Contacts of the strand formed by residues 272 - 278 (chain B) in PDB entry 1ZVM


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 GLN 272 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76A  GLU*     4.1    41.4    +      -       +      +
     77A  MET*     4.3     6.9    -      -       -      +
     79A  HIS*     6.1     2.2    -      -       +      -
    114A  THR      5.0     0.5    -      -       -      +
    115A  GLN*     3.8     9.8    -      -       -      +
    116A  THR*     2.8    48.8    +      -       -      +
    236B  GLN      3.0    13.0    +      -       -      +
    237B  THR*     3.0    26.3    -      -       +      -
    238B  LEU      2.9    26.2    +      -       -      -
    266B  ILE*     3.9     1.0    -      -       -      +
    270B  ASN      5.6     1.6    -      -       -      -
    271B  ILE*     1.3    78.1    +      -       -      +
    273B  PHE*     1.3    59.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 273 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  THR*     4.6    13.5    -      -       -      +
    116A  THR*     2.7    24.9    +      -       +      +
    237B  THR*     5.4     0.2    -      -       -      -
    238B  LEU*     3.4    17.7    -      -       +      -
    240B  ALA*     4.0    12.1    -      -       +      -
    259B  ILE*     3.8    28.3    -      -       +      -
    262B  LEU*     3.6    35.4    -      -       +      -
    263B  GLU*     3.6    42.2    -      -       +      +
    266B  ILE*     4.0    27.1    -      -       +      -
    272B  GLN*     1.3    74.7    -      -       -      +
    274B  SER*     1.3    71.9    +      -       -      +
    275B  CYS*     4.1    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 274 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  THR*     6.1     1.1    -      -       -      -
    237B  THR*     4.7     9.0    -      -       -      -
    238B  LEU      3.0     7.2    +      -       -      +
    239B  GLU*     2.9    37.6    +      -       -      +
    240B  ALA      2.8    23.6    +      -       -      -
    273B  PHE*     1.3    82.3    -      -       -      +
    275B  CYS*     1.3    64.0    +      -       -      +
    276B  LYS*     3.8    11.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 275 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240B  ALA*     3.4     9.6    -      -       -      -
    242B  VAL*     3.7    19.1    -      -       -      -
    254B  CYS*     2.0    57.2    -      -       +      +
    259B  ILE*     4.0    10.3    -      -       +      -
    273B  PHE*     4.1    15.0    -      -       +      -
    274B  SER*     1.3    77.6    +      -       -      +
    276B  LYS*     1.3    76.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 276 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111A  LYS*     5.8     7.1    -      -       -      +
    239B  GLU*     3.7    33.2    -      -       +      +
    240B  ALA      2.8     9.6    +      -       -      +
    241B  TRP*     3.4    13.1    -      -       +      +
    242B  VAL      2.9    24.9    +      -       -      -
    254B  CYS*     3.7     4.0    -      -       -      -
    274B  SER*     3.8     9.2    +      -       -      -
    275B  CYS*     1.3    83.2    +      -       -      +
    277B  ASN*     1.3    67.3    +      -       -      +
    278B  ILE*     4.3     2.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 277 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242B  VAL*     3.8     4.3    -      -       -      +
    244B  HIS*     2.8    22.1    +      -       -      +
    252B  ASP*     2.7    28.9    +      -       -      -
    253B  LEU*     3.0    23.9    +      -       -      +
    254B  CYS*     3.8     8.9    +      -       -      -
    276B  LYS*     1.3    77.8    -      -       -      +
    278B  ILE*     1.3    63.5    +      -       -      +
    279B  TYR*     3.5    41.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 278 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241B  TRP*     3.5    38.8    -      -       +      -
    242B  VAL      3.0    15.1    +      -       -      +
    243B  ILE*     3.5    19.3    -      -       +      -
    244B  HIS*     3.1    23.6    +      -       -      -
    276B  LYS*     4.3     4.5    -      -       +      +
    277B  ASN*     1.3    79.6    -      -       -      +
    279B  TYR*     1.3    60.8    +      -       -      +
    280B  ARG      4.1     2.0    -      -       -      +
    281B  PRO*     4.0    16.7    -      -       +      +
    284B  PHE*     3.9    50.0    -      -       +      -
----------------------------------------------------------
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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