Contacts of the strand formed by residues 77 - 86 (chain A) 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 LEU 77 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  MET*     3.7    36.8    -      -       +      -
      8A  THR      3.3     8.3    -      -       -      +
      9A  VAL*     3.5    32.3    -      -       +      -
     71A  LEU*     4.5     9.6    -      -       +      -
     73A  PHE*     3.3    25.8    -      -       +      +
     74A  PHE*     2.9    24.4    +      -       -      +
     75A  PRO      3.5     0.7    -      -       -      -
     76A  TYR*     1.3    79.3    -      -       -      +
     78A  THR*     1.3    62.3    +      -       -      +
     79A  ILE*     3.8    28.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 78 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  ARG*     3.5     4.7    -      -       -      +
      7A  MET*     3.6     1.0    -      -       -      -
      8A  THR*     2.9    44.3    +      -       -      +
     10A  ASN*     3.9    11.7    +      -       -      -
     76A  TYR      4.0     0.4    +      -       -      -
     77A  LEU*     1.3    72.1    -      -       -      +
     79A  ILE*     1.3    65.6    +      -       -      +
     80A  ASP*     5.1     9.9    -      -       -      +
     49C  LYS*     5.3     4.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 79 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  VAL*     4.0    14.6    -      -       +      -
      6A  ARG      3.3     4.9    -      -       -      +
      7A  MET*     4.6     4.7    -      -       +      -
     68A  LEU*     4.4    18.6    -      -       +      +
     74A  PHE*     3.8    26.7    -      -       +      -
     77A  LEU*     3.8    29.5    +      -       +      +
     78A  THR*     1.3    79.5    -      -       -      +
     80A  ASP*     1.3    62.5    +      -       -      +
     81A  VAL*     3.8    24.2    -      -       +      -
     48C  GLY      3.6    25.8    -      -       -      +
     49C  LYS*     2.6    39.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 80 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  LEU      3.5     1.6    -      -       -      +
      5A  VAL*     3.2     6.9    -      -       -      +
      6A  ARG*     2.9    59.6    +      -       +      +
     78A  THR*     5.1    10.6    -      -       -      +
     79A  ILE*     1.3    79.2    -      -       -      +
     81A  VAL*     1.3    62.1    +      -       -      +
     49C  LYS*     4.2     9.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 81 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  TYR*     4.0    16.6    -      -       +      -
      4A  LEU      3.6     2.2    -      -       -      +
      5A  VAL*     4.3     5.6    -      -       +      -
     64A  LEU*     3.8    22.0    -      -       +      -
     68A  LEU*     4.0    17.0    -      -       +      -
     79A  ILE*     3.8    20.3    +      -       +      +
     80A  ASP*     1.3    78.6    -      -       -      +
     82A  GLU*     1.3    67.6    +      -       -      +
     83A  PRO*     4.6     1.3    -      -       -      +
     81B  VAL      5.4     1.7    -      -       -      +
     83B  PRO*     4.1    24.6    -      -       +      +
     47C  THR*     4.0    21.1    -      -       +      +
     49C  LYS*     5.4     4.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 82 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  TYR*     3.5     2.3    -      -       -      -
      4A  LEU*     2.8    61.9    +      -       +      +
     81A  VAL*     1.3    79.7    -      -       -      +
     83A  PRO*     1.3    77.3    -      -       +      +
     84A  LEU*     4.7     1.6    -      -       +      +
     81B  VAL      5.9     1.3    -      -       -      +
      6D  ARG*     2.7    45.3    +      -       -      -
     46D  THR*     4.2    11.3    -      -       -      +
     53D  ILE*     4.2     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 83 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  LEU      3.8     6.3    -      -       -      +
      3A  TYR*     4.3     4.7    -      -       +      -
     82A  GLU*     1.3    92.8    -      -       +      +
     84A  LEU*     1.3    65.1    +      -       -      +
      3B  TYR*     4.6     6.5    -      -       +      -
     61B  HIS*     3.4    35.4    -      -       +      +
     81B  VAL*     4.1    29.4    -      -       +      +
     83B  PRO*     4.2    21.3    -      -       +      -
     46D  THR*     4.8     0.9    -      -       -      -
     47D  THR*     3.3    27.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 84 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  MET*     5.5     0.2    -      -       -      +
      2A  LEU*     2.9    34.2    +      -       +      +
      3A  TYR      4.2     4.3    -      -       -      -
      4A  LEU*     3.9    35.7    -      -       +      +
     55A  VAL*     4.4     8.7    -      -       +      -
     82A  GLU*     4.6     4.7    -      -       +      +
     83A  PRO*     1.3    79.8    -      -       -      +
     85A  SER*     1.3    61.2    +      -       -      +
     61B  HIS*     3.2    21.3    -      -       -      +
     44D  TRP*     3.8    44.6    -      -       +      -
     45D  ARG      3.6     6.1    -      -       -      +
     46D  THR*     5.2     0.9    -      -       -      -
     47D  THR*     3.5     2.5    -      -       -      -
     53D  ILE*     3.9    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 85 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  LEU*     6.1     2.0    -      -       -      -
     84A  LEU*     1.3    72.9    -      -       -      +
     86A  HIS*     1.3    61.6    +      -       -      +
     87A  HIS      3.4     0.3    +      -       -      -
     61B  HIS*     3.4    17.2    +      -       -      -
     62B  ASP*     3.2    12.6    -      -       -      -
     65B  HIS*     3.8     9.1    -      -       -      +
     44D  TRP*     3.6     9.8    -      -       -      +
     45D  ARG*     2.7    52.0    +      -       -      -
     47D  THR*     2.5    27.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 86 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  LEU*     6.5     0.2    -      -       -      -
     85A  SER*     1.3    74.0    -      -       -      +
     87A  HIS*     1.3    80.7    +      -       -      +
     88A  PRO*     3.8     9.5    +      -       +      +
     90A  ARG*     3.8    32.1    +      -       +      +
     92A  GLY      5.3     6.7    -      -       -      -
     62B  ASP*     2.7    26.2    +      -       -      +
     65B  HIS*     5.9     1.7    -      -       -      -
     44D  TRP*     5.5     3.8    -      -       -      +
     45D  ARG*     3.7     7.5    -      -       -      +
----------------------------------------------------------
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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