Contacts of the strand formed by residues 329 - 334 (chain A) in PDB entry 2IZV


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 ARG 329 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    325A  ARG*     3.6    12.2    -      -       -      +
    326A  ARG      3.0    30.2    +      -       -      +
    327A  TYR*     3.6    14.1    +      -       +      +
    328A  SER*     1.3    99.9    +      -       -      +
    330A  SER*     1.3    61.6    +      -       -      +
    331A  LEU*     3.6    20.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 330 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    297A  GLU*     3.9    35.9    +      -       -      +
    300A  LEU*     4.0    19.0    -      -       -      +
    301A  GLU*     4.6     0.7    +      -       -      -
    324A  PHE      3.6     6.5    -      -       -      -
    325A  ARG*     3.5    23.0    +      -       -      +
    329A  ARG*     1.3    70.4    -      -       -      +
    331A  LEU*     1.3    62.4    +      -       -      +
    332A  HIS*     4.2    10.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 331 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323A  SER*     3.4     4.5    -      -       -      -
    324A  PHE*     2.8    65.8    +      -       +      +
    326A  ARG*     3.7    29.4    -      -       +      +
    327A  TYR*     4.6     9.2    -      -       +      -
    329A  ARG*     3.9    20.0    -      -       +      +
    330A  SER*     1.3    75.0    -      -       -      +
    332A  HIS*     1.3    67.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 332 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293A  LYS*     3.5    41.3    -      -       +      +
    296A  ALA*     4.2     1.6    -      -       +      -
    297A  GLU*     2.6    37.3    +      -       +      +
    300A  LEU*     5.8     0.2    -      -       +      -
    311A  ARG*     3.2    14.4    +      -       -      +
    321A  SER*     5.5     0.9    -      -       -      -
    322A  VAL      3.3     7.2    -      -       -      +
    323A  SER*     2.7    32.2    +      -       -      -
    324A  PHE*     4.4     3.9    -      -       -      -
    330A  SER*     4.2     7.0    +      -       -      -
    331A  LEU*     1.3    83.2    -      -       -      +
    333A  ALA*     1.3    65.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 333 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    321A  SER*     3.3     3.2    -      -       -      -
    322A  VAL*     2.9    54.0    +      -       +      +
    324A  PHE*     4.2     3.8    -      -       +      -
    332A  HIS*     1.3    76.6    -      -       -      +
    334A  ARG*     1.3    64.5    +      -       -      +
    335A  ILE      3.6     0.7    +      -       -      -
    344A  PHE*     3.7    21.4    -      -       +      -
    375A  PRO*     4.1    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 334 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    313A  SER*     5.0     0.2    -      -       -      +
    315A  GLN*     3.4    38.6    +      -       -      +
    318A  TYR*     3.4    47.3    +      -       +      -
    320A  PHE      4.4     2.0    -      -       -      +
    321A  SER*     3.7    17.2    +      -       -      +
    332A  HIS*     5.6     0.2    -      -       -      +
    333A  ALA*     1.3    73.3    -      -       -      +
    335A  ILE*     1.3    60.1    +      -       -      +
    336A  GLU*     3.3    28.8    +      -       +      +
    344A  PHE*     3.4    21.2    -      -       -      +
----------------------------------------------------------
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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