Contacts of the strand formed by residues 202 - 209 (chain A) in PDB entry 1YH3


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 ASP 202 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  ASN*     3.2    20.6    -      -       +      +
    201A  CYS*     1.3    90.7    -      -       -      +
    203A  VAL*     1.3    63.0    +      -       -      +
    234A  LYS      3.0    15.3    +      -       -      +
    235A  VAL*     3.5     3.5    -      -       -      +
    236A  GLN*     2.6    32.4    +      -       -      +
    237A  THR      3.4     4.5    +      -       -      +
     53B  PRO*     3.6     5.4    -      -       -      +
     54B  GLY*     2.7    37.7    +      -       -      +
     55B  THR      4.0     7.8    -      -       -      +
     56B  THR*     4.9     4.2    -      -       -      -
     57B  LYS      5.0     2.1    +      -       -      +
    170B  TYR      3.4    18.6    -      -       -      +
    171B  GLN      4.3     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 203 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  ASN      3.6    19.1    +      -       -      +
    121A  LYS*     5.4     0.2    -      -       -      -
    122A  ILE      4.8     1.9    +      -       -      +
    201A  CYS      3.6     3.5    -      -       -      +
    202A  ASP*     1.3    81.8    -      -       -      +
    204A  VAL*     1.3    64.5    +      -       -      +
    205A  HIS*     3.7    29.1    +      -       +      +
    236A  GLN*     4.2     9.0    -      -       +      -
    237A  THR*     3.4    31.2    -      -       +      +
    239A  GLU*     4.7     6.5    -      -       +      +
    170B  TYR*     4.1    10.8    -      -       +      +
    171B  GLN*     3.4    39.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 204 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119A  CYS      5.3     0.7    -      -       -      +
    122A  ILE*     4.0    15.0    -      -       +      +
    124A  LEU*     3.9    25.1    -      -       +      -
    200A  ALA*     3.8    23.3    -      -       +      -
    201A  CYS      3.9     9.2    -      -       -      +
    203A  VAL*     1.3    77.0    -      -       -      +
    205A  HIS*     1.3    72.3    +      -       -      +
    230A  LEU*     4.4     7.6    -      -       +      -
    235A  VAL*     3.7    25.4    -      -       +      -
    237A  THR      2.9     9.6    +      -       -      +
    238A  LEU*     3.2    15.4    -      -       +      +
    239A  GLU      2.9    24.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 205 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  ASN      5.6     0.2    +      -       -      -
    121A  LYS      6.1     0.2    -      -       -      -
    122A  ILE      3.1     9.9    +      -       -      +
    123A  LEU*     3.6    19.8    -      -       +      -
    124A  LEU*     2.8    27.9    +      -       -      +
    142A  MET*     3.3    31.0    -      -       +      +
    203A  VAL*     3.7    18.9    +      -       +      +
    204A  VAL*     1.3    78.6    -      -       -      +
    206A  VAL*     1.3    61.5    +      -       -      +
    239A  GLU*     3.3    35.4    +      -       +      +
    241A  TRP*     3.5    28.5    -      +       +      -
     45B  ARG      4.3     3.8    +      -       -      -
     48B  GLN*     4.3     5.0    +      -       -      -
    171B  GLN*     3.3    32.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 206 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123A  LEU*     4.3     3.1    -      -       -      -
    124A  LEU*     3.3    17.9    -      -       +      +
    125A  TRP*     4.2     1.8    -      -       -      +
    205A  HIS*     1.3    75.8    -      -       -      +
    207A  MET*     1.3    64.0    +      -       -      +
    208A  LEU*     3.9    20.5    +      -       +      -
    222A  PHE*     3.6    44.0    -      -       +      -
    238A  LEU*     4.0    17.7    -      -       +      -
    239A  GLU      2.9     9.9    +      -       -      +
    240A  ALA*     3.3    23.5    -      -       +      +
    241A  TRP*     2.8    27.5    +      -       -      +
    262A  LEU*     5.2     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 207 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123A  LEU*     3.9    10.9    -      -       +      +
    124A  LEU      2.9    13.2    +      -       -      +
    125A  TRP*     3.3     4.9    -      -       +      -
    126A  SER      2.9    26.7    +      -       -      -
    128A  ILE*     3.5    15.4    -      -       +      +
    131A  LEU*     3.9    22.0    -      -       +      +
    132A  ALA*     3.7    36.8    -      -       -      -
    135A  PHE*     4.0    17.9    -      -       +      -
    206A  VAL*     1.3    72.2    -      -       -      +
    208A  LEU*     1.4    60.5    +      -       -      +
    241A  TRP*     3.4    35.0    -      -       +      +
    243A  ILE*     3.8    21.3    -      -       +      -
    284A  PHE*     4.5     3.8    -      -       +      -
----------------------------------------------------------
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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
----------------------------------------------------------
    126A  SER*     3.7    26.9    -      -       -      -
    128A  ILE*     4.2     4.9    -      -       -      -
    206A  VAL*     3.9    20.2    -      -       +      +
    207A  MET*     1.4    76.0    -      -       -      +
    209A  ASP*     1.3    56.9    +      -       -      +
    210A  GLY      3.2     1.2    +      -       -      -
    215A  ILE*     3.8    28.9    -      -       +      +
    216A  PHE*     4.8     3.1    -      -       -      +
    222A  PHE*     4.3    11.2    -      -       +      -
    240A  ALA*     4.1    16.4    -      -       +      -
    241A  TRP      2.9    12.8    +      -       -      +
    242A  VAL*     3.5     3.3    -      -       +      -
    243A  ILE*     2.7    34.5    +      -       -      +
    259A  ILE*     3.7    29.8    -      -       +      -
    262A  LEU*     4.6     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 209 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126A  SER      3.6     5.9    +      -       -      -
    127A  ARG*     3.1    38.3    -      -       +      +
    128A  ILE*     4.2    16.9    -      -       +      +
    208A  LEU*     1.3    69.4    -      -       -      +
    210A  GLY*     1.3    58.4    +      -       -      +
    211A  SER*     3.0    30.9    +      -       -      -
    212A  ARG*     3.3    44.8    +      -       +      +
    215A  ILE*     3.8    11.6    +      -       -      +
    243A  ILE      4.2     3.4    -      -       -      +
----------------------------------------------------------
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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