Contacts of the strand formed by residues 104 - 111 (chain A) in PDB entry 4O65


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 104 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  PHE*     4.4    17.9    -      -       +      -
     42A  VAL*     3.6    30.1    -      -       +      -
     98A  SER*     5.0     1.1    -      -       -      +
    100A  VAL*     3.6    29.6    -      -       +      -
    102A  GLN*     4.0     9.0    -      -       +      +
    103A  ASP*     1.3    81.6    -      -       -      +
    105A  ASN*     1.3    66.4    +      -       -      +
    134A  THR*     3.3     5.5    -      -       -      +
    135A  ILE*     2.7    47.6    +      -       +      +
    163A  ILE*     3.9    26.2    -      -       +      -
    164A  ALA      5.3     2.7    -      -       -      +
    165A  SER*     5.9     0.7    -      -       -      +
    166A  VAL*     5.0     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 105 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104A  LEU*     1.3    77.4    -      -       -      +
    106A  ALA*     1.3    62.8    +      -       -      +
    132A  VAL*     3.7    19.4    -      -       +      +
    133A  PHE      3.3     4.5    -      -       -      +
    134A  THR*     3.7    16.6    +      -       -      +
    163A  ILE*     3.7     5.4    -      -       -      +
    164A  ALA*     2.8    41.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 106 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104A  LEU*     5.7     0.2    -      -       +      -
    105A  ASN*     1.3    77.2    -      -       -      +
    107A  TRP*     1.3    67.4    +      -       -      +
    132A  VAL*     3.3     5.2    -      -       -      +
    133A  PHE*     2.8    41.3    +      -       +      -
    135A  ILE*     3.7    29.2    -      -       +      -
    161A  LEU*     3.8    12.6    -      -       +      -
    162A  ASN      3.1    15.9    -      -       -      +
    163A  ILE*     4.3     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 107 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  ALA*     1.3    77.5    -      -       -      +
    108A  ILE*     1.3    67.1    +      -       -      +
    109A  SER*     5.4     4.3    -      -       -      -
    126A  ARG*     6.2     1.3    -      -       -      +
    131A  ASN      3.2    25.8    -      -       -      +
    132A  VAL*     4.2    17.5    -      -       +      -
    133A  PHE*     3.9     7.6    -      -       -      -
    160A  GLN      4.0     0.2    -      -       -      +
    161A  LEU*     3.6     4.5    -      -       -      +
    162A  ASN*     2.8    70.0    +      -       +      +
    163A  ILE      4.9     1.1    -      -       -      -
    164A  ALA*     3.8    35.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  LEU*     4.3    15.7    -      -       +      -
    107A  TRP*     1.3    81.1    -      -       -      +
    109A  SER*     1.3    65.4    +      -       -      +
    123A  PHE*     4.8     0.2    -      -       -      -
    126A  ARG*     3.0    45.1    +      -       +      +
    127A  ASP      5.3     4.7    -      -       -      +
    128A  PRO      5.4     1.1    -      -       -      +
    133A  PHE*     4.0    18.6    -      -       +      -
    143A  TYR*     3.6    42.2    -      -       +      -
    145A  LEU*     3.7    23.3    -      -       +      -
    159A  THR*     3.9    17.9    -      -       +      -
    160A  GLN      3.4    10.3    -      -       -      +
    161A  LEU*     4.7     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107A  TRP*     5.4     5.4    -      -       -      -
    108A  ILE*     1.3    76.6    -      -       -      +
    110A  LEU*     1.3    64.1    +      -       -      +
    123A  PHE*     3.8    15.3    -      -       -      -
    126A  ARG*     4.1     9.0    -      -       -      -
    145A  LEU*     3.8    11.0    -      -       -      +
    159A  THR*     3.8     1.0    -      -       -      -
    160A  GLN*     2.8    53.5    +      -       -      +
    162A  ASN*     4.6     4.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  PHE*     4.5     1.8    -      -       +      -
     90A  LEU*     4.5     7.9    -      -       +      -
     92A  VAL*     4.2    23.6    -      -       +      -
    109A  SER*     1.3    80.6    +      -       -      +
    111A  PHE*     1.3    62.6    +      -       -      +
    112A  THR      3.9    21.3    +      -       -      +
    121A  TRP*     4.3    19.3    -      -       +      -
    123A  PHE*     3.9     5.7    -      -       +      -
    145A  LEU*     4.8     3.8    -      -       +      -
    147A  LEU*     3.9    37.5    -      -       +      -
    157A  ALA*     4.2    16.2    -      -       +      -
    158A  HIS      3.5    20.6    -      -       -      +
    159A  THR*     4.4     3.8    -      -       -      +
    160A  GLN*     4.8     0.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109A  SER      4.1     1.0    -      -       -      -
    110A  LEU*     1.3    72.2    -      -       -      +
    112A  THR*     1.4    88.3    +      -       +      +
    156A  HIS      3.7     0.4    -      -       -      +
    157A  ALA*     3.3     2.6    -      -       -      +
    158A  HIS*     2.8    61.5    +      +       +      +
    160A  GLN*     3.3    27.0    -      -       +      +
    170A  LEU*     3.9    32.1    -      -       +      -
----------------------------------------------------------
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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