Contacts of the strand formed by residues 103 - 115 (chain V) in PDB entry 1H2I


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 PHE 103 (chain V).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96V  VAL*     4.2    15.3    -      -       +      -
     97V  ASP      3.2    13.5    -      -       -      -
     98V  LEU*     3.8    34.1    -      -       +      -
    101V  GLY      4.8     0.9    -      -       -      -
    102V  LYS*     1.3    72.7    -      -       -      +
    104V  TYR*     1.3    64.7    +      -       -      +
    105V  VAL*     4.5     3.4    -      -       +      -
    129V  SER      3.3     7.0    -      -       -      +
    130V  GLU*     3.6     0.2    -      -       -      -
    131V  GLY      3.0    22.3    +      -       -      -
    132V  LEU      2.8    12.5    +      -       -      +
    133V  LYS*     3.3    31.0    -      -       -      -
    134V  SER      3.8     0.7    -      -       -      -
    135V  LYS*     3.5    50.3    -      -       +      -
    138V  SER*     3.8    19.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 104 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95V  PHE*     3.2    18.0    -      -       +      -
     96V  VAL*     3.5     0.2    -      -       -      -
     97V  ASP*     2.7    52.3    +      -       +      +
     99V  ASN*     3.9    24.9    -      -       +      +
    100V  ASN*     3.4    24.9    +      -       -      -
    102V  LYS*     3.5    29.7    -      -       +      +
    103V  PHE*     1.3    72.4    -      -       -      +
    105V  VAL*     1.3    60.6    +      -       -      +
    129V  SER      3.4     2.5    -      -       -      -
    130V  GLU*     3.6    33.4    -      -       +      +
    131V  GLY*     3.7    17.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 105 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136U  ALA*     4.8     0.2    -      -       -      -
     93V  VAL*     4.7     0.2    -      -       +      -
     95V  PHE*     3.4    14.3    -      -       -      +
     96V  VAL*     4.1    21.1    -      -       +      -
    103V  PHE*     4.5     1.6    -      -       +      -
    104V  TYR*     1.3    83.3    -      -       -      +
    106V  GLY*     1.3    62.4    +      -       -      +
    107V  VAL*     4.0     6.7    -      -       +      -
    127V  GLY      3.6     0.5    -      -       -      +
    128V  VAL*     3.4    10.6    -      -       -      +
    129V  SER*     2.8    38.8    +      -       -      +
    130V  GLU*     4.9     1.4    -      -       -      +
    135V  LYS*     6.3     0.2    -      -       -      -
    138V  SER*     3.8    27.1    -      -       -      +
    139V  LEU*     3.6    26.9    -      -       +      +
    142V  ALA*     4.0    17.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 106 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136U  ALA*     4.5     1.1    -      -       -      -
     93V  VAL*     3.9     0.2    -      -       -      -
     94V  ASP*     2.8    29.1    +      -       -      +
     95V  PHE*     3.2    22.7    +      -       -      +
    105V  VAL*     1.3    76.5    -      -       -      +
    107V  VAL*     1.3    64.0    +      -       -      +
    126V  TYR*     3.3    24.2    -      -       -      -
    127V  GLY      3.5     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 107 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91V  GLN*     3.7    28.0    -      -       +      +
     92V  ASN      3.6    11.7    -      -       -      +
     93V  VAL*     3.8    22.7    -      -       +      -
    105V  VAL*     4.0     9.2    -      -       +      -
    106V  GLY*     1.3    80.0    -      -       -      +
    108V  CYS*     1.3    71.5    +      -       -      +
    126V  TYR*     3.2     8.6    -      -       -      -
    127V  GLY      2.6    40.8    +      -       -      -
    139V  LEU*     4.6     0.9    -      -       +      -
    142V  ALA*     3.8    27.6    -      -       +      +
    143V  ARG*     4.1    11.7    -      -       +      +
    146V  ALA*     3.5     4.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 108 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143U  ARG*     3.4    39.0    -      -       -      +
     91V  GLN*     3.3     6.2    -      -       -      +
     92V  ASN*     2.8    49.5    +      -       -      -
     94V  ASP*     4.7     0.2    +      -       -      -
    107V  VAL*     1.3    75.2    -      -       -      +
    109V  ALA*     1.3    60.5    +      -       -      +
    110V  PHE*     3.8    18.6    -      -       -      -
    124V  VAL*     4.5     4.9    -      -       +      -
    125V  GLY      3.3     8.1    -      -       -      +
    126V  TYR*     3.6    21.7    -      -       +      -
    146V  ALA*     4.1     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 109 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88V  ILE*     5.1     2.0    -      -       +      -
     90V  GLN      3.4     9.4    -      -       -      +
     91V  GLN*     4.0    11.2    -      -       +      +
    108V  CYS*     1.3    75.4    -      -       -      +
    110V  PHE*     1.3    65.6    +      -       -      +
    111V  VAL*     3.9     7.7    +      -       +      +
    123V  ASP      3.6     0.9    -      -       -      +
    124V  VAL*     3.2     3.9    -      -       -      -
    125V  GLY*     2.8    31.8    +      -       -      -
    146V  ALA*     3.7    30.0    -      -       +      +
    147V  VAL*     3.9    13.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 110 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88U  ILE*     3.7    29.6    -      -       +      -
     91U  GLN*     3.2    44.9    -      -       +      -
    143U  ARG*     4.5     4.7    -      -       -      -
     88V  ILE*     3.5     4.9    -      -       -      -
     89V  THR*     2.8    45.1    +      -       -      +
     90V  GLN*     2.7    41.3    +      -       +      +
     92V  ASN*     5.6     0.2    -      -       +      -
    108V  CYS*     3.8    23.6    -      -       -      -
    109V  ALA*     1.3    71.9    -      -       -      +
    111V  VAL*     1.3    62.6    +      -       -      +
    122V  GLU*     3.8     6.1    -      -       -      +
    123V  ASP      3.4     2.7    -      -       -      +
    124V  VAL*     3.0    24.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 111 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86V  HIS*     3.9    26.2    -      -       +      -
     87V  SER      3.4    11.0    -      -       -      +
     88V  ILE*     4.7     4.7    -      -       +      -
    109V  ALA*     4.5     7.0    -      -       +      -
    110V  PHE*     1.3    78.5    -      -       -      +
    112V  ARG*     1.3    63.0    +      -       -      +
    122V  GLU*     3.3     4.0    -      -       -      -
    123V  ASP      3.0    29.9    +      -       -      +
    147V  VAL*     3.7    35.9    -      -       +      +
    150V  GLY*     3.8    15.7    -      -       -      +
    151V  LEU*     3.8    22.9    -      -       +      +
    154V  ALA*     3.7     7.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 112 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120L  TYR*     5.0     5.4    +      -       -      -
     87U  SER*     5.1     4.8    -      -       -      -
     86V  HIS*     3.1     3.9    -      -       -      -
     87V  SER*     2.9    42.9    +      -       -      +
     89V  THR*     3.9    23.3    -      -       +      +
    110V  PHE      4.1     1.0    +      -       -      -
    111V  VAL*     1.3    71.9    -      -       -      +
    113V  VAL*     1.3    63.6    +      -       -      +
    114V  GLN*     3.1    33.2    +      -       -      +
    118V  GLY      4.8     0.8    +      -       -      -
    120V  TYR*     3.4    47.9    -      -       +      +
    121V  HIS      3.6     6.3    -      -       -      +
    122V  GLU*     3.8    25.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 113 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84V  TRP*     4.1    11.2    -      -       +      -
     85V  ALA      3.1    12.8    -      -       -      +
     86V  HIS*     4.0     7.4    -      -       +      +
    111V  VAL      4.1     0.2    +      -       -      -
    112V  ARG*     1.3    75.8    -      -       -      +
    114V  GLN*     1.3    67.5    +      -       -      +
    120V  TYR*     3.2     6.5    -      -       -      +
    121V  HIS      2.9    42.2    +      -       -      +
    151V  LEU*     4.8     3.6    -      -       +      -
    154V  ALA*     3.4    30.7    -      -       +      -
    155V  LEU*     3.6    24.2    -      -       +      +
    158V  PHE*     4.0    19.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 114 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120L  TYR*     3.2    22.1    +      -       -      +
     26V  PHE*     3.4    14.8    -      -       +      -
     27V  GLY*     3.5    24.5    -      -       -      -
     84V  TRP*     3.1     4.5    -      -       -      +
     85V  ALA      2.7    40.5    +      -       -      +
    112V  ARG*     3.1    26.0    +      -       -      +
    113V  VAL*     1.3    76.5    -      -       -      +
    115V  LEU*     1.3    81.1    +      -       -      +
    118V  GLY*     3.5    15.1    -      -       -      +
    119V  SER      3.2    13.5    -      -       -      +
    120V  TYR*     4.2     4.0    -      -       +      +
    158V  PHE*     5.3     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 115 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81U  TYR*     4.1    13.9    -      -       +      -
     26V  PHE*     3.4     3.8    -      -       -      -
     31V  TYR*     3.6    18.4    -      -       +      +
     79V  PHE*     4.0    20.9    -      -       +      -
     83V  GLY      3.3     4.3    -      -       -      +
     84V  TRP*     3.8    19.1    -      -       +      -
    113V  VAL*     5.0     0.4    -      -       +      -
    114V  GLN*     1.3    92.4    +      -       -      +
    116V  LYS*     1.3    58.4    +      -       -      +
    117V  ASP*     2.8    14.3    +      -       +      -
    118V  GLY      2.9    12.3    +      -       -      -
    119V  SER*     2.9    28.3    +      -       -      +
    158V  PHE*     3.2    48.0    -      -       +      -
----------------------------------------------------------
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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