Contacts of the strand formed by residues 12 - 21 (chain B) in PDB entry 1OZ7


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 TYR 12 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2B  CYS*     4.4     0.2    -      -       -      -
      7B  SER      3.6     0.3    -      -       -      +
      8B  VAL*     3.5     7.2    -      -       -      +
      9B  TYR      2.7    38.1    +      -       -      +
     10B  GLU*     3.1    31.9    -      -       +      -
     11B  GLY*     1.3    80.4    -      -       -      -
     13B  CYS*     1.3    64.1    +      -       -      +
     14B  TYR*     3.2    36.3    -      -       +      +
     43B  ARG*     2.7    33.2    +      -       -      -
     45B  SER*     4.8    12.1    +      -       -      -
     47B  GLU*     4.3     7.9    -      -       +      -
    120B  LYS*     3.9    13.2    -      -       +      -
    121B  CYS      3.8     5.6    -      -       -      +
    122B  PRO*     3.8    30.1    -      -       +      -
    123B  ALA      4.3     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 13 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  ASN      3.4    11.0    -      -       -      -
      2B  CYS*     2.0    49.6    -      -       +      -
      3B  LEU      5.0     0.4    -      -       -      +
      6B  TRP*     4.1    18.8    -      -       +      -
      7B  SER      3.2     4.0    -      -       -      +
     12B  TYR*     1.3    73.2    -      -       -      +
     14B  TYR*     1.3    64.8    +      -       -      +
    120B  LYS*     3.3     8.3    -      -       -      +
    121B  CYS*     3.0    43.6    +      -       -      +
    123B  ALA*     4.2    11.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 14 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  TRP*     3.4     3.3    -      -       -      -
      7B  SER*     2.7    44.0    +      -       -      +
      9B  TYR*     3.9    17.6    +      -       +      -
     12B  TYR*     3.2    46.1    -      -       +      +
     13B  CYS*     1.3    75.9    -      -       -      +
     15B  LYS*     1.3    61.1    +      -       -      +
     16B  VAL*     5.6     0.2    -      -       -      +
     40B  VAL*     4.1     9.0    -      -       +      -
     47B  GLU*     2.8    27.8    +      -       +      +
     50B  PHE*     3.6    17.0    -      +       +      -
     51B  VAL*     3.9    25.1    -      -       +      -
     55B  ALA*     4.0    20.7    -      -       +      +
    118B  VAL*     4.5     4.0    -      -       +      -
    119B  CYS      3.6     4.9    -      -       -      +
    120B  LYS*     3.4    30.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 15 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  PRO      5.2     0.2    -      -       -      -
      5B  ASP*     2.8    48.1    +      -       -      +
      6B  TRP*     3.2    50.8    -      -       +      +
     14B  TYR*     1.3    75.5    -      -       -      +
     16B  VAL*     1.3    70.8    +      -       -      +
     17B  PHE*     3.6    34.9    -      -       +      -
     33B  GLN*     5.5     0.7    -      -       -      +
    118B  VAL*     3.5     5.5    -      -       -      +
    119B  CYS      3.2    28.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 16 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  LYS*     1.3    88.5    +      -       -      +
     17B  PHE*     1.3    72.3    +      -       -      +
     55B  ALA*     2.8    42.6    -      -       +      +
     56B  PHE*     4.1     0.7    -      -       -      +
     58B  MET*     4.2    25.1    -      -       +      +
     59B  LEU*     3.1    48.0    -      -       +      -
    117B  PHE      3.8     6.3    -      -       -      +
    118B  VAL*     4.2     5.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 17 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  TRP*     4.5     0.7    -      +       -      -
     15B  LYS*     3.6    52.9    -      -       +      -
     16B  VAL*     1.3    77.4    -      -       -      +
     18B  LYS*     1.3    62.5    +      -       -      +
     19B  GLU*     2.9    18.6    -      -       -      +
     29B  PHE*     3.7    15.9    -      +       -      -
     33B  GLN*     3.2    38.6    -      -       +      -
     59B  LEU*     3.4    14.1    -      -       -      +
    116B  SER*     4.0     0.3    -      -       -      -
    117B  PHE*     3.1    38.7    +      +       +      +
    119B  CYS*     3.4    33.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 18 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  PHE*     1.3    71.2    -      -       -      +
     19B  GLU*     1.3    71.6    +      -       -      +
     20B  ARG*     4.4    11.8    +      -       -      +
     58B  MET      4.8    11.2    -      -       -      +
     59B  LEU*     3.8    22.9    -      -       +      -
     60B  LYS*     4.9     7.6    -      -       +      +
    116B  SER*     4.4     5.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 19 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  PHE*     2.9    31.2    -      -       -      +
     18B  LYS*     1.3    77.8    +      -       -      +
     20B  ARG*     1.3    59.2    +      -       -      +
     21B  MET*     3.9    15.3    -      -       +      -
     29B  PHE*     4.4    13.7    -      -       +      -
    115B  PHE      3.4     0.5    -      -       -      +
    116B  SER*     3.3    22.9    +      -       -      -
    117B  PHE*     3.0    25.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 20 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18B  LYS      4.4     8.0    +      -       -      +
     19B  GLU*     1.3    74.7    +      -       -      +
     21B  MET*     1.3    64.8    +      -       -      +
     60B  LYS*     2.7    52.3    -      -       -      +
     62B  ASP*     3.8     3.2    +      -       -      -
    114B  THR*     4.0    26.0    -      -       +      +
    115B  PHE*     3.7    20.0    -      -       -      +
    116B  SER*     3.6    22.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 21 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  GLU*     3.9    13.7    -      -       +      -
     20B  ARG*     1.3    81.3    -      -       -      +
     22B  ASN*     1.3    63.2    -      -       -      +
     25B  ASP*     3.8    21.8    -      -       +      +
     26B  ALA*     3.9     3.4    -      -       +      +
     29B  PHE*     3.6    37.9    -      -       +      -
     65B  TRP*     2.5    27.9    +      -       -      -
    114B  THR*     3.8     7.0    -      -       -      -
    115B  PHE      2.9    16.5    +      -       -      +
    117B  PHE*     3.1    39.9    -      -       +      -
----------------------------------------------------------
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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