Contacts of the strand formed by residues 25 - 36 (chain A) in PDB entry 4ZIN


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 HIS 25 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  SER*     3.1     4.0    -      -       -      -
     22A  VAL      2.9    34.1    +      -       -      +
     23A  ASN      3.3     2.1    +      -       -      +
     24A  GLY*     1.3    75.3    -      -       -      +
     26A  GLU*     1.3    75.3    +      -       -      +
     27A  PHE*     3.4     5.9    -      -       -      -
     51A  GLY*     2.7    33.6    +      -       -      -
     53A  PRO      4.6     2.2    +      -       -      -
     54A  LEU*     4.6     2.2    -      -       +      -
     55A  PRO*     3.5    41.2    -      -       +      +
     56A  PHE*     4.4     6.9    -      -       +      -
    136A  MET*     6.1     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 26 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  GLY      3.4     6.3    -      -       -      +
     21A  SER*     3.9    15.5    -      -       -      -
     24A  GLY      3.4     9.2    +      -       -      +
     25A  HIS*     1.3    86.6    -      -       -      +
     27A  PHE*     1.3    63.9    +      -       -      +
     50A  LYS      4.7     0.2    -      -       -      -
     51A  GLY*     3.6     9.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 27 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  MET*     3.7    25.6    -      -       +      -
     19A  GLU*     3.7     1.7    -      -       -      +
     20A  GLY*     2.9    58.0    +      -       -      +
     21A  SER*     3.6     7.2    -      -       -      -
     22A  VAL*     4.0     5.2    -      -       +      -
     25A  HIS*     3.4    14.4    -      -       -      +
     26A  GLU*     1.3    75.7    -      -       -      +
     28A  GLU*     1.3    71.5    +      -       -      +
     29A  ILE*     4.0    16.8    -      -       +      -
     50A  LYS*     3.2    17.5    -      -       -      +
     51A  GLY*     4.4     1.3    -      -       -      +
     54A  LEU*     3.6    20.9    -      -       +      -
     56A  PHE*     3.5    23.3    -      +       -      -
     61A  LEU*     3.7    31.6    -      -       +      -
    124A  LEU*     4.4     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 28 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  HIS*     3.1    26.8    +      -       -      +
     18A  MET      3.2    11.4    -      -       -      +
     19A  GLU*     4.4    14.7    -      -       +      +
     27A  PHE*     1.3    80.5    -      -       -      +
     29A  ILE*     1.3    69.9    +      -       -      +
     30A  GLU*     5.3     1.9    -      -       -      +
     48A  VAL*     3.5     1.2    -      -       -      +
     49A  THR*     3.0    35.2    +      -       -      +
     50A  LYS*     3.0    41.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 29 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  VAL*     4.7     0.7    -      -       +      -
     17A  HIS*     3.5     4.3    -      -       -      -
     18A  MET*     2.8    38.6    +      -       +      +
     27A  PHE*     4.0    14.1    -      -       +      -
     28A  GLU*     1.3    80.8    -      -       -      +
     30A  GLU*     1.3    74.4    +      -       -      +
     46A  LEU*     4.1    14.4    -      -       +      -
     47A  LYS      3.3     9.9    -      -       -      +
     48A  VAL*     4.0    17.9    -      -       +      -
     49A  THR*     4.2     0.2    -      -       -      -
     54A  LEU*     4.4     0.7    -      -       +      -
     58A  TRP*     3.6    18.6    -      -       +      -
     61A  LEU*     3.5    32.3    -      -       +      -
     65A  PHE*     3.8    26.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 30 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  VAL      3.4     7.4    -      -       -      +
     17A  HIS*     3.9    20.1    +      -       +      -
     28A  GLU*     5.3     1.9    -      -       -      +
     29A  ILE*     1.3    82.1    -      -       -      +
     31A  GLY*     1.3    58.9    +      -       -      +
     46A  LEU*     3.4     1.3    -      -       -      -
     47A  LYS*     2.7    53.6    +      -       -      +
     49A  THR*     3.7    30.7    +      -       +      +
    141B  MET*     5.3    10.6    -      -       +      +
    168B  LYS*     3.0    45.7    +      -       -      +
    208B  TYR*     5.6     0.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 31 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  LYS*     3.5     4.2    -      -       -      -
     16A  VAL*     2.9    43.8    +      -       -      +
     30A  GLU*     1.3    77.8    -      -       -      +
     32A  GLU*     1.3    64.3    +      -       -      +
     45A  LYS      3.2    13.0    -      -       -      -
     46A  LEU*     3.9     3.6    -      -       -      -
    141B  MET*     4.0     9.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 32 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  ARG*     5.8     3.5    -      -       -      -
     14A  PHE*     3.3    16.4    -      -       -      +
     15A  LYS*     4.4     9.5    +      -       +      +
     16A  VAL*     4.5     0.2    -      -       -      +
     31A  GLY*     1.3    72.6    -      -       -      +
     33A  GLY*     1.3    58.7    +      -       -      +
     44A  ALA*     3.5     1.0    -      -       -      -
     45A  LYS*     2.9    38.5    +      -       +      +
     46A  LEU*     4.9     0.4    -      -       -      +
    117A  GLU*     5.3     1.0    -      -       -      +
    141B  MET*     3.4    32.7    -      -       +      +
    166B  LYS*     3.0    40.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 33 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  ARG*     3.3     7.7    +      -       -      +
     14A  PHE*     2.8    47.1    +      -       -      +
     32A  GLU*     1.3    77.5    -      -       -      +
     34A  GLU*     1.3    65.9    +      -       -      +
     43A  THR      3.1    14.6    -      -       -      -
     44A  ALA*     4.0     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 34 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  PHE*     3.8    23.0    -      -       +      -
     12A  MET      3.3     8.5    -      -       -      +
     13A  ARG*     2.2    43.0    +      -       +      +
     14A  PHE*     3.8     3.0    -      -       -      -
     33A  GLY*     1.3    75.9    -      -       -      +
     35A  GLY*     1.3    60.8    +      -       -      +
     42A  GLN*     3.3     5.1    -      -       -      -
     43A  THR*     2.8    44.5    +      -       -      +
     45A  LYS*     6.2     2.6    -      -       -      -
     72A  TYR*     4.3     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  PHE*     3.4    11.0    -      -       -      -
     12A  MET      3.0    31.1    +      -       -      +
     34A  GLU*     1.3    79.3    -      -       -      +
     36A  ARG*     1.3    67.5    -      -       -      -
     37A  PRO*     3.4     0.7    -      -       -      +
     41A  THR      3.2    12.8    -      -       -      -
     42A  GLN*     3.9     1.3    -      -       -      -
     72A  TYR*     3.5     9.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 36 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  GLU*     3.3    37.8    +      -       -      +
     11A  PHE*     3.9    23.3    -      -       -      +
     35A  GLY*     1.3    76.7    -      -       -      -
     37A  PRO*     1.3    70.9    -      -       -      +
     38A  TYR      3.2     2.5    -      -       -      -
     39A  GLU*     3.0    53.6    +      -       +      +
     40A  GLY      3.0    10.0    +      -       -      -
     41A  THR*     2.9    29.1    +      -       -      +
     72A  TYR*     4.1     0.2    -      -       -      -
----------------------------------------------------------
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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