Contacts of the strand formed by residues 134 - 142 (chain H) in PDB entry 2Q5E


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 THR 134 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195B  HIS*     6.2     0.7    -      -       +      -
    198B  CYS*     5.8     2.2    -      -       -      -
    220B  PRO*     4.1     9.9    -      -       -      +
    221B  ALA*     4.2    10.0    +      -       +      -
    224B  ILE*     3.8    34.8    -      -       +      -
    131H  ILE      2.8    38.5    +      -       -      +
    132H  GLU      4.0     6.7    -      -       -      +
    133H  GLY*     1.3    75.1    -      -       -      +
    135H  THR*     1.3    59.5    +      -       -      +
    136H  HIS*     3.2    33.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 135 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220B  PRO*     3.7    16.2    +      -       -      +
    223B  TYR*     4.1    12.3    -      -       -      -
    224B  ILE*     5.2     6.6    -      -       -      +
    227B  PRO*     3.5    40.4    -      -       +      +
    128H  PRO*     4.2    13.4    -      -       -      +
    129H  ILE      3.2    12.8    -      -       -      -
    130H  GLU*     3.8    15.5    -      -       +      +
    133H  GLY      5.0     3.1    -      -       -      +
    134H  THR*     1.3    74.3    +      -       -      +
    136H  HIS*     1.3    62.7    +      -       -      +
    137H  GLN*     4.6     3.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 136 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220B  PRO*     3.4    35.8    -      -       +      +
    221B  ALA      5.4     0.9    -      -       -      -
    223B  TYR*     5.9     0.7    -      -       -      -
    194C  PHE*     4.0    37.0    -      +       -      +
    195C  HIS*     5.7     1.1    -      -       -      -
    196C  GLN      5.9     2.5    +      -       -      -
    117H  PHE*     3.6    30.8    -      +       +      +
    128H  PRO*     3.4     3.3    -      -       -      +
    129H  ILE*     2.7    33.7    +      -       -      +
    131H  ILE*     4.0    20.7    -      -       +      +
    134H  THR*     3.2    38.2    +      -       -      +
    135H  THR*     1.3    73.1    -      -       -      +
    137H  GLN*     1.3    62.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 137 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220B  PRO*     5.7     1.0    -      -       -      +
    223B  TYR*     5.2     5.6    -      -       +      +
    227B  PRO      5.5     5.5    +      -       -      -
    230B  ALA*     5.6     0.4    +      -       -      +
    232B  PRO*     3.9    24.9    -      -       +      +
    269B  ARG*     4.0    29.5    -      -       -      +
    117H  PHE*     4.0    12.5    -      -       -      +
    126H  ILE*     3.7    21.8    -      -       +      +
    127H  VAL      3.5     1.6    -      -       -      -
    128H  PRO*     3.2    36.0    -      -       -      +
    135H  THR*     4.6     3.8    +      -       -      +
    136H  HIS*     1.3    77.4    -      -       -      +
    138H  VAL*     1.3    64.0    +      -       -      +
    139H  TYR*     3.3    34.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 138 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115H  SER*     3.5    31.2    -      -       -      +
    116H  SER      3.6    11.4    -      -       -      +
    117H  PHE*     3.4    36.3    -      -       +      -
    125H  PHE      3.8     0.5    -      -       -      +
    126H  ILE*     3.2     6.2    -      -       -      -
    127H  VAL*     2.7    39.3    +      -       +      +
    129H  ILE*     3.3    31.4    -      -       +      -
    137H  GLN*     1.3    75.2    -      -       -      +
    139H  TYR*     1.3    63.6    +      -       -      +
    140H  VAL*     4.0     5.0    +      -       +      +
    169H  TYR*     4.3    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 139 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232B  PRO*     3.7    26.9    +      -       -      +
    114H  HIS      3.9     0.9    -      -       -      +
    115H  SER*     3.4     2.6    -      -       -      -
    116H  SER*     3.1    35.1    +      -       -      +
    117H  PHE      3.8     5.2    -      -       -      -
    118H  LYS      3.4    17.5    -      -       -      +
    119H  PRO*     3.3    25.4    -      -       +      +
    120H  ILE*     3.6    46.1    -      -       +      +
    123H  ALA*     4.7     1.8    -      -       +      -
    125H  PHE      3.6     3.1    -      -       -      -
    126H  ILE*     3.5    34.7    -      -       +      +
    137H  GLN*     3.3    38.2    -      -       +      +
    138H  VAL*     1.3    71.7    -      -       -      +
    140H  VAL*     1.3    61.0    +      -       -      +
    141H  LEU*     4.1     0.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 140 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113H  VAL*     3.8    31.4    -      -       +      -
    114H  HIS      3.6     2.7    -      -       -      +
    115H  SER*     3.3    22.7    -      -       -      +
    123H  ALA*     3.8     2.2    -      -       -      +
    124H  ASP*     3.0    24.6    +      -       -      +
    125H  PHE*     2.7    48.0    +      -       +      +
    127H  VAL*     4.6     7.9    -      -       +      -
    138H  VAL*     4.4    10.8    -      -       +      +
    139H  TYR*     1.3    76.1    -      -       -      +
    141H  LEU*     1.3    64.0    +      -       -      +
    173H  VAL*     4.0    23.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 141 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113H  VAL*     3.4     2.9    -      -       -      +
    114H  HIS*     3.1    36.9    +      -       +      +
    120H  ILE*     4.1    22.0    -      -       +      -
    123H  ALA*     3.7    31.4    -      -       -      +
    124H  ASP*     3.4     8.7    -      -       -      +
    139H  TYR      5.4     0.9    -      -       -      +
    140H  VAL*     1.3    76.9    -      -       -      +
    142H  LYS*     1.3    62.5    +      -       -      +
    236H  TRP*     3.3    14.6    -      -       +      -
    237H  PHE      4.2     5.2    -      -       -      +
    238H  ASP*     4.1    26.7    -      -       +      +
    240H  MET*     5.8     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 142 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112H  LEU      4.3     3.4    -      -       -      -
    113H  VAL*     4.3     4.7    -      -       -      -
    124H  ASP*     2.9    34.0    +      -       +      +
    125H  PHE*     3.4    34.9    -      -       +      -
    141H  LEU*     1.3    72.4    -      -       -      +
    143H  ARG*     1.3    61.5    +      -       -      +
    146H  VAL*     3.8    12.1    -      -       +      -
    147H  ASP*     2.6    42.4    +      -       -      -
    176H  LEU      5.9     0.2    +      -       -      -
    177H  LEU*     4.0    13.3    +      -       +      +
    179H  ARG*     3.7    12.1    -      -       -      +
    236H  TRP*     3.1    14.3    -      -       -      -
    240H  MET*     4.4     9.5    -      -       -      +
----------------------------------------------------------
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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