Contacts of the strand formed by residues 124 - 134 (chain O) in PDB entry 2GTL


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 HIS 124 (chain O).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109O  ILE*     4.7    12.5    -      -       +      +
    110O  GLY      3.2    14.8    +      -       -      +
    111O  ASP*     3.5    27.7    +      -       +      -
    122O  PRO*     3.4    22.7    -      -       -      +
    123O  GLU*     1.3    95.5    +      -       +      +
    125O  MET*     1.3    69.7    +      -       -      +
    126O  THR*     5.8     1.3    -      -       -      +
    150O  ILE*     4.9     3.6    -      -       -      +
    151O  GLU      5.6     1.6    +      -       -      -
    216O  PHE*     4.3     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 125 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109O  ILE*     4.8     0.7    -      -       -      -
    110O  GLY*     2.9    28.0    +      -       -      -
    118O  THR*     4.6     9.4    -      -       +      -
    122O  PRO*     4.9     1.1    -      -       +      -
    124O  HIS*     1.3    85.3    -      -       -      +
    126O  THR*     1.3    62.8    +      -       -      +
    148O  ILE*     4.1    25.4    -      -       +      -
    149O  GLU      3.8     8.5    -      -       -      +
    150O  ILE*     4.2    22.2    -      -       +      +
    188O  LEU*     5.3     5.2    -      -       -      -
    204O  ILE*     3.5    31.2    -      -       +      -
    216O  PHE*     3.9    25.1    -      -       +      -
    218O  PHE*     3.7    29.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 126 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107O  LYS*     4.8    17.9    -      -       +      +
    108O  PHE      3.5     6.3    -      -       -      +
    109O  ILE*     2.9    29.5    -      -       +      +
    124O  HIS*     5.8     0.9    -      -       -      +
    125O  MET*     1.3    73.6    +      -       -      +
    127O  LEU*     1.3    69.4    +      -       -      +
    128O  ALA      4.0     2.0    -      -       -      +
    148O  ILE*     3.6     6.2    -      -       -      +
    149O  GLU*     2.9    60.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 127 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107O  LYS*     3.6     0.2    -      -       -      -
    108O  PHE*     2.7    38.3    +      -       +      +
    125O  MET*     6.2     0.2    -      -       -      -
    126O  THR*     1.3    78.1    -      -       -      +
    128O  ALA*     1.3    58.7    +      -       -      +
    129O  PHE*     3.6    33.3    -      -       +      -
    146O  VAL*     4.7     4.7    -      -       +      -
    147O  HIS      3.9     2.2    -      -       -      +
    148O  ILE*     3.6    35.9    -      -       +      -
    176O  LEU*     4.8     0.9    -      -       +      -
    178O  ILE*     3.9    25.4    -      -       +      -
    188O  LEU*     4.0    18.4    -      -       +      -
    200O  PHE*     4.1    20.4    -      -       +      -
    218O  PHE*     4.0    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 128 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106O  ASP      3.9     4.3    -      -       -      -
    107O  LYS*     4.2    26.2    -      -       +      -
    126O  THR*     4.0     2.3    -      -       +      +
    127O  LEU*     1.3    72.1    -      -       -      +
    129O  PHE*     1.3    64.3    +      -       -      +
    130O  GLU      3.6     1.3    +      -       -      -
    146O  VAL*     3.4     3.9    -      -       -      +
    147O  HIS*     2.9    49.9    +      -       +      +
    149O  GLU*     4.7    13.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 129 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102O  THR*     3.1    55.6    -      -       +      -
    103O  LYS      4.3    16.2    -      -       -      +
    104O  ALA*     4.4     1.3    -      -       -      +
    105O  GLY*     2.9    26.7    +      -       -      -
    106O  ASP      3.1    20.5    +      -       -      +
    108O  PHE*     3.8    11.0    -      +       -      -
    127O  LEU*     3.6    38.6    -      -       +      -
    128O  ALA*     1.3    72.6    -      -       -      +
    130O  GLU*     1.3    61.4    +      -       -      +
    131O  SER      3.8     2.0    -      -       -      +
    144O  LEU*     3.6    20.9    -      -       +      -
    145O  HIS      4.0     2.5    -      -       -      +
    146O  VAL*     3.3    22.2    -      -       +      -
    176O  LEU*     3.5    17.3    -      -       +      -
    200O  PHE*     5.8     0.2    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLU 130 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104O  ALA*     3.4    13.1    -      -       -      +
    105O  GLY      4.3     1.4    +      -       -      -
    128O  ALA      3.6     4.3    +      -       -      +
    129O  PHE*     1.3    74.8    -      -       -      +
    131O  SER*     1.3    60.5    +      -       -      +
    145O  HIS*     2.9    38.7    +      -       +      +
    146O  VAL*     5.0     1.6    -      -       -      -
    147O  HIS*     2.8    39.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 131 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104O  ALA*     4.0     6.9    +      -       -      -
    129O  PHE*     5.1     2.1    -      -       -      +
    130O  GLU*     1.3    83.1    +      -       -      +
    132O  SER*     1.3    64.2    +      -       -      +
    144O  LEU*     3.5     3.7    -      -       -      +
    145O  HIS*     3.0    45.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 132 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100O  LEU*     4.5    12.4    -      -       -      +
    103O  LYS*     4.1     7.2    -      -       -      +
    104O  ALA*     3.5    27.2    +      -       -      +
    129O  PHE*     6.2     0.2    -      -       -      -
    131O  SER*     1.3    78.8    -      -       -      +
    133O  SER*     1.3    62.0    +      -       -      +
    134O  ILE*     5.9     0.2    -      -       -      -
    142O  ALA*     6.0     0.2    -      -       -      -
    143O  ASP      3.3     7.9    -      -       -      -
    144O  LEU*     3.4    23.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 133 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132O  SER*     1.3    76.5    -      -       -      +
    134O  ILE*     1.3    65.1    +      -       -      +
    135O  ALA      4.1     0.7    +      -       -      -
    142O  ALA*     4.8     0.4    -      -       -      -
    143O  ASP*     3.1    37.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 134 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100O  LEU*     4.8     9.0    -      -       +      -
    132O  SER      5.9     0.2    -      -       -      -
    133O  SER*     1.3    76.5    -      -       -      +
    135O  ALA*     1.3    77.2    +      -       -      +
    136O  ALA*     3.2     5.0    +      -       -      -
    138O  PHE      4.1     2.2    -      -       -      +
    139O  THR*     4.0    29.4    -      -       +      +
    141O  ILE      4.2     7.0    -      -       -      +
    142O  ALA*     3.5    28.0    -      -       +      -
    171O  PHE*     4.1    19.5    -      -       +      -
----------------------------------------------------------
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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