Contacts of the strand formed by residues 121 - 127 (chain A) 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 PHE 121 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  PRO*     3.7     6.3    -      -       -      -
     21A  LYS      2.9    22.7    +      -       -      +
     62A  MET*     5.4     1.6    -      -       +      -
     63A  TYR*     5.2    11.4    -      +       +      -
     64A  LYS*     3.4    57.4    -      -       +      +
     65A  ILE      4.6     0.2    -      -       -      +
     66A  TRP*     3.5    27.7    -      +       +      +
    102A  VAL*     5.3     0.4    -      -       +      -
    115A  THR*     4.1    11.7    -      -       -      -
    119A  ASN*     3.4    35.6    +      -       +      -
    120A  THR*     1.3    79.0    -      -       -      +
    122A  PRO*     1.3    79.3    -      -       +      +
    123A  PHE*     4.0     2.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 122 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  PHE      3.4    15.7    -      -       -      +
     18A  LYS*     3.9    21.5    -      -       +      +
     19A  GLU      4.2     5.4    -      -       -      +
     20A  PRO*     4.1    13.7    -      -       +      -
     59A  ILE*     4.0    20.4    -      -       +      -
     62A  MET*     3.8    24.9    -      -       +      -
     64A  LYS      3.4    16.6    -      -       -      +
     65A  ILE*     3.6     6.3    -      -       +      -
     66A  TRP*     3.0    19.2    +      -       -      +
    121A  PHE*     1.3    92.9    -      -       +      +
    123A  PHE*     1.3    63.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 123 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  LEU*     3.3     4.2    -      -       -      +
     17A  PHE*     2.7    55.9    +      +       +      -
     19A  GLU*     3.1    28.7    -      -       +      -
     21A  LYS*     4.0    17.5    -      -       +      -
     26A  ALA*     3.6    19.5    -      -       +      -
     29A  PHE*     3.3    41.7    -      +       +      -
     30A  CYS*     3.7    19.1    -      -       -      -
     39A  LEU*     3.9     5.8    -      -       +      -
     59A  ILE*     4.2     0.9    -      -       -      +
     65A  ILE*     3.8    12.1    -      -       -      -
     66A  TRP*     3.8    18.6    -      -       +      -
    121A  PHE      4.0     2.2    -      -       -      +
    122A  PRO*     1.3    81.5    -      -       -      +
    124A  MET*     1.3    57.8    +      -       -      +
    125A  CYS*     3.6    11.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 124 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  TYR*     6.2     2.2    -      -       +      -
     15A  MET      3.3     8.5    -      -       -      +
     16A  LEU*     4.5     7.9    -      -       +      -
     30A  CYS*     4.4     0.9    -      -       -      -
     39A  LEU*     3.6     7.6    -      -       -      +
     40A  LEU*     2.9    39.2    +      -       +      -
     51A  VAL*     4.5    17.9    -      -       +      -
     54A  VAL*     5.4     3.4    -      -       +      -
     55A  VAL*     5.3     2.5    -      -       +      -
     65A  ILE*     4.6     7.0    -      -       +      -
     66A  TRP      3.5     9.9    +      -       -      +
     67A  THR*     5.8     1.3    -      -       +      -
    103A  LEU*     6.3     0.2    -      -       +      -
    123A  PHE*     1.3    78.2    -      -       -      +
    125A  CYS*     1.3    64.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 125 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  TRP*     4.0    13.7    -      -       +      -
     14A  TYR*     3.4     7.1    -      -       -      +
     15A  MET      2.7    27.6    +      -       -      +
     17A  PHE*     3.5    29.6    -      -       +      -
     29A  PHE*     4.0     2.9    -      -       -      -
     30A  CYS*     2.0    52.7    -      -       +      +
     33A  GLN*     4.7     2.5    -      -       -      -
     38A  HIS      3.4     4.3    -      -       -      -
     40A  LEU*     4.6     0.7    -      -       -      +
    123A  PHE*     3.6    10.1    -      -       -      -
    124A  MET*     1.3    77.1    -      -       -      +
    126A  LYS*     1.3    65.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 126 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  TRP*     4.6     0.8    -      -       -      -
     12A  TYR*     3.7    35.7    -      -       +      -
     13A  CYS      3.2    13.0    -      -       -      +
     14A  TYR*     3.6    23.6    -      -       +      -
     36A  ASP      4.0     0.7    -      -       -      +
     37A  GLY*     3.1     1.2    -      -       -      -
     38A  HIS*     2.8    32.9    +      -       -      +
     39A  LEU      4.9     0.9    -      -       -      +
     40A  LEU*     4.0    13.2    -      -       +      -
     41A  SER*     2.8    42.0    +      -       -      +
     43A  GLU*     4.1    10.1    +      -       -      -
     47A  GLU*     2.8    26.3    +      -       -      +
    125A  CYS*     1.3    79.8    -      -       -      +
    127A  TYR*     1.3    69.1    +      -       -      +
     81B  ASP*     4.4     5.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 127 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  PRO*     2.8    37.6    -      -       +      +
      6A  TRP*     3.3    47.1    -      +       -      -
     12A  TYR*     3.6     5.7    -      -       -      -
     13A  CYS*     3.0    44.7    +      -       +      +
     33A  GLN*     5.2     3.1    -      -       +      -
     34A  GLY*     5.0    18.6    -      -       -      -
     35A  LYS      4.5     6.3    -      -       -      +
     36A  ASP      3.8     2.5    -      -       -      +
     37A  GLY*     3.3    22.4    -      -       -      +
    126A  LYS*     1.3    80.6    -      -       -      +
    128A  PRO*     1.3    78.2    -      -       +      +
    129A  VAL*     4.2    13.4    -      -       +      +
----------------------------------------------------------
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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