Contacts of the strand formed by residues 122 - 128 (chain A) in PDB entry 4OI9


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 122 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89A  PRO*     5.3     4.3    -      -       +      -
    113A  VAL*     5.1     0.9    -      -       +      +
    116A  ALA*     3.3    45.1    -      -       +      +
    118A  PRO      3.7     9.2    -      -       -      +
    119A  ARG*     2.8    19.1    +      -       -      +
    120A  ALA      4.3     0.9    -      -       -      +
    121A  SER*     1.3    79.5    -      -       -      +
    123A  THR*     1.3    63.0    +      -       -      +
    124A  LEU*     4.3    12.8    -      -       +      -
    137A  SER*     4.6     0.7    +      -       -      -
    138A  PHE*     3.3    31.6    +      -       +      +
    147A  GLY      4.2     3.4    -      -       -      -
    148A  ALA*     3.7    22.9    -      -       +      -
    169A  ALA*     5.4     1.3    -      -       +      -
    170A  GLU      3.3    10.3    -      -       -      +
    171A  LEU*     3.8    30.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 123 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121A  SER      4.6     2.1    +      -       -      -
    122A  LEU*     1.3    77.0    +      -       -      +
    124A  LEU*     1.3    63.6    +      -       -      +
    125A  THR*     4.3     3.9    +      -       -      +
    135A  ARG*     4.1    41.7    -      -       +      +
    136A  ARG      3.3    12.3    -      -       -      +
    137A  SER*     4.1    14.3    +      -       -      -
    168A  ARG      3.5     3.5    -      -       -      +
    170A  GLU*     2.7    40.8    +      -       -      +
   2327A  EDO      3.7    22.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 124 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111A  CYS*     4.5     6.5    -      -       -      -
    113A  VAL*     3.7    31.2    -      -       +      -
    122A  LEU*     4.2    11.0    -      -       +      -
    123A  THR*     1.3    77.6    -      -       -      +
    125A  THR*     1.3    65.4    +      -       -      +
    136A  ARG      2.8    36.7    +      -       -      +
    138A  PHE*     3.8    10.1    -      -       +      -
    148A  ALA*     3.7    28.5    -      -       +      +
    149A  VAL*     3.9     7.0    -      -       -      -
    150A  LEU*     3.4    45.2    -      -       +      +
    167A  CYS*     4.8     3.8    -      -       -      -
    168A  ARG      3.3     5.8    -      -       -      +
    169A  ALA*     4.2     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 125 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123A  THR*     4.3     3.8    +      -       -      +
    124A  LEU*     1.3    79.7    +      -       -      +
    126A  LEU*     1.3    67.8    +      -       -      +
    127A  LEU*     3.6    13.7    -      -       +      +
    132A  GLU*     3.8    37.2    -      -       +      +
    134A  ILE      3.4    12.6    -      -       -      +
    135A  ARG*     3.4    22.8    +      -       -      +
    150A  LEU*     4.4     0.7    -      -       -      -
    167A  CYS*     3.4     4.1    -      -       -      -
    168A  ARG*     2.7    57.4    +      -       -      +
    170A  GLU*     5.3     0.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 126 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  LEU*     4.1    13.7    -      -       +      -
    109A  LEU*     3.7    28.5    -      -       +      -
    111A  CYS*     3.8     8.7    -      -       +      +
    125A  THR*     1.3    72.3    -      -       -      +
    127A  LEU*     1.3    53.6    +      -       -      +
    132A  GLU*     3.7     2.4    -      -       -      -
    133A  LEU*     2.7    35.4    +      -       +      +
    134A  ILE*     2.9    26.9    +      -       +      +
    150A  LEU*     4.0    19.2    -      -       +      +
    152A  ALA*     3.7    36.1    -      -       +      +
    166A  SER      3.7     4.3    -      -       -      +
    167A  CYS*     3.6    32.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 127 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109A  LEU*     5.2     0.7    -      -       -      +
    125A  THR*     3.6    26.9    -      -       +      +
    126A  LEU*     1.3    76.1    -      -       -      +
    128A  ARG*     1.3    61.1    +      -       -      +
    129A  GLY      3.8    11.7    -      -       -      +
    130A  ALA*     3.9    17.7    -      -       -      +
    131A  GLN      3.2    13.0    -      -       -      +
    132A  GLU*     3.9    17.0    -      -       +      +
    133A  LEU*     4.2     5.4    -      -       -      +
    164A  ASN      3.9     0.2    -      -       -      +
    165A  PHE*     3.3     9.2    -      -       -      +
    166A  SER*     2.9    49.7    +      -       -      +
    168A  ARG*     3.7    30.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 128 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127A  LEU*     1.3    70.4    -      -       -      +
    129A  GLY*     1.3    60.8    +      -       -      +
    130A  ALA      3.3     0.2    +      -       -      -
    131A  GLN*     2.7    63.5    +      -       +      +
    133A  LEU*     3.6    31.0    -      -       +      +
    154A  VAL*     4.0    18.2    -      -       -      +
    155A  LEU      5.0     1.2    +      -       -      -
    157A  ARG*     3.2    48.1    -      -       -      +
    160A  ASP*     3.5    11.7    +      -       -      -
    163A  ALA*     4.7     7.9    -      -       +      -
    164A  ASN      3.5     5.4    -      -       -      +
    165A  PHE*     3.5    27.4    -      -       +      -
   2336A  EDO      5.0     6.3    +      -       -      -
----------------------------------------------------------
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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