Contacts of the strand formed by residues 254 - 260 (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 ILE 254 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164A  THR*     5.0     5.8    -      -       -      +
    165A  ILE*     3.7    29.8    -      -       +      -
    246A  ALA*     4.0     7.0    -      -       +      -
    247A  THR      3.9    14.8    -      -       -      +
    248A  LYS*     4.2     7.0    -      -       +      +
    252A  GLY      5.1     0.9    -      -       -      +
    253A  LYS*     1.3    76.5    -      -       -      +
    255A  ASP*     1.3    73.8    +      -       -      +
    256A  VAL*     3.9     2.5    +      -       +      -
    269A  ILE      3.8     0.2    -      -       -      +
    270A  THR*     3.4     4.3    -      -       -      -
    271A  CYS*     3.0    58.4    +      -       -      +
    272A  ASP      4.3    10.5    -      -       -      +
    274A  LEU*     3.4    37.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 255 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246A  ALA*     3.3     4.7    -      -       -      +
    247A  THR*     3.1    45.4    +      -       +      +
    249A  LYS*     3.1    32.5    -      -       -      +
    253A  LYS      4.4     0.2    +      -       -      -
    254A  ILE*     1.3    72.9    -      -       -      +
    256A  VAL*     1.3    61.7    +      -       -      +
    257A  SER      4.1     0.7    +      -       -      -
    268A  VAL*     4.1    15.9    -      -       +      +
    269A  ILE      3.4     3.7    -      -       -      +
    270A  THR*     2.5    32.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 256 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182A  VAL*     3.8    26.9    -      -       +      -
    243A  VAL*     3.5    35.0    -      -       +      -
    245A  GLY      3.6     5.4    -      -       -      +
    246A  ALA*     4.4     4.0    -      -       +      -
    254A  ILE*     4.4     2.5    -      -       +      +
    255A  ASP*     1.3    76.0    -      -       -      +
    257A  SER*     1.3    61.9    +      -       -      +
    258A  ILE*     3.6     9.2    +      -       +      -
    268A  VAL*     3.5     3.8    -      -       -      -
    269A  ILE*     2.9    49.2    +      -       +      +
    271A  CYS*     4.2    11.2    -      -       -      -
    274A  LEU*     4.1    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 257 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243A  VAL*     3.8     1.0    -      -       -      +
    244A  THR*     2.9    44.3    +      -       -      -
    245A  GLY*     3.0    24.7    +      -       -      +
    247A  THR*     6.1     0.7    -      -       -      +
    255A  ASP      4.1     1.8    +      -       -      -
    256A  VAL*     1.3    72.5    -      -       -      +
    258A  ILE*     1.3    61.6    +      -       -      +
    267A  GLU      3.9     4.9    -      -       -      -
    268A  VAL*     4.2    14.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 258 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207A  VAL*     4.3     5.4    -      -       +      -
    238A  LYS*     3.9    25.4    -      -       +      -
    241A  THR*     3.7    17.5    -      -       +      -
    242A  LYS      3.2    15.9    -      -       -      +
    243A  VAL*     4.0    20.4    -      -       +      -
    244A  THR*     4.4     2.1    -      -       -      +
    256A  VAL*     4.1    11.7    -      -       +      +
    257A  SER*     1.3    81.1    -      -       -      +
    259A  GLU*     1.3    68.9    +      -       -      +
    266A  ALA*     3.4     4.0    -      -       -      +
    267A  GLU*     3.0    57.0    +      -       +      +
    268A  VAL*     5.0     0.2    -      -       -      -
    269A  ILE*     4.2    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 259 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241A  THR*     3.3     8.0    -      -       -      +
    242A  LYS*     2.8    56.7    +      -       -      +
    244A  THR*     3.8    22.2    -      -       +      +
    258A  ILE*     1.3    83.0    -      -       -      +
    260A  ALA*     1.3    65.7    +      -       -      +
    262A  SER      4.2     5.5    -      -       -      +
    264A  GLY*     3.8    16.7    +      -       -      -
    265A  LYS      4.4     2.7    -      -       -      -
    266A  ALA*     3.7    27.6    -      -       +      +
    267A  GLU*     5.8     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 260 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240A  ASN      3.7     8.3    -      -       -      +
    241A  THR*     4.3     2.9    -      -       -      +
    242A  LYS*     4.1     0.9    +      -       -      -
    259A  GLU*     1.3    87.1    -      -       -      +
    261A  ALA*     1.3    66.5    +      -       -      +
    262A  SER*     3.1    14.0    +      -       -      +
    263A  GLY      3.0    22.4    -      -       -      +
    265A  LYS*     3.4    29.6    -      -       +      +
----------------------------------------------------------
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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