Contacts of the strand formed by residues 202 - 208 (chain A) in PDB entry 5HOO


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 VAL 202 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195A  VAL*     4.1    15.7    -      -       +      -
    196A  TRP      3.9     8.7    -      -       -      +
    197A  TRP*     3.7    11.2    -      -       +      -
    201A  GLY*     1.3    76.6    -      -       -      -
    203A  ILE*     1.3    66.4    +      -       -      +
    204A  TYR      3.9    12.6    -      -       -      +
    205A  TYR*     4.5     6.1    -      -       +      -
    233A  LYS*     5.3     1.2    -      -       -      +
    234A  ARG*     3.9     7.8    +      -       -      -
    287A  LEU*     5.3     2.2    -      -       +      -
    314A  PHE*     3.7    50.9    -      -       +      -
    322A  TYR*     3.8    18.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 203 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  VAL*     3.4    36.6    -      -       +      -
    196A  TRP      3.2    10.4    +      -       -      +
    197A  TRP*     4.1     1.6    -      -       -      +
    198A  ASP*     3.7    24.0    -      -       +      +
    202A  VAL*     1.3    79.1    -      -       -      +
    204A  TYR*     1.3    63.0    +      -       +      +
    226A  LEU*     3.9    16.6    -      -       +      -
    229A  ALA*     4.2     2.0    -      -       +      -
    230A  LEU*     4.1    39.5    -      -       +      +
    233A  LYS*     3.2    35.0    +      -       +      +
    234A  ARG*     3.6    21.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 204 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195A  VAL*     4.0     0.5    -      -       -      +
    196A  TRP*     3.2    45.4    +      +       -      +
    202A  VAL*     3.9     2.0    -      -       -      +
    203A  ILE*     1.3    80.3    -      -       -      +
    205A  TYR*     1.3    80.0    +      -       -      +
    206A  GLU*     2.7    41.6    +      -       +      +
    222A  GLN      3.8     7.0    -      -       -      -
    225A  ASN*     3.4    38.2    +      -       +      +
    226A  LEU*     3.7    24.2    -      -       +      +
    229A  ALA*     3.7    19.5    -      -       +      -
    232A  ARG*     5.7     3.1    -      -       -      -
    233A  LYS*     6.0     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 205 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193A  LEU*     3.5    28.0    -      -       +      -
    194A  CYS      3.2    14.1    -      -       -      +
    195A  VAL*     3.7    17.3    -      -       +      +
    196A  TRP*     4.2     2.9    -      -       -      -
    202A  VAL*     4.5     7.2    -      -       +      -
    204A  TYR*     1.3    99.2    -      -       -      +
    206A  GLU*     1.3    64.5    +      -       -      +
    207A  LEU*     4.1    11.4    -      -       +      -
    307A  LYS*     3.3    21.0    +      -       +      +
    310A  LEU*     4.0    14.8    -      -       +      +
    311A  ASP*     2.5    30.2    +      -       -      -
    314A  PHE*     4.4    21.8    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLU 206 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193A  LEU*     3.8     9.2    -      -       -      +
    194A  CYS      2.8    28.9    +      -       -      +
    196A  TRP*     4.5     1.2    -      -       +      -
    204A  TYR*     2.7    36.5    +      -       +      +
    205A  TYR*     1.3    72.9    -      -       -      +
    207A  LEU*     1.3    63.5    +      -       -      +
    208A  LEU*     4.2     7.0    -      -       +      -
    218A  ARG*     4.5    10.9    +      -       -      -
    221A  GLN*     5.8     2.3    -      -       -      +
    222A  GLN*     3.3    46.2    +      -       -      +
    225A  ASN*     4.4     6.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 207 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160A  ILE*     5.1     1.1    -      -       +      -
    191A  THR*     3.5    27.2    -      -       +      +
    192A  MET      3.6     3.1    -      -       -      +
    193A  LEU*     3.7    26.5    -      -       +      -
    205A  TYR*     4.1     5.6    -      -       +      -
    206A  GLU*     1.3    79.6    -      -       -      +
    208A  LEU*     1.3    63.3    +      -       -      +
    209A  LYS*     3.8     9.0    +      -       -      +
    212A  GLU*     4.7     1.0    -      -       -      +
    303A  TYR*     4.4    10.1    -      -       +      +
    306A  VAL*     4.1    16.6    -      -       +      -
    307A  LYS*     3.6    47.8    -      -       +      +
    310A  LEU*     4.0     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 208 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159A  TRP*     5.3     0.2    -      -       -      -
    191A  THR*     3.0    20.1    -      -       -      +
    192A  MET*     2.9    33.1    +      -       +      +
    194A  CYS*     4.0    17.3    -      -       -      -
    206A  GLU*     4.2     9.6    -      -       +      +
    207A  LEU*     1.3    75.3    -      -       -      +
    209A  LYS*     1.3    66.1    +      -       -      +
    212A  GLU*     3.5    31.9    -      -       -      +
    214A  VAL*     3.6    27.1    -      -       +      -
    218A  ARG*     4.0    22.7    -      -       -      +
    222A  GLN*     3.8    23.1    -      -       -      +
----------------------------------------------------------
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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