22.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 362 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323B  ARG*     5.2     0.2    -      -       -      +
    327B  GLU*     3.6    14.8    -      -       +      +
    330B  ALA*     5.8     0.2    -      -       +      -
    331B  ILE*     4.7    12.1    -      -       +      -
    360B  CYS*     3.1    32.3    +      -       -      +
    361B  LEU*     1.3    76.6    -      -       -      +
    363B  LEU*     1.3    61.9    +      -       -      +
    364B  ASN*     4.3     4.5    -      -       -      +
    423B  VAL*     3.3    20.9    -      -       +      +
    425B  HIS*     3.5    23.1    -      -       +      -
     22C  HIS*     3.3     3.8    +      -       -      -
     23C  TYR*     2.9    79.0    +      -       +      +
     25C  VAL*     4.9     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 363 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    361B  LEU*     4.8     7.9    -      -       +      +
    362B  ILE*     1.3    78.6    -      -       -      +
    364B  ASN*     1.3    60.9    +      -       -      +
    365B  GLY      3.2     5.4    +      -       -      +
    370B  CYS*     3.6    19.7    -      -       -      -
    375B  VAL*     3.7    36.1    -      -       +      -
    422B  LEU*     5.0     7.4    -      -       +      -
    423B  VAL      2.8    14.6    +      -       -      +
    424B  VAL*     4.2    18.4    -      -       +      -
    425B  HIS*     2.9    28.9    +      -       -      +
    432B  ILE*     3.6    29.8    -      -       +      -
    437B  PHE*     4.3     7.0    -      -       +      -
    441B  LEU*     4.9     5.6    -      -       +      -
     22C  HIS*     4.1    10.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 364 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323B  ARG*     3.9    10.9    -      -       -      +
    362B  ILE*     4.8     0.4    -      -       -      +
    363B  LEU*     1.3    71.5    -      -       -      +
    365B  GLY*     1.3    59.7    +      -       -      +
    366B  TYR*     2.6    47.2    +      -       +      -
    367B  ASN*     3.3    22.6    -      -       +      +
    370B  CYS*     4.1     7.6    -      -       -      +
    425B  HIS*     3.8    15.3    +      -       -      -
     17C  ASP      3.6    11.8    -      -       -      +
     18C  ALA      4.1     2.2    +      -       -      -
     20C  ARG      2.9    29.5    -      -       -      +
     21C  SER*     4.3     3.6    -      -       -      -
     22C  HIS      4.1     7.1    +      -       -      +
     23C  TYR*     3.7    16.2    -      -       -      -
----------------------------------------------------------
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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