Contacts of the strand formed by residues 265 - 268 (chain A) in PDB entry 4ZTZ


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 LEU 265 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150A  TYR*     3.2    45.3    -      -       +      +
    153A  ALA*     3.7    17.0    -      -       +      -
    154A  ALA*     3.5    23.8    -      -       +      +
    157A  LEU*     4.8     0.6    -      -       +      +
    193A  ARG      3.2     5.9    +      -       -      -
    194A  ALA*     3.2    24.1    -      -       +      +
    195A  LEU*     3.3     6.6    +      -       -      +
    264A  GLN*     1.3    78.5    +      -       -      +
    266A  VAL*     1.3    66.7    +      -       -      +
    267A  VAL*     4.1    15.4    +      -       +      -
    290A  ARG      3.7    13.2    -      -       -      +
    291A  PHE      4.5     0.4    -      -       -      -
    292A  LEU*     4.3    30.3    -      -       +      +
    407A  PHE*     5.2     0.2    -      -       +      -
    428A  LEU*     4.7     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 266 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195A  LEU*     3.5    14.6    -      -       +      +
    197A  PHE*     3.6    36.1    -      -       +      -
    244A  LEU*     3.6    24.5    -      -       +      -
    264A  GLN*     5.0     2.2    -      -       -      +
    265A  LEU*     1.3    78.7    -      -       -      +
    267A  VAL*     1.3    64.4    +      -       -      +
    271A  VAL*     3.5     9.0    -      -       +      +
    274A  ASP*     6.0     0.2    -      -       +      -
    289A  MET*     3.7    22.7    -      -       +      -
    290A  ARG      3.2     7.3    +      -       -      -
    291A  PHE*     3.3    25.7    -      -       +      -
    292A  LEU      3.0    20.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 267 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157A  LEU*     3.9    15.3    -      -       +      -
    195A  LEU      3.2     5.2    +      -       -      +
    196A  VAL*     3.4    31.8    -      -       +      -
    197A  PHE*     3.0    25.6    +      -       -      +
    265A  LEU*     4.4     9.6    -      -       +      -
    266A  VAL*     1.3    80.1    -      -       -      +
    268A  GLY*     1.3    59.8    +      -       -      +
    271A  VAL*     4.0     2.9    -      -       -      +
    292A  LEU*     3.2    22.4    -      -       +      +
    294A  THR*     5.1     1.1    -      -       +      -
    403A  THR*     5.4     1.6    -      -       +      -
    407A  PHE*     3.6    48.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 268 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197A  PHE      3.9    13.0    -      -       -      -
    267A  VAL*     1.3    77.9    -      -       -      +
    269A  HIS*     1.3    61.6    +      -       -      -
    270A  ASN      3.5     0.2    +      -       -      -
    271A  VAL*     3.5    12.5    -      -       -      +
    274A  ASP*     4.9     0.2    -      -       -      -
    292A  LEU      3.1     6.1    +      -       -      -
    293A  ASP*     3.1    19.9    -      -       -      +
    294A  THR*     3.2    15.5    +      -       -      +
    403A  THR*     3.7    12.3    -      -       -      +
----------------------------------------------------------
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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