Contacts of the strand formed by residues 99 - 108 (chain A) in PDB entry 1HS6


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 GLU 99 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  LYS*     5.0     6.3    -      -       -      +
     41A  THR*     3.8    23.0    -      -       +      +
     42A  VAL      3.0    13.2    -      -       -      +
     43A  GLN*     3.5    26.5    -      -       +      +
     94A  LEU*     4.6     4.5    -      -       -      +
     97A  ASN      3.8     8.5    -      -       -      +
     98A  GLN*     1.3    80.8    +      -       -      +
    100A  ILE*     1.3    63.1    +      -       -      +
    101A  VAL*     5.8     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 100 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  THR*     3.6     3.2    -      -       -      +
     42A  VAL*     2.9    42.5    +      -       +      +
     52A  LEU*     4.7     1.8    -      -       +      -
     66A  ILE*     4.3    18.6    -      -       +      -
     67A  ASN*     5.1     8.3    -      -       -      +
     90A  LEU*     4.5    14.8    -      -       +      -
     91A  PRO*     5.6     5.8    -      -       +      -
     92A  ILE*     5.9     8.5    -      -       +      +
     94A  LEU*     3.5    32.1    -      -       +      -
     99A  GLU*     1.3    76.0    -      -       -      +
    101A  VAL*     1.3    67.6    +      -       -      +
    102A  ILE*     3.0    42.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 101 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  ALA*     4.6    13.7    -      -       +      -
     40A  LEU      3.3    11.9    -      -       -      +
     41A  THR*     4.1    17.3    -      -       +      +
     66A  ILE*     3.2    26.2    -      -       -      +
     67A  ASN*     4.6     3.6    +      -       -      +
    100A  ILE*     1.3    79.3    -      -       -      +
    102A  ILE*     1.3    69.5    +      -       -      +
    103A  GLU*     4.2     3.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 102 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  ALA      3.1     4.7    -      -       -      +
     40A  LEU*     2.8    44.9    +      -       +      +
     42A  VAL*     4.3    10.8    -      -       +      -
     52A  LEU*     3.9    27.1    -      -       +      -
     54A  LEU*     6.1     1.1    -      -       +      -
     64A  VAL*     3.8    27.8    -      -       +      -
     65A  VAL      3.8     1.8    -      -       -      -
     66A  ILE*     3.9    13.7    -      -       +      -
     88A  ILE*     4.1    16.2    -      -       +      -
     90A  LEU*     4.3     6.5    -      -       +      -
    100A  ILE*     3.0    35.4    -      -       +      -
    101A  VAL*     1.3    75.1    -      -       -      +
    103A  GLU*     1.3    59.2    +      -       -      +
    104A  ILE*     4.5     6.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 103 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  ARG*     3.9    18.3    +      -       -      -
     37A  THR*     3.8    32.0    +      -       +      +
     38A  ALA      3.5     2.2    -      -       -      -
     39A  ALA*     4.0    18.5    -      -       +      +
     63A  LYS*     4.0     5.5    +      -       -      +
     64A  VAL*     3.5     3.3    -      -       -      +
     65A  VAL*     2.8    59.1    +      -       +      +
    101A  VAL*     4.1     4.6    -      -       +      -
    102A  ILE*     1.3    70.6    -      -       -      +
    104A  ILE*     1.3    62.8    +      -       -      +
    105A  SER*     4.2     2.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 104 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  THR*     2.8    12.3    -      -       -      -
     38A  ALA*     2.6    48.0    +      -       +      +
     40A  LEU*     4.3    11.9    -      -       +      -
     54A  LEU*     3.8    29.4    -      -       +      -
     61A  ILE*     4.0    18.6    -      -       +      -
     63A  LYS      3.7     7.0    -      -       -      +
     64A  VAL*     3.9    15.3    -      -       +      -
     86A  MET*     4.4     2.0    -      -       +      -
     88A  ILE*     4.3     6.3    -      -       +      -
    102A  ILE*     4.5    11.0    -      -       +      +
    103A  GLU*     1.3    78.9    -      -       -      +
    105A  SER*     1.3    62.5    -      -       -      +
    106A  PHE*     3.4     8.4    -      -       +      -
    145A  PRO*     3.8    29.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 105 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  GLY      3.4     5.2    +      -       -      -
     37A  THR*     3.6    16.7    -      -       -      +
     61A  ILE*     3.4     6.8    -      -       -      +
     62A  GLU*     2.6    48.5    +      -       -      -
     63A  LYS*     2.7    49.0    +      -       -      +
    103A  GLU*     4.2     1.6    +      -       -      -
    104A  ILE*     1.3    68.2    -      -       -      +
    106A  PHE*     1.3    55.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 106 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  LEU*     3.9    17.9    -      -       +      -
     25A  CYS*     4.8     4.0    -      -       +      -
     34A  LEU*     4.2    18.6    -      -       +      -
     35A  THR*     3.4     5.7    -      -       -      +
     36A  GLY*     2.8    52.0    +      -       -      +
     37A  THR      3.6    23.3    -      -       -      -
     38A  ALA*     3.6    15.3    -      -       +      -
     59A  LEU*     4.9     4.3    -      -       +      -
     60A  THR      3.2     9.4    -      -       -      +
     61A  ILE*     4.5     8.1    -      -       +      -
     62A  GLU*     4.4     3.1    -      -       -      +
    104A  ILE*     3.4    21.8    -      -       +      -
    105A  SER*     1.3    75.4    -      -       -      +
    107A  GLU*     1.3    69.8    +      -       -      +
    108A  THR*     4.5     1.6    -      -       +      -
    143A  ILE*     3.2    29.8    -      -       +      -
    144A  LEU*     4.1     8.3    -      -       +      -
    145A  PRO*     4.3    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 107 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  THR*     4.4    15.2    -      -       +      +
     34A  LEU      3.4     3.1    -      -       -      +
     35A  THR*     3.6    28.4    +      -       +      +
     59A  LEU*     3.8     2.4    -      -       -      +
     60A  THR*     2.7    61.9    +      -       +      +
    106A  PHE*     1.3    76.5    -      -       -      +
    108A  THR*     1.3    66.0    +      -       -      +
    802A   YB      3.8    12.2    -      -       -      -
    803A   YB      2.2    30.0    -      -       -      -
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Residues in contact with THR 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  ARG      4.8     0.3    +      -       -      -
     33A  THR*     3.3    24.8    -      -       -      +
     34A  LEU*     3.0    46.0    +      -       +      +
     59A  LEU*     3.7     7.4    -      -       +      -
     60A  THR*     5.7     1.1    -      -       -      -
    106A  PHE*     4.5     1.3    -      -       +      -
    107A  GLU*     1.3    79.0    -      -       -      +
    109A  SER*     1.3    65.5    +      -       -      +
    110A  PRO*     4.4     0.5    -      -       -      +
    112A  SER*     4.6     3.1    -      -       -      -
    115A  LEU*     4.5     8.6    -      -       +      +
    142A  ALA      3.6    20.4    -      -       -      +
    143A  ILE*     3.2    32.5    -      -       +      +
----------------------------------------------------------
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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