Contacts of the strand formed by residues 235 - 241 (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 LYS 235 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229A  LYS*     3.4     8.8    -      -       -      +
    230A  ALA*     3.4    10.9    +      -       -      -
    233A  THR*     2.8    23.4    +      -       -      +
    234A  GLY*     1.3    85.1    -      -       -      +
    236A  GLY*     1.3    58.8    +      -       -      +
    329A  PHE      3.1     6.5    -      -       -      +
    330A  ASN*     3.0    35.5    +      -       +      +
    341A  ILE*     3.5    27.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 236 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226A  GLY      4.2     5.2    -      -       -      -
    229A  LYS*     4.5    11.0    -      -       -      -
    230A  ALA*     4.2     7.0    -      -       -      -
    235A  LYS*     1.3    75.7    -      -       -      +
    237A  SER*     1.3    61.0    +      -       -      -
    327A  PHE      3.6     0.5    -      -       -      +
    328A  GLY*     3.5     3.7    -      -       -      -
    329A  PHE*     2.8    42.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 237 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226A  GLY*     3.3    20.8    +      -       -      -
    229A  LYS*     5.3     5.0    +      -       -      +
    236A  GLY*     1.3    73.0    -      -       -      -
    238A  ILE*     1.3    64.5    +      -       -      +
    326A  ASN*     5.9     5.4    -      -       -      -
    327A  PHE      3.4     7.9    -      -       -      -
    328A  GLY*     5.0     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 238 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213A  PRO*     4.2    16.2    -      -       +      -
    215A  PHE*     4.5     2.5    -      -       +      -
    221A  VAL*     5.1     7.6    -      -       +      -
    222A  MET      4.2     2.7    -      -       -      +
    223A  GLY*     3.9    10.1    -      -       -      +
    226A  GLY      3.7     2.5    -      -       -      -
    227A  ILE*     3.6    36.3    -      -       +      +
    237A  SER*     1.3    79.5    -      -       -      +
    239A  VAL*     1.3    66.7    +      -       -      +
    240A  LEU*     3.8    22.9    -      -       +      -
    326A  ASN*     3.5     6.9    -      -       -      +
    327A  PHE*     2.9    51.8    +      -       +      +
    329A  PHE*     3.6    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 239 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221A  VAL*     3.3     7.3    -      -       -      +
    222A  MET*     2.9    58.9    +      -       +      +
    223A  GLY*     5.7     0.4    -      -       -      -
    238A  ILE*     1.3    78.0    -      -       -      +
    240A  LEU*     1.3    68.9    +      -       -      +
    324A  GLN*     4.0    29.6    -      -       +      +
    325A  THR      3.7    10.8    -      -       -      +
    326A  ASN*     4.0    11.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 240 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215A  PHE*     3.7    36.8    -      -       +      -
    219A  ALA*     5.8     1.6    -      -       +      -
    220A  LEU      3.4     9.0    -      -       -      +
    221A  VAL*     4.6     4.0    -      -       +      -
    238A  ILE*     3.8    16.8    -      -       +      -
    239A  VAL*     1.3    86.4    -      -       -      +
    241A  ARG*     1.3    60.1    +      -       -      +
    262A  PRO*     4.1    10.2    -      -       +      +
    263A  TYR*     4.3    26.0    -      -       +      +
    324A  GLN*     3.2     6.2    -      -       -      +
    325A  THR*     2.9    52.8    +      -       -      +
    326A  ASN      5.0     1.1    -      -       -      +
    327A  PHE*     4.1    23.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 241 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219A  ALA*     3.3     5.6    -      -       -      +
    220A  LEU*     2.9    39.9    +      -       +      +
    222A  MET*     3.6    45.3    -      -       +      +
    239A  VAL      4.2     0.2    -      -       -      -
    240A  LEU*     1.3    75.0    -      -       -      +
    242A  SER*     1.3    74.4    +      -       -      +
    244A  THR*     5.6     0.4    -      -       -      -
    262A  PRO*     4.4     1.6    -      -       -      -
    315A  ASN*     5.7     4.2    -      -       -      +
    318A  PHE*     3.5    40.1    -      -       +      +
    323A  MET      3.8     2.9    -      -       -      -
    324A  GLN*     2.9    33.0    +      -       -      +
----------------------------------------------------------
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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