Contacts of the strand formed by residues 254 - 260 (chain C) 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 C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164C  THR*     3.6    25.6    -      -       -      +
    165C  ILE*     4.1    13.2    -      -       +      -
    246C  ALA*     4.5     2.5    -      -       +      -
    247C  THR      3.5    13.7    -      -       -      +
    248C  LYS*     4.2    10.5    -      -       +      -
    252C  GLY      4.1     6.5    -      -       -      +
    253C  LYS*     1.3    79.3    -      -       -      +
    255C  ASP*     1.3    72.2    +      -       -      +
    256C  VAL*     4.4     0.7    -      -       +      -
    269C  ILE      3.5     0.9    -      -       -      +
    270C  THR*     3.0     6.4    -      -       -      -
    271C  CYS*     2.9    41.0    +      -       -      +
    272C  ASP      3.5    24.5    -      -       -      +
    273C  VAL      4.0     0.7    -      -       -      +
    274C  LEU*     3.7    37.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 255 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246C  ALA*     3.1     4.3    -      -       -      +
    247C  THR*     2.9    46.7    +      -       -      +
    249C  LYS*     2.7    44.0    +      -       +      +
    253C  LYS      4.2     0.4    -      -       -      -
    254C  ILE*     1.3    72.0    -      -       -      +
    256C  VAL*     1.3    61.5    +      -       -      +
    257C  SER*     4.0     3.2    +      -       -      +
    268C  VAL*     3.6    20.5    -      -       +      +
    269C  ILE      3.2     1.8    -      -       -      -
    270C  THR*     2.8    21.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 256 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182C  VAL*     4.3    15.7    -      -       +      -
    184C  ILE*     5.4     0.9    -      -       +      -
    243C  VAL*     3.7    29.4    -      -       +      -
    245C  GLY      3.6     3.6    -      -       -      +
    246C  ALA*     4.1     8.5    -      -       +      -
    254C  ILE*     4.4     1.8    -      -       +      -
    255C  ASP*     1.3    75.9    -      -       -      +
    257C  SER*     1.3    63.6    +      -       -      +
    258C  ILE*     3.8    12.9    +      -       +      +
    268C  VAL*     3.3     5.0    -      -       -      -
    269C  ILE*     2.4    54.7    +      -       +      +
    271C  CYS*     4.1    15.5    -      -       -      -
    274C  LEU*     3.6    29.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 257 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243C  VAL*     3.4     6.4    -      -       -      +
    244C  THR*     2.9    42.6    +      -       -      -
    245C  GLY      2.8    17.8    +      -       -      +
    246C  ALA*     5.3     0.2    -      -       -      -
    255C  ASP*     4.0     3.7    +      -       -      +
    256C  VAL*     1.3    73.8    -      -       -      +
    258C  ILE*     1.3    64.2    +      -       -      +
    267C  GLU      3.7     7.6    -      -       -      -
    268C  VAL*     4.1    12.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 258 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207C  VAL*     4.3    10.3    -      -       +      -
    238C  LYS*     3.4    34.3    -      -       +      -
    241C  THR*     3.5    19.3    -      -       +      -
    242C  LYS      3.3     5.6    -      -       -      +
    243C  VAL*     3.9    21.1    -      -       +      -
    244C  THR*     4.4     0.9    -      -       -      +
    256C  VAL*     4.1    14.4    -      -       +      +
    257C  SER*     1.3    81.2    -      -       -      +
    259C  GLU*     1.3    62.4    +      -       -      +
    266C  ALA*     3.5     3.6    -      -       -      +
    267C  GLU*     2.7    69.6    +      -       +      +
    268C  VAL      4.7     0.2    -      -       -      +
    269C  ILE*     4.3    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 259 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241C  THR*     2.9    10.7    -      -       -      +
    242C  LYS*     2.7    41.7    +      -       +      +
    244C  THR*     3.7    25.4    -      -       +      +
    258C  ILE*     1.3    77.0    -      -       -      +
    260C  ALA*     1.3    65.1    +      -       -      +
    263C  GLY*     4.3     6.4    -      -       -      -
    264C  GLY      3.3    25.4    +      -       -      +
    265C  LYS*     4.1     4.3    -      -       -      -
    266C  ALA*     4.3    14.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 260 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240C  ASN      3.6     7.9    -      -       -      +
    241C  THR*     4.3     1.8    -      -       -      +
    242C  LYS*     4.2     3.0    -      -       -      +
    259C  GLU*     1.3    79.9    -      -       -      +
    261C  ALA*     1.3    66.9    +      -       -      +
    262C  SER*     4.2     9.4    -      -       -      +
    263C  GLY*     2.9    31.6    +      -       -      +
    264C  GLY      2.9    11.3    +      -       -      +
    265C  LYS*     4.0    22.8    -      -       +      +
----------------------------------------------------------
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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