Contacts of the strand formed by residues 142 - 152 (chain H) in PDB entry 3HI6


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 142 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141H  SER*     1.3    86.9    -      -       -      +
    143H  ALA*     1.3    60.1    +      -       -      +
    144H  ALA      4.3     0.7    +      -       -      -
    190H  THR*     4.1    17.3    -      -       -      +
    191H  VAL      3.2    19.5    -      -       -      -
    192H  PRO*     5.1     2.2    -      -       +      -
    193H  SER*     4.1     2.0    -      -       -      +
    115L  PHE*     4.5    15.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 143 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133H  PRO*     4.1    22.0    -      -       +      -
    142H  THR*     1.3    74.5    -      -       -      +
    144H  ALA*     1.3    59.6    +      -       -      +
    189H  VAL      3.8     0.2    -      -       -      +
    190H  THR*     3.2     4.1    -      -       -      -
    191H  VAL*     2.6    50.1    +      -       +      +
    193H  SER*     4.0    12.5    -      -       -      +
    196H  LEU*     4.2    16.6    -      -       +      -
    115L  PHE*     4.9     0.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 144 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133H  PRO*     3.3    22.0    -      -       -      +
    143H  ALA*     1.3    73.0    -      -       -      +
    145H  LEU*     1.3    61.8    +      -       -      +
    189H  VAL      3.5     5.4    -      -       -      +
    190H  THR*     4.1    10.3    -      -       +      +
    115L  PHE*     3.4    46.7    -      -       +      -
    117L  PHE*     3.5    18.4    -      -       +      -
    134L  LEU*     4.4     7.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 145 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131H  LEU      3.3    13.7    -      -       -      +
    133H  PRO*     3.7    30.1    -      -       +      -
    144H  ALA*     1.3    76.0    -      -       -      +
    146H  GLY*     1.3    56.1    +      -       -      +
    161H  TRP*     3.4    31.4    -      -       +      -
    188H  VAL*     3.3     3.9    -      -       -      +
    189H  VAL*     2.7    52.9    +      -       +      +
    191H  VAL*     4.5     7.4    -      -       +      -
    196H  LEU*     4.1     8.3    -      -       +      -
    201H  TYR*     3.8    34.1    -      -       +      -
    218H  VAL*     4.1    12.1    -      -       +      +
    117L  PHE*     4.2     7.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 146 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131H  LEU*     2.8    45.3    +      -       -      +
    145H  LEU*     1.3    78.2    -      -       -      +
    147H  CYS*     1.3    57.6    +      -       -      -
    161H  TRP*     3.6    11.9    -      -       -      -
    187H  SER      3.0    13.5    -      -       -      -
    188H  VAL*     3.9     1.8    -      -       -      -
    218H  VAL*     3.4    15.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 147 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128H  VAL*     4.1    13.0    -      -       +      -
    129H  PHE      3.2     7.4    -      -       -      +
    131H  LEU*     3.8     4.4    -      -       -      +
    146H  GLY*     1.3    71.4    -      -       -      -
    148H  LEU*     1.3    60.1    +      -       -      +
    149H  VAL*     3.7     8.8    +      -       +      +
    159H  VAL*     5.5     0.2    -      -       +      -
    161H  TRP*     3.8     1.1    -      -       +      -
    186H  SER*     3.3     3.5    -      -       -      -
    187H  SER*     2.8    35.4    +      -       -      +
    203H  CYS*     2.0    52.0    -      -       +      -
    216H  LYS*     4.4     2.9    -      -       -      -
    218H  VAL*     3.5    25.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 148 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127H  SER      3.3     5.0    -      -       -      +
    128H  VAL*     3.4     0.9    -      -       -      -
    129H  PHE*     2.7    56.0    +      -       +      +
    131H  LEU*     4.1    12.9    -      -       +      +
    147H  CYS*     1.3    69.9    -      -       -      +
    149H  VAL*     1.3    59.6    +      -       -      +
    150H  LYS*     4.2    17.0    -      -       +      -
    184H  SER*     3.7    18.6    -      -       -      +
    185H  LEU      3.6    16.6    -      -       -      +
    186H  SER*     3.6    15.5    -      -       -      +
    123L  GLN*     4.3     4.7    -      -       -      +
    130L  SER*     3.7    33.4    -      -       -      +
    132L  VAL*     4.8    11.0    -      -       +      -
    177L  THR*     5.3     7.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 149 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126H  PRO*     3.5    26.0    -      -       +      -
    127H  SER      3.5     2.7    -      -       -      -
    128H  VAL*     4.4     7.9    -      -       +      +
    147H  CYS*     4.3     9.6    -      -       +      +
    148H  LEU*     1.3    72.1    -      -       -      +
    150H  LYS*     1.3    59.2    +      -       -      +
    152H  TYR*     3.6    13.6    -      -       +      -
    157H  VAL*     4.3     7.0    -      -       +      -
    159H  VAL*     4.3     6.1    -      -       +      -
    184H  SER*     3.4     4.3    -      -       -      -
    185H  LEU*     2.7    54.9    +      -       +      +
    187H  SER      5.5     0.4    -      -       -      +
    205H  VAL*     3.8    41.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 150 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126H  PRO*     3.3     2.4    -      -       -      +
    127H  SER*     2.7    44.4    +      -       -      +
    129H  PHE*     4.3    14.8    -      -       +      -
    148H  LEU*     4.2    13.7    -      -       +      -
    149H  VAL*     1.3    74.8    -      -       -      +
    151H  ASP*     1.3    92.5    +      -       -      +
    152H  TYR*     3.6     2.0    -      -       -      -
    178H  GLN*     3.2    22.0    +      -       -      +
    183H  TYR      4.2     0.2    -      -       -      -
    184H  SER*     3.6    16.4    -      -       -      +
    123L  GLN*     3.6    19.7    -      -       -      +
    128L  THR*     4.4    12.4    +      -       -      +
    130L  SER*     3.5    21.3    -      -       -      +
    177L  THR*     6.4     0.7    -      -       -      -
    179L  THR*     5.6    10.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 151 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124H  LYS*     3.4    30.6    +      -       -      +
    125H  GLY      3.4    14.9    -      -       -      +
    127H  SER*     4.8     7.2    +      -       -      +
    129H  PHE*     6.0     0.3    -      -       -      -
    150H  LYS*     1.3   103.2    +      -       -      +
    152H  TYR*     1.3    56.9    +      -       -      +
    178H  GLN*     3.0    21.5    +      -       -      +
    180H  SER*     4.5     2.3    +      -       -      -
    182H  LEU*     3.9    19.5    -      -       +      +
    183H  TYR      2.9    14.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 152 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124H  LYS*     3.3    13.2    -      -       -      +
    126H  PRO*     3.6    29.4    -      -       +      -
    149H  VAL*     3.6    25.8    -      -       +      -
    151H  ASP*     1.3    77.5    -      -       -      +
    153H  PHE*     1.3    64.5    +      -       -      +
    154H  PRO      3.8    14.6    -      -       -      -
    155H  GLU*     2.5    41.8    +      -       -      -
    157H  VAL*     3.3    37.3    -      -       +      +
    175H  ALA*     3.2    12.8    -      -       -      +
    182H  LEU*     4.5     1.3    -      -       -      -
    183H  TYR*     2.8    52.6    +      +       +      +
    184H  SER*     4.0     2.5    -      -       -      -
    185H  LEU*     3.4     4.0    -      -       -      +
    207H  HIS*     3.8     2.0    -      +       -      +
----------------------------------------------------------
 Back to top of page


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