Contacts of the strand formed by residues 373 - 379 (chain A) in PDB entry 2ZH2


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 373 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    345A  MET*     3.5    38.1    -      -       -      +
    346A  GLY      2.8    25.2    +      -       -      -
    347A  PRO*     3.3    17.9    -      -       -      +
    348A  GLN*     3.5    35.9    -      -       +      +
    349A  PHE      4.1     1.6    -      -       -      +
    369A  ILE*     3.4     5.6    -      -       -      +
    370A  GLU      3.0    28.2    +      -       -      +
    371A  ASN*     4.3     4.9    -      -       +      +
    372A  GLY*     1.3    82.2    -      -       -      +
    374A  TRP*     1.3    63.3    +      -       -      +
    375A  TRP*     3.2    32.1    -      -       +      +
     15B    C      4.2     5.3    -      -       -      +
     16B    G      6.0     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 374 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    346A  GLY*     2.7    33.4    +      -       -      +
    347A  PRO*     2.9    15.8    +      -       +      +
    349A  PHE*     4.3    15.1    +      -       +      +
    355A  VAL*     3.5    40.9    -      -       +      +
    358A  PHE*     3.9    18.4    -      -       +      -
    359A  LEU*     3.7    37.9    -      -       +      -
    367A  PRO*     3.8    19.1    -      -       +      -
    368A  PHE*     3.3    24.0    -      -       -      -
    369A  ILE*     3.6    33.7    -      -       +      +
    373A  ARG*     1.3    76.7    -      -       -      +
    375A  TRP*     1.3    59.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 375 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343A  ARG*     3.0    49.3    -      -       +      +
    344A  ARG      3.2     8.7    -      -       -      -
    345A  MET*     3.4    56.1    -      -       +      -
    358A  PHE*     4.0     1.3    -      -       -      -
    367A  PRO*     3.0     6.1    -      -       -      +
    368A  PHE*     2.8    54.7    +      +       +      -
    370A  GLU*     3.6    28.3    +      -       +      +
    373A  ARG*     3.2    44.1    -      -       +      +
    374A  TRP*     1.3    73.8    -      -       -      +
    376A  ALA*     1.3    61.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 376 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343A  ARG*     3.3     4.6    -      -       -      -
    344A  ARG*     2.7    43.9    +      -       +      +
    358A  PHE*     3.4    21.7    -      -       +      -
    363A  ARG*     3.2    35.4    -      -       -      +
    367A  PRO*     3.9     7.2    -      -       +      -
    368A  PHE*     4.9     1.1    -      -       -      -
    375A  TRP*     1.3    75.0    -      -       -      +
    377A  PHE*     1.3    63.3    +      -       -      +
    378A  GLU*     4.5     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 377 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341A  VAL*     4.1    20.6    -      -       +      -
    342A  PHE      3.5    11.7    -      -       -      -
    343A  ARG*     4.6     9.0    -      -       +      -
    363A  ARG*     3.8    13.9    -      -       -      +
    364A  ALA      5.5     0.3    +      -       -      -
    365A  PHE*     3.9    35.9    +      +       +      +
    366A  ARG      4.3     9.6    +      -       -      +
    367A  PRO*     5.1     2.4    -      -       -      +
    368A  PHE*     3.5    39.5    -      +       -      -
    376A  ALA*     1.3    74.8    -      -       -      +
    378A  GLU*     1.3    70.4    +      -       -      +
    379A  MET*     5.7     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 378 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341A  VAL*     3.0    10.0    -      -       -      +
    342A  PHE*     2.7    62.6    +      -       +      +
    344A  ARG*     2.5    44.9    +      -       +      +
    363A  ARG*     3.1    37.3    +      -       -      +
    376A  ALA*     4.8     2.5    -      -       -      -
    377A  PHE*     1.3    95.7    -      -       -      +
    379A  MET*     1.3    67.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 379 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    340A  ARG*     3.2    41.3    -      -       +      +
    341A  VAL*     3.8    22.4    -      -       +      +
    342A  PHE*     4.0     8.8    -      -       -      -
    364A  ALA*     5.3     8.7    -      -       +      -
    365A  PHE*     4.3    22.0    -      -       +      -
    377A  PHE      5.7     0.2    -      -       -      +
    378A  GLU*     1.3    88.3    -      -       -      +
    380A  ARG*     1.3    62.7    +      -       -      +
    381A  LYS*     4.1     2.1    +      -       -      +
----------------------------------------------------------
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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