Contacts of the strand formed by residues 254 - 260 (chain A) in PDB entry 4Z2C


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 GLU 254 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246A  ILE*     4.2    14.1    -      -       +      +
    247A  GLU      3.7     5.6    -      -       -      +
    248A  THR*     4.9     3.1    -      -       -      +
    249A  THR*     4.4     2.9    -      -       -      +
    253A  ARG*     1.3    79.0    -      -       -      +
    255A  ARG*     1.3    60.5    +      -       -      +
    303A  GLU*     4.2     1.0    -      -       -      +
    304A  VAL*     3.2    33.9    +      -       +      +
    305A  LYS      5.4     1.2    +      -       -      +
    308A  ALA      3.3    12.9    -      -       -      +
    309A  SER*     3.7     2.8    -      -       -      -
    310A  ALA*     2.8    46.9    +      -       +      +
    311A  ASN*     4.5    10.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 255 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245A  GLU      3.7     0.2    -      -       -      +
    246A  ILE*     3.3     7.1    -      -       -      +
    247A  GLU*     2.7    64.3    +      -       -      +
    248A  THR      4.7     0.6    +      -       -      -
    249A  THR*     3.3    39.6    -      -       +      +
    250A  LYS      4.8     0.8    -      -       -      +
    254A  GLU*     1.3    77.8    -      -       -      +
    256A  ILE*     1.3    63.4    +      -       -      +
    257A  VAL*     3.7    22.8    +      -       +      -
    292A  GLU*     4.9     6.1    +      -       -      -
    299A  ARG*     3.9     9.5    -      -       -      +
    301A  VAL*     3.6    26.3    -      -       +      +
    302A  ILE      4.0     3.8    -      -       -      -
    303A  GLU*     2.3    37.3    +      -       +      +
    304A  VAL      4.7     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 256 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244A  THR*     4.9     1.8    -      -       +      -
    245A  GLU      3.8     3.1    -      -       -      +
    246A  ILE*     3.8    17.3    -      -       +      -
    255A  ARG*     1.3    73.4    -      -       -      +
    257A  VAL*     1.3    63.4    +      -       -      +
    258A  VAL*     4.3    17.7    -      -       +      -
    300A  PHE      3.4     1.2    -      -       -      +
    301A  VAL*     3.4     6.1    -      -       -      +
    302A  ILE*     2.9    51.4    +      -       +      +
    304A  VAL*     4.5     3.6    -      -       +      -
    310A  ALA*     3.3    32.8    -      -       +      +
    313A  ILE*     3.9    15.7    -      -       +      -
    314A  LEU*     3.7    38.8    -      -       +      +
    317A  LEU*     4.7     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 257 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244A  THR*     3.2     4.3    -      -       -      -
    245A  GLU*     2.8    47.9    +      -       +      +
    247A  GLU*     3.7    25.8    -      -       +      +
    255A  ARG*     3.7    27.4    -      -       +      +
    256A  ILE*     1.3    75.8    -      -       -      +
    258A  VAL*     1.3    63.5    +      -       -      +
    259A  THR*     3.5    18.8    +      -       +      +
    299A  ARG*     3.8    35.7    -      -       +      +
    300A  PHE      3.5     3.4    -      -       -      +
    301A  VAL*     4.8     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 258 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242A  SER*     3.7    20.2    -      -       -      -
    243A  ARG      4.0     1.1    -      -       -      +
    244A  THR*     3.7    26.9    -      -       +      -
    256A  ILE*     4.3    10.1    -      -       +      -
    257A  VAL*     1.3    71.2    -      -       -      +
    259A  THR*     1.3    61.6    +      -       -      +
    260A  GLU      4.1     1.3    -      -       -      +
    261A  PHE*     3.5    26.0    -      -       +      -
    298A  VAL*     3.9     2.9    -      -       -      +
    299A  ARG*     3.8     2.6    -      -       -      -
    300A  PHE*     2.8    64.6    +      -       +      +
    302A  ILE*     6.0     1.8    -      -       +      +
    317A  LEU*     6.1     0.2    -      -       +      -
    323A  MET*     3.8    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 259 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243A  ARG*     2.8    37.4    +      -       -      +
    244A  THR*     4.6     1.2    -      -       -      -
    245A  GLU*     4.6    15.5    +      -       -      +
    257A  VAL*     3.5    22.6    +      -       +      +
    258A  VAL*     1.3    77.2    -      -       -      +
    260A  GLU*     1.3    68.0    +      -       -      +
    298A  VAL*     3.3    41.2    +      -       -      +
    299A  ARG*     5.2     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 260 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217A  THR*     3.3    17.7    -      -       -      +
    218A  GLY*     3.3     5.0    -      -       -      -
    219A  ALA*     2.4    40.5    +      -       -      +
    242A  SER*     3.0    10.4    -      -       -      -
    243A  ARG*     2.9    69.0    +      -       +      -
    258A  VAL*     3.7     0.6    -      -       -      -
    259A  THR*     1.3    87.5    -      -       -      +
    261A  PHE*     1.3    63.8    +      -       -      +
    298A  VAL*     5.3     0.2    -      -       -      -
    481A  ARG*     4.2     3.9    -      -       -      +
----------------------------------------------------------
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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