Contacts of the strand formed by residues 131 - 136 (chain T) in PDB entry 5A0Q


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 GLY 131 (chain T).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29T  VAL*     3.8    18.4    -      -       -      +
     75T  ALA      3.0    33.1    +      -       -      +
    129T  GLY      3.6     2.6    +      -       -      -
    130T  VAL*     1.4    77.0    -      -       -      +
    132T  LEU*     1.3    58.8    +      -       -      -
    147T  THR      3.4    10.1    -      -       -      -
    148T  CYS*     4.9     0.2    -      -       -      -
    149T  PRO*     4.4     5.4    -      -       -      -
    161T  ILE*     3.2    12.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 132 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72T  ILE*     3.7    46.2    -      -       +      -
     73T  SER      3.5     2.5    -      -       -      +
     74T  ILE*     3.9    14.8    -      -       +      -
     81T  ALA*     4.5     3.8    -      -       +      -
     84T  LEU*     4.5    18.4    -      -       +      -
     88T  MET*     5.4     2.5    -      -       +      -
    112T  ILE*     4.5     8.5    -      -       +      -
    130T  VAL*     3.5    35.4    -      -       +      +
    131T  GLY*     1.3    72.7    -      -       -      +
    133T  LEU*     1.3    59.2    +      -       -      +
    134T  ILE*     3.9    13.2    -      -       +      -
    146T  GLN*     3.3     6.9    -      -       -      +
    147T  THR*     2.9    45.3    +      -       -      +
    161T  ILE*     3.7     6.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 133 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35T  THR      3.7    24.9    -      -       -      +
     36T  VAL      4.2     0.2    -      -       -      -
     37T  GLY*     3.9    18.4    -      -       -      +
     46T  LEU*     3.8     9.4    -      -       +      +
     71T  GLY      3.7     0.5    -      -       -      +
     72T  ILE*     3.4     1.8    -      -       -      -
     73T  SER*     3.0    44.7    +      -       -      +
    132T  LEU*     1.3    72.8    -      -       -      +
    134T  ILE*     1.3    61.1    +      -       -      +
    135T  ALA      3.3     6.0    +      -       -      +
    144T  ILE*     4.6    14.6    -      -       +      -
    145T  PHE      3.8     2.5    -      -       -      -
    146T  GLN*     3.9    25.8    -      -       +      +
    159T  MET*     3.9    22.4    -      -       +      -
    160T  SER*     4.3     1.6    -      -       -      -
    161T  ILE*     3.9    24.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 134 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70T  ILE*     3.5    30.3    -      -       +      -
     71T  GLY      3.9     2.9    -      -       -      -
     72T  ILE*     3.7    20.0    -      -       +      -
    105T  VAL*     4.1     6.7    -      -       +      +
    108T  LEU*     4.9     6.3    -      -       +      -
    109T  VAL*     4.0    21.1    -      -       +      -
    112T  ILE*     3.4    22.9    -      -       +      -
    132T  LEU*     4.0     7.4    -      -       +      -
    133T  LEU*     1.3    66.9    -      -       -      +
    135T  ALA*     1.4    58.8    +      -       -      +
    136T  GLY      3.9     0.5    +      -       -      -
    143T  HIS      4.1     0.5    -      -       -      +
    144T  ILE*     3.5     1.9    -      -       -      -
    145T  PHE*     2.9    41.9    +      -       -      +
    147T  THR*     3.3    41.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 135 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44T  ALA*     4.2    12.3    -      -       +      -
     45T  VAL      5.1     0.4    -      -       -      -
     46T  LEU*     3.7    33.2    -      -       +      +
     70T  ILE*     3.5     4.5    -      -       -      +
     71T  GLY      2.9    31.6    +      -       -      +
    133T  LEU      3.3     3.6    +      -       -      -
    134T  ILE*     1.4    75.7    -      -       -      +
    136T  GLY*     1.3    59.7    +      -       -      +
    143T  HIS      3.7     4.5    -      -       -      -
    144T  ILE*     3.7    22.6    -      -       +      +
    221T  PHE*     4.5     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 136 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44T  ALA*     4.1     2.9    -      -       -      +
     69T  HIS      3.5    11.4    -      -       -      -
     70T  ILE*     4.0    10.5    -      -       -      -
    105T  VAL*     4.0     8.3    -      -       -      +
    134T  ILE      3.9     0.6    +      -       -      -
    135T  ALA*     1.3    76.9    -      -       -      +
    137T  TYR*     1.3    62.3    +      -       -      -
    142T  PRO*     3.5     5.2    -      -       -      +
    143T  HIS      2.8    33.4    +      -       -      +
    215T  VAL*     4.2     7.6    -      -       -      -
----------------------------------------------------------
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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