Contacts of the strand formed by residues 72 - 79 (chain A) in PDB entry 1X0O


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 72 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  SER*     3.2    36.3    -      -       -      +
     63A  GLN*     3.5    25.8    -      -       +      +
     64A  VAL*     3.5    13.5    -      -       +      +
     67A  LEU*     3.5    21.8    -      -       +      -
     70A  GLN*     4.3     1.8    -      -       +      +
     71A  VAL*     1.3    76.7    -      -       -      +
     73A  SER*     1.3    65.5    +      -       -      +
     74A  VAL*     3.6     0.3    +      -       -      +
     90A  THR      3.3     1.2    -      -       -      +
     91A  SER*     4.3     1.1    -      -       -      -
     92A  SER*     2.7    52.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 73 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  SER*     5.3     1.0    +      -       -      -
     71A  VAL*     4.1     3.5    +      -       -      -
     72A  LEU*     1.3    78.6    -      -       -      +
     74A  VAL*     1.3    60.5    +      -       -      +
     89A  ARG*     3.7    31.8    -      -       -      -
     90A  THR      3.4     5.2    -      -       -      -
     91A  SER*     4.3     6.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 74 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  LEU*     3.9    22.2    -      -       +      +
     57A  LEU*     3.6    32.5    -      -       +      -
     60A  SER*     3.5    31.2    -      -       -      +
     61A  PHE*     3.8    16.8    -      -       +      -
     72A  LEU      4.9     0.4    -      -       -      +
     73A  SER*     1.3    74.8    -      -       -      +
     75A  MET*     1.3    66.3    +      -       -      +
     76A  PHE*     3.9     2.8    -      -       -      -
     89A  ARG*     3.4     2.4    -      -       -      -
     90A  THR*     2.8    50.9    +      -       -      +
     92A  SER*     4.1     6.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 75 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  ASP*     4.5     1.4    -      -       -      +
     56A  LEU*     3.2    24.6    -      -       -      +
     73A  SER      4.3     0.2    -      -       -      -
     74A  VAL*     1.3    76.1    -      -       -      +
     76A  PHE*     1.3    63.0    +      -       -      +
     87A  TRP*     3.8    46.0    -      -       +      -
     88A  MET      3.6     9.0    -      -       -      +
     89A  ARG*     4.3    14.8    -      -       +      -
    113A  VAL*     4.4    23.1    -      -       +      -
    114A  LYS*     5.2     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 76 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  ILE*     3.9    11.9    -      -       +      -
     49A  CYS*     3.7     8.7    -      -       +      -
     53A  ASP*     3.9    23.6    -      -       +      +
     56A  LEU*     4.9     1.3    -      -       +      -
     57A  LEU*     3.5    43.3    -      -       +      -
     74A  VAL      3.9     6.1    -      -       -      -
     75A  MET*     1.3    75.0    -      -       -      +
     77A  ARG*     1.3    72.9    +      -       -      +
     78A  PHE*     3.4    45.1    -      +       +      -
     87A  TRP*     3.6     9.3    -      -       -      -
     88A  MET*     2.8    49.0    +      -       +      +
     90A  THR*     3.0    29.6    -      -       -      -
    110A  ASN*     4.5     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 77 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  HIS*     2.9    78.6    +      -       +      +
     53A  ASP*     4.1     2.5    +      -       -      +
     76A  PHE*     1.3    82.5    -      -       -      +
     78A  PHE*     1.3    61.9    +      -       -      +
     85A  TRP*     3.5    30.2    +      -       +      +
     86A  LEU      2.9     9.9    -      -       -      +
     87A  TRP*     3.3    48.0    -      -       +      +
    116A  SER*     4.6    13.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 78 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  PHE*     4.3     7.9    -      +       -      -
     22A  PHE*     4.7     3.4    -      +       -      -
     33A  VAL*     3.3    35.9    -      -       +      -
     35A  TYR*     3.8    11.9    -      +       -      -
     40A  LEU*     4.3    18.2    -      -       +      -
     45A  ILE*     3.8    21.5    -      -       +      -
     48A  PHE*     3.8    12.8    -      +       +      -
     76A  PHE*     3.4    29.7    +      +       +      -
     77A  ARG*     1.3    72.8    -      -       -      +
     79A  ARG*     1.3    82.1    +      -       -      +
     80A  SER      3.2     1.0    +      -       -      -
     84A  GLU      3.1     9.6    -      -       -      +
     85A  TRP*     4.3     0.9    -      -       -      -
     86A  LEU*     2.8    33.2    +      -       +      +
     88A  MET*     3.6    26.2    -      -       +      -
    110A  ASN*     3.7    16.2    -      -       -      -
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Residues in contact with ARG 79 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  TYR*     3.0    40.2    +      -       -      +
     47A  GLU      4.6     8.5    +      -       -      -
     48A  PHE*     2.8    52.9    +      -       -      +
     77A  ARG      3.9     0.6    +      -       -      -
     78A  PHE*     1.3    75.6    -      -       -      +
     80A  SER*     1.3    60.8    +      -       -      +
     83A  GLN*     3.5    38.5    +      -       -      +
     84A  GLU      2.9    12.8    -      -       -      +
     85A  TRP*     3.4    35.7    -      -       +      -
----------------------------------------------------------
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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