Contacts of the strand formed by residues 40 - 46 (chain C) in PDB entry 3ZO7


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 TRP 40 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90B  ARG*     4.0     0.2    +      -       -      -
      7C  MET*     4.0    22.2    -      -       +      -
     31C  SER*     3.5    31.4    -      -       -      -
     34C  LEU*     3.2    22.0    +      -       +      -
     35C  GLN*     3.5    43.3    -      -       +      +
     38C  GLY      4.0     1.6    -      -       -      -
     39C  GLN*     1.3    74.8    -      -       -      +
     41C  ARG*     1.3    66.7    +      -       -      +
     42C  TYR      3.2    22.7    +      -       -      -
     43C  LEU*     3.6    28.0    -      -       +      +
     52C  ASN*     4.5     4.5    -      -       -      -
     54C  SER*     3.0    30.2    +      -       -      -
     55C  VAL      4.3     1.3    -      -       -      -
     56C  PHE*     3.4    24.7    -      +       +      -
     71C  LEU*     3.9    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 41 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90B  ARG*     3.1    23.6    +      -       -      -
      2C  LEU*     3.7    24.9    -      -       -      +
     38C  GLY*     4.0    12.8    +      -       -      +
     39C  GLN      3.4     2.2    +      -       -      -
     40C  TRP*     1.3    74.0    -      -       -      +
     42C  TYR*     1.3    99.0    +      -       +      +
     55C  VAL*     2.9    19.3    +      -       -      +
     57C  ASP*     3.3    28.9    +      -       +      -
     93C  LYS*     5.9     1.8    -      -       -      +
     94C  ASP*     3.3    24.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 42 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42B  TYR*     3.2    42.9    +      +       -      -
     44B  TRP*     4.2    14.1    -      +       -      -
     90B  ARG*     4.0    12.6    -      -       -      +
     93B  LYS      4.7     4.7    -      -       -      -
     94B  ASP      4.6     4.0    -      -       -      -
     40C  TRP*     3.2    13.5    -      -       -      -
     41C  ARG*     1.3   127.0    +      -       +      +
     43C  LEU*     1.3    61.6    +      -       -      +
     44C  TRP*     3.5    37.5    -      +       +      -
     53C  ILE      4.7     0.4    -      -       -      -
     54C  SER*     3.3     2.4    -      -       -      -
     55C  VAL*     3.1    40.2    +      -       +      -
     94C  ASP*     3.7     6.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 43 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87B  HIS*     3.6    39.7    +      -       +      +
     89B  ALA*     4.1    10.5    -      -       +      +
     90B  ARG*     3.8    28.3    +      -       -      +
     94B  ASP*     4.4     1.4    -      -       -      +
     31C  SER*     4.9     2.0    -      -       -      +
     35C  GLN*     3.7    26.7    -      -       -      +
     40C  TRP*     3.6    22.2    -      -       +      +
     42C  TYR*     1.3    77.3    -      -       -      +
     44C  TRP*     1.3    70.0    +      -       -      +
     52C  ASN*     3.6    27.8    -      -       +      +
     53C  ILE      3.8     2.0    -      -       -      -
     54C  SER*     3.3    18.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 44 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2B  LEU*     3.6    21.4    -      -       +      +
      4B  LEU*     5.6     0.7    -      -       +      -
     42B  TYR*     3.9    13.5    -      +       -      -
     44B  TRP*     4.6     2.5    -      +       -      -
     55B  VAL*     4.0    25.4    -      -       +      -
     84B  LEU*     3.9    34.1    -      -       +      -
     85B  SER      3.6    11.0    -      -       -      +
     87B  HIS*     4.0     5.6    -      -       -      -
     94B  ASP*     3.3    43.7    +      -       +      +
      4C  LEU*     5.4     1.1    -      -       +      -
     42C  TYR*     3.5    42.4    -      +       +      -
     43C  LEU*     1.3    80.9    +      -       -      +
     45C  ARG*     1.3    59.8    +      -       -      +
     52C  ASN*     3.1     8.7    -      -       -      +
     53C  ILE*     3.0    57.2    +      -       +      +
     55C  VAL*     4.3    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 45 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  HIS*     3.3    42.7    +      -       +      +
     69A  TRP*     4.1    21.6    -      -       -      -
     84B  LEU*     3.5     7.2    -      -       -      +
     85B  SER*     2.8    46.4    +      -       -      +
     86B  HIS      3.8    14.1    -      -       -      +
     87B  HIS*     3.5    31.1    +      -       -      +
     88B  PRO*     3.5    30.7    -      -       -      +
     44C  TRP*     1.3    74.0    -      -       -      +
     46C  THR*     1.3    63.5    +      -       -      +
     47C  THR      3.3     0.5    +      -       -      -
     49C  LYS      3.5     8.3    +      -       -      -
     50C  TYR*     4.4    11.5    -      -       -      -
     51C  GLY*     3.1    34.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 46 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82B  GLU*     3.7    16.8    -      -       -      +
     83B  PRO      4.5     4.3    -      -       -      -
     84B  LEU*     4.9     1.6    -      -       +      -
      6C  ARG*     4.2     9.0    -      -       +      +
      7C  MET      5.6     0.4    -      -       -      +
     44C  TRP      3.8     0.4    +      -       -      -
     45C  ARG*     1.3    75.6    -      -       -      +
     47C  THR*     1.3    67.3    +      -       -      +
     48C  GLY      3.3     0.3    +      -       -      -
     49C  LYS*     2.9    43.7    +      -       +      +
     51C  GLY*     3.2    21.1    +      -       -      -
     52C  ASN*     4.0    11.4    -      -       -      +
     53C  ILE*     3.6    31.4    -      -       +      -
----------------------------------------------------------
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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