Contacts of the strand formed by residues 103 - 115 (chain E) 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 E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96E  VAL*     4.3    13.0    -      -       +      -
     97E  ASP      3.2    14.6    -      -       -      -
     98E  LEU*     3.7    33.9    -      -       +      -
    101E  GLY      4.9     0.9    -      -       -      -
    102E  LYS*     1.3    72.0    -      -       -      +
    104E  TYR*     1.3    64.8    +      -       -      +
    105E  VAL*     4.1     4.7    -      -       +      -
    129E  SER      3.4     7.0    -      -       -      +
    131E  GLY      3.0    22.9    +      -       -      -
    132E  LEU      2.9    11.4    +      -       -      +
    133E  LYS*     3.2    31.0    -      -       -      -
    134E  SER      3.8     1.8    -      -       -      -
    135E  LYS*     3.4    52.9    -      -       +      -
    138E  SER*     3.7    20.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 104 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95E  PHE*     3.2    17.2    -      -       +      -
     96E  VAL*     3.5     0.2    -      -       -      -
     97E  ASP*     2.6    48.5    +      -       +      +
     99E  ASN*     4.0    25.1    -      -       +      +
    100E  ASN*     3.4    25.2    +      -       -      -
    102E  LYS*     3.4    33.7    -      -       +      +
    103E  PHE*     1.3    72.0    -      -       -      +
    105E  VAL*     1.3    60.2    +      -       -      +
    129E  SER      3.4     2.5    -      -       -      -
    130E  GLU*     3.6    34.1    -      -       +      +
    131E  GLY*     3.7    17.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 105 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136D  ALA*     4.9     0.4    -      -       -      -
     95E  PHE*     3.5    13.9    -      -       -      +
     96E  VAL*     4.2    20.4    -      -       +      -
    103E  PHE*     4.5     2.0    -      -       +      -
    104E  TYR*     1.3    84.8    -      -       -      +
    106E  GLY*     1.3    62.2    +      -       -      +
    107E  VAL*     4.0     6.7    -      -       +      -
    127E  GLY      3.7     0.5    -      -       -      +
    128E  VAL*     3.4    10.2    -      -       -      +
    129E  SER*     2.8    42.7    +      -       -      +
    130E  GLU*     4.9     1.2    -      -       -      +
    135E  LYS*     5.6     0.4    -      -       -      +
    138E  SER*     3.9    24.5    -      -       -      +
    139E  LEU*     3.6    28.7    -      -       +      -
    142E  ALA*     3.9    15.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 106 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136D  ALA*     4.6     0.9    -      -       -      -
     94E  ASP*     2.7    32.9    +      -       -      +
     95E  PHE*     3.3    23.8    +      -       -      +
    105E  VAL*     1.3    74.7    -      -       -      +
    107E  VAL*     1.3    60.0    +      -       -      +
    126E  TYR*     3.4    25.1    -      -       -      -
    127E  GLY      3.6     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 107 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91E  GLN*     3.6    35.9    -      -       +      +
     92E  ASN      3.5    12.3    -      -       -      +
     93E  VAL*     3.7    23.3    -      -       +      -
     94E  ASP      4.3     0.2    -      -       -      +
    105E  VAL*     4.0     9.2    -      -       +      -
    106E  GLY*     1.3    79.1    -      -       -      +
    108E  CYS*     1.3    64.1    +      -       -      +
    126E  TYR*     3.2     9.3    -      -       -      -
    127E  GLY      2.6    38.4    +      -       -      -
    139E  LEU*     4.7     0.7    -      -       +      -
    142E  ALA*     3.8    26.0    -      -       +      +
    143E  ARG*     4.0    11.0    -      -       +      -
    146E  ALA*     3.4     4.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 108 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143D  ARG*     3.2    42.8    -      -       -      -
     91E  GLN*     3.2     6.2    -      -       -      +
     92E  ASN*     2.9    49.0    +      -       -      -
     94E  ASP*     4.7     0.4    +      -       -      -
    107E  VAL*     1.3    74.4    -      -       -      +
    109E  ALA*     1.3    61.5    +      -       -      +
    110E  PHE*     3.8    16.2    -      -       -      -
    124E  VAL*     4.4     5.6    -      -       +      -
    125E  GLY      3.2     7.6    -      -       -      +
    126E  TYR*     3.6    20.1    -      -       +      -
    146E  ALA*     4.1     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 109 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88E  ILE*     4.9     2.2    -      -       +      -
     90E  GLN      3.3     8.7    -      -       -      +
     91E  GLN*     4.0    11.2    -      -       +      +
    108E  CYS*     1.3    77.5    -      -       -      +
    110E  PHE*     1.3    65.4    +      -       -      +
    111E  VAL*     3.9     7.3    +      -       +      +
    123E  ASP      3.7     0.3    -      -       -      +
    124E  VAL*     3.2     5.4    -      -       -      +
    125E  GLY      2.7    31.7    +      -       -      -
    146E  ALA*     3.8    29.4    -      -       +      +
    147E  VAL*     4.0    13.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 110 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88D  ILE*     3.8    30.7    -      -       +      -
     91D  GLN*     3.2    44.4    -      -       +      -
    143D  ARG*     4.5     3.6    -      -       -      -
     88E  ILE*     3.5     5.5    -      -       -      -
     89E  THR*     2.8    47.5    +      -       -      +
     90E  GLN*     2.8    40.1    +      -       +      +
     92E  ASN*     5.6     0.4    -      -       +      -
    108E  CYS*     3.8    23.6    -      -       -      -
    109E  ALA*     1.3    72.4    -      -       -      +
    111E  VAL*     1.3    57.9    +      -       -      +
    122E  GLU*     3.8     6.1    -      -       -      +
    123E  ASP      3.4     2.5    -      -       -      +
    124E  VAL*     3.1    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 111 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86E  HIS*     3.9    25.1    -      -       +      -
     87E  SER      3.4    12.1    -      -       -      +
     88E  ILE*     4.6     9.4    -      -       +      -
    109E  ALA*     4.5     7.9    -      -       +      -
    110E  PHE*     1.3    76.3    -      -       -      +
    112E  ARG*     1.3    63.1    +      -       -      +
    113E  VAL      4.8     0.9    -      -       -      +
    122E  GLU*     3.2     4.6    -      -       -      -
    123E  ASP      3.0    30.9    +      -       -      -
    147E  VAL*     3.6    30.3    -      -       +      +
    150E  GLY*     3.8    17.3    -      -       -      +
    151E  LEU*     3.7    23.6    -      -       +      +
    154E  ALA*     3.7     7.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 112 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87D  SER*     5.1     5.4    -      -       -      -
     86E  HIS*     3.2     3.3    -      -       -      -
     87E  SER*     2.9    38.0    +      -       -      +
     89E  THR*     4.0    23.8    -      -       +      +
    110E  PHE      4.2     0.4    +      -       -      -
    111E  VAL*     1.3    72.0    -      -       -      +
    113E  VAL*     1.3    64.6    +      -       -      +
    114E  GLN*     2.9    34.2    +      -       -      +
    118E  GLY      4.8     0.4    +      -       -      -
    120E  TYR*     3.5    47.0    -      -       +      +
    121E  HIS      3.6     6.3    -      -       -      +
    122E  GLU*     3.9    24.7    -      -       +      -
    120F  TYR*     5.0     5.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 113 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84E  TRP*     4.1    11.4    -      -       +      -
     85E  ALA      3.1    14.4    -      -       -      +
     86E  HIS*     4.0     7.6    -      -       +      -
    111E  VAL*     5.3     0.2    -      -       +      -
    112E  ARG*     1.3    74.3    -      -       -      +
    114E  GLN*     1.3    67.5    +      -       -      +
    120E  TYR*     3.2     7.1    -      -       -      +
    121E  HIS      3.0    42.1    +      -       -      +
    151E  LEU*     4.7     3.4    -      -       +      -
    154E  ALA*     3.3    32.5    -      -       +      +
    155E  LEU*     3.6    25.1    -      -       +      +
    158E  PHE*     4.1    18.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 114 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26E  PHE*     3.4    15.4    -      -       +      -
     27E  GLY*     3.5    29.7    -      -       -      -
     84E  TRP*     3.1     3.6    -      -       -      +
     85E  ALA      2.7    38.4    +      -       -      +
    112E  ARG*     2.9    26.0    +      -       -      +
    113E  VAL*     1.3    75.4    -      -       -      +
    115E  LEU*     1.3    74.8    +      -       -      +
    118E  GLY*     3.6    13.7    -      -       -      +
    119E  SER      3.2    15.0    -      -       -      +
    120E  TYR*     4.3     2.9    -      -       +      -
    158E  PHE*     5.4     0.2    -      -       -      -
    120F  TYR*     3.2    22.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 115 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81D  TYR*     4.1    23.6    -      -       +      -
     26E  PHE*     3.5     5.9    -      -       -      -
     31E  TYR*     3.7    14.8    -      -       +      +
     79E  PHE*     4.1    14.8    -      -       +      -
     83E  GLY      3.3     9.9    -      -       -      +
     84E  TRP*     3.9    12.6    -      -       +      -
    113E  VAL*     5.0     0.4    -      -       +      -
    114E  GLN*     1.3    89.3    +      -       -      +
    116E  LYS*     1.3    60.8    +      -       -      +
    117E  ASP*     2.8    14.6    +      -       +      -
    118E  GLY      2.9    10.4    +      -       -      -
    119E  SER*     3.0    30.5    +      -       -      +
    158E  PHE*     3.2    47.3    -      -       +      -
----------------------------------------------------------
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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