Contacts of the strand formed by residues 202 - 208 (chain H) in PDB entry 1YPO


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 202 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197G  TYR*     3.9    23.1    -      +       +      -
    158H  PHE*     3.5    29.6    -      +       +      -
    159H  SER      5.5     0.2    -      -       -      -
    195H  ILE*     4.1    19.7    -      -       +      -
    198H  SER*     3.4    22.4    -      -       -      -
    200H  PHE*     3.1    25.4    -      -       +      -
    201H  PRO*     1.3    75.1    -      -       -      +
    203H  TRP*     1.3    62.6    +      -       -      +
    245H  TYR*     3.2     3.7    -      -       -      +
    246H  ILE*     2.9    45.2    +      -       +      +
    261H  PHE*     3.0    20.6    -      -       +      +
    262H  SER      3.7     9.4    -      -       -      -
    263H  ILE*     3.5    37.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 203 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163H  PHE      3.4    16.2    +      -       -      -
    165H  TRP*     3.5    29.9    -      +       +      +
    168H  SER*     3.5    25.1    -      -       -      -
    179H  LEU*     4.3     4.3    -      -       +      +
    180H  LEU*     4.6     1.2    -      -       -      +
    201H  PRO      4.3     0.4    -      -       -      -
    202H  PHE*     1.3    76.9    -      -       -      +
    204H  MET*     1.3    59.9    +      -       -      +
    243H  CYS*     3.5    33.7    -      -       +      -
    244H  ALA      3.4    17.5    -      -       -      -
    245H  TYR*     3.7    19.9    -      +       +      +
    254H  GLU*     4.0    12.6    -      -       +      -
    255H  ASN      3.4    22.4    -      -       -      -
    256H  CYS*     4.1     7.9    -      -       -      -
    258H  LEU*     3.2    22.8    +      -       +      -
    260H  ALA*     3.8    24.1    -      -       +      +
    261H  PHE      2.8    11.6    +      -       -      +
    262H  SER*     4.1     9.6    -      -       -      -
    263H  ILE*     3.5    23.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 204 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165H  TRP*     2.7    28.4    +      -       -      -
    179H  LEU*     3.8     6.6    -      -       -      +
    180H  LEU*     3.4    28.3    -      -       +      +
    182H  ILE*     3.4    28.3    -      -       +      -
    203H  TRP*     1.3    75.0    -      -       -      +
    205H  GLY*     1.3    56.8    +      -       -      +
    206H  LEU*     3.2     9.1    +      -       -      +
    217H  TRP*     4.2    17.9    -      -       +      -
    228H  PHE*     4.7     2.9    -      -       -      -
    244H  ALA*     3.1    35.7    +      -       +      +
    245H  TYR*     4.0     1.3    -      -       -      -
    246H  ILE*     3.4    33.4    -      -       +      -
    251H  VAL*     4.2    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 205 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165H  TRP*     3.8    11.2    -      -       -      -
    179H  LEU*     3.5    20.7    -      -       -      +
    180H  LEU      2.9    18.2    +      -       -      -
    204H  MET*     1.3    70.5    -      -       -      +
    206H  LEU*     1.3    58.1    +      -       -      +
    207H  SER      4.1     0.3    +      -       -      -
    217H  TRP*     2.9    38.8    -      -       -      -
    218H  GLU*     3.1     9.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 206 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165H  TRP*     4.4     0.4    +      -       -      -
    204H  MET*     3.2     8.6    +      -       +      +
    205H  GLY*     1.3    77.5    -      -       -      +
    207H  SER*     1.3    65.4    +      -       -      +
    215H  TRP*     3.9    27.1    -      -       +      -
    216H  LEU*     3.4    25.1    -      -       -      +
    217H  TRP*     3.5    39.2    -      -       +      +
    223H  LEU*     4.0    12.3    -      -       +      -
    228H  PHE*     4.2    25.8    -      -       +      -
    230H  VAL*     4.4     3.1    -      -       +      -
    243H  CYS*     3.9     0.7    -      -       -      +
    244H  ALA*     3.0    45.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 207 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165H  TRP*     3.8    20.0    -      -       -      -
    205H  GLY      5.0     0.7    +      -       -      -
    206H  LEU*     1.3    78.4    -      -       -      +
    208H  ARG*     1.3    67.8    +      -       -      +
    214H  PRO      4.3     0.7    -      -       -      +
    215H  TRP*     3.6     9.3    -      -       -      -
    216H  LEU*     3.0    29.8    +      -       -      +
    217H  TRP      5.1     2.3    +      -       -      -
    242H  THR      3.5    14.4    -      -       -      -
    243H  CYS*     3.8    18.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 208 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207H  SER*     1.3    80.6    +      -       -      +
    209H  ARG*     1.3    64.0    +      -       -      +
    210H  ASN      3.3    14.4    +      -       -      +
    211H  PRO*     3.8    22.8    +      -       -      +
    213H  TYR*     2.9    37.0    +      -       +      +
    214H  PRO*     4.0     7.4    -      -       -      +
    215H  TRP*     3.5    56.9    -      -       +      +
    234H  VAL*     2.8    37.2    +      -       -      +
    241H  GLY*     4.1     0.4    -      -       -      -
    242H  THR*     3.0    29.5    +      -       -      +
----------------------------------------------------------
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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