Contacts of the strand formed by residues 140 - 150 (chain H) in PDB entry 4OQT


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 140 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135H  SER*     5.1     3.3    -      -       -      -
    136H  THR*     5.4     2.6    +      -       -      -
    139H  GLY*     1.3    75.2    -      -       -      -
    141H  ALA*     1.3    60.6    +      -       -      +
    188H  THR*     5.0    10.8    -      -       -      +
    189H  VAL      3.2    15.5    -      -       -      +
    190H  PRO*     4.4     4.0    -      -       +      -
    191H  SER*     4.2     1.1    -      -       -      +
    115L  SER*     5.3     3.5    +      -       -      -
    117L  PHE*     4.4    17.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 141 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131H  PRO*     4.8     5.2    -      -       +      -
    132H  SER      5.4     1.1    -      -       -      +
    135H  SER*     4.0    12.1    -      -       -      +
    139H  GLY      3.7     0.6    +      -       -      -
    140H  THR*     1.3    74.5    -      -       -      +
    142H  ALA*     1.3    60.6    -      -       -      +
    187H  VAL      4.0     0.2    -      -       -      +
    188H  THR*     3.3     5.6    -      -       -      -
    189H  VAL*     2.8    35.0    +      -       -      +
    191H  SER*     3.6    22.9    -      -       -      -
    194H  LEU*     3.9    24.5    -      -       +      -
    117L  PHE*     4.4     5.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 142 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131H  PRO*     3.4    20.4    -      -       -      +
    132H  SER      4.3     2.5    +      -       -      +
    141H  ALA*     1.3    74.0    -      -       -      +
    143H  LEU*     1.3    60.4    -      -       -      +
    187H  VAL      3.5     6.1    -      -       -      +
    188H  THR*     4.1     7.2    -      -       +      -
    117L  PHE*     3.5    46.6    -      -       +      -
    119L  PHE*     3.5    14.2    -      -       +      -
    136L  LEU*     3.9    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 143 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129H  LEU*     3.3    17.0    -      -       -      +
    131H  PRO*     4.0    10.3    -      -       +      -
    142H  ALA*     1.3    74.3    -      -       -      +
    144H  GLY*     1.3    60.9    +      -       -      +
    159H  TRP*     3.6    26.7    -      -       +      -
    186H  VAL*     3.2     7.5    -      -       -      +
    187H  VAL*     2.9    41.7    +      -       +      +
    189H  VAL*     4.2     9.9    -      -       +      -
    194H  LEU*     3.7    22.2    -      -       +      -
    199H  TYR*     3.5    36.1    -      -       +      -
    216H  VAL*     3.6    22.0    -      -       +      +
    119L  PHE*     4.3     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 144 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129H  LEU*     2.7    40.5    +      -       -      +
    143H  LEU*     1.3    81.1    -      -       -      +
    145H  CYS*     1.3    56.4    +      -       -      -
    159H  TRP*     3.4    16.8    -      -       -      -
    185H  SER      3.0    13.5    -      -       -      -
    186H  VAL*     4.0     0.2    -      -       -      -
    216H  VAL*     3.2    12.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 145 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126H  VAL*     4.1    13.0    -      -       +      -
    127H  PHE      3.4     5.4    -      -       -      +
    129H  LEU*     4.3     3.6    -      -       -      -
    144H  GLY*     1.3    71.7    -      -       -      -
    146H  LEU*     1.3    60.9    +      -       -      +
    147H  VAL*     3.8     4.8    +      -       +      +
    157H  VAL*     5.5     1.1    -      -       +      -
    159H  TRP*     3.7     4.0    -      -       +      -
    184H  SER*     3.4     3.8    +      -       -      -
    185H  SER*     2.9    33.8    +      -       -      +
    201H  CYS*     2.0    53.4    -      -       +      -
    203H  VAL*     4.9     3.6    -      -       +      -
    214H  LYS*     4.3     6.3    -      -       -      -
    216H  VAL*     3.9    19.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 146 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125H  SER      3.2     8.8    -      -       -      +
    126H  VAL*     3.4     1.1    -      -       -      -
    127H  PHE*     2.6    46.7    +      -       +      +
    129H  LEU*     4.4    11.2    -      -       +      +
    145H  CYS*     1.3    71.8    -      -       -      +
    147H  VAL*     1.3    59.6    +      -       -      +
    148H  LYS*     3.5    14.3    +      -       +      -
    182H  SER*     4.0    14.8    -      -       -      +
    183H  LEU      3.5    13.2    -      -       -      +
    184H  SER*     3.2    22.2    -      -       -      +
    125L  GLN*     4.4     8.3    -      -       -      +
    132L  SER*     3.6    33.2    -      -       -      +
    134L  VAL*     5.0     9.9    -      -       +      -
    179L  THR*     5.1     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 147 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124H  PRO*     3.5    26.2    -      -       +      -
    125H  SER      3.7     3.4    -      -       -      -
    126H  VAL*     4.5     3.1    -      -       +      -
    145H  CYS*     3.8     4.9    +      -       +      +
    146H  LEU*     1.3    70.3    -      -       -      +
    148H  LYS*     1.3    57.9    +      -       -      +
    150H  TYR*     3.8    17.3    -      -       +      -
    155H  VAL*     4.1     9.0    -      -       +      -
    157H  VAL*     3.9    19.1    -      -       +      -
    182H  SER*     3.2     4.0    +      -       -      -
    183H  LEU*     2.8    50.2    +      -       +      +
    203H  VAL*     3.6    39.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 148 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124H  PRO*     3.6     0.7    -      -       -      +
    125H  SER*     2.9    38.1    +      -       -      +
    127H  PHE*     4.3    14.1    -      -       +      -
    146H  LEU*     4.1    14.8    -      -       +      +
    147H  VAL*     1.3    75.5    -      -       -      +
    149H  ASP*     1.3    98.7    +      -       -      +
    150H  TYR*     3.8     2.2    -      -       -      -
    176H  GLN*     3.6    12.2    +      -       -      +
    181H  TYR      3.9     0.4    -      -       -      -
    182H  SER*     3.5    15.5    -      -       -      +
    125L  GLN*     3.9    27.1    -      -       -      +
    130L  THR*     4.4    23.0    -      -       -      +
    132L  SER*     4.0    11.7    +      -       -      +
    181L  THR*     5.4     5.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 149 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122H  LYS*     3.0    33.0    +      -       -      +
    123H  GLY      3.1     8.5    -      -       -      +
    125H  SER*     5.6     3.2    -      -       -      -
    148H  LYS*     1.3   112.8    +      -       -      +
    150H  TYR*     1.3    56.2    +      -       -      +
    176H  GLN*     3.3    15.8    +      -       -      +
    178H  SER*     4.0    10.8    +      -       -      -
    180H  LEU*     3.9    18.2    -      -       +      -
    181H  TYR      3.0    14.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 150 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122H  LYS*     3.3    15.3    -      -       -      +
    124H  PRO*     3.8    19.3    -      -       +      -
    147H  VAL*     3.8    25.4    -      -       +      -
    149H  ASP*     1.3    78.4    -      -       -      +
    151H  PHE*     1.3    65.0    +      -       -      +
    152H  PRO      3.8    10.3    -      -       -      -
    153H  GLU*     2.8    28.3    +      -       -      -
    155H  VAL*     3.3    26.9    -      -       +      +
    173H  ALA*     3.2    17.7    -      -       -      +
    180H  LEU*     3.7     4.4    -      -       -      +
    181H  TYR*     3.0    58.7    +      +       +      +
    182H  SER*     3.9     7.2    -      -       -      -
    183H  LEU*     3.8     5.3    -      -       -      +
    205H  HIS*     3.8    18.6    -      +       -      +
----------------------------------------------------------
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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