Contacts of the strand formed by residues 242 - 247 (chain G) 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 THR 242 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207G  SER*     3.2     3.6    -      -       -      -
    208G  ARG*     2.6    61.0    +      -       +      +
    209G  ARG      4.4     7.9    -      -       -      +
    210G  ASN*     5.2     0.7    -      -       -      -
    215G  TRP*     3.0    16.6    -      -       -      -
    233G  ALA      4.4    10.5    -      -       -      +
    234G  VAL*     5.8     0.4    -      -       -      -
    236G  GLN      3.5    24.7    -      -       -      +
    238G  TYR*     4.4    13.7    -      -       +      -
    241G  GLY*     1.3    75.2    -      -       -      +
    243G  CYS*     1.3    58.9    +      -       -      +
    253G  ALA*     4.3     9.4    -      -       +      -
    254G  GLU      3.2     6.5    -      -       -      -
    256G  CYS*     3.6     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 243 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165G  TRP*     3.4    31.2    -      -       +      -
    203G  TRP*     2.9    34.3    -      -       +      -
    207G  SER*     3.5    20.6    -      -       -      -
    215G  TRP*     5.2     0.4    -      -       -      -
    242G  THR*     1.3    73.2    -      -       -      +
    244G  ALA*     1.3    60.1    +      -       -      +
    252G  TYR      3.7     1.4    -      -       -      +
    253G  ALA*     4.5     1.3    -      -       -      -
    254G  GLU*     2.7    27.6    +      -       -      +
    256G  CYS*     2.0    45.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 244 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203G  TRP*     2.8    15.9    -      -       -      -
    204G  MET*     3.0    32.1    +      -       +      +
    206G  LEU*     2.9    31.5    +      -       +      +
    207G  SER*     4.6     0.4    -      -       -      +
    215G  TRP*     4.9     4.4    -      -       +      -
    230G  VAL*     4.9     7.9    -      -       +      -
    242G  THR      4.3     0.2    +      -       -      -
    243G  CYS*     1.3    71.9    -      -       -      +
    245G  TYR*     1.3    62.3    +      -       -      +
    251G  VAL*     3.8    17.7    -      -       +      -
    252G  TYR      3.3     9.0    -      -       -      +
    253G  ALA*     4.6     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 245 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201G  PRO*     3.6    31.6    -      -       +      -
    202G  PHE      3.1    18.6    -      -       -      +
    203G  TRP*     3.3    28.7    -      +       +      +
    204G  MET*     4.1     4.0    -      -       -      +
    244G  ALA*     1.3    74.5    -      -       -      +
    246G  ILE*     1.3    64.8    +      -       -      +
    247G  GLN*     3.7    22.5    +      -       +      -
    250G  ALA      3.9     0.2    -      -       -      +
    251G  VAL*     3.4     4.8    -      -       -      -
    252G  TYR*     2.9    68.5    +      +       +      +
    253G  ALA      4.2     0.8    +      -       -      -
    254G  GLU*     3.6    32.8    +      -       +      -
    260G  ALA*     5.8     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 246 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180G  LEU*     5.1     3.1    -      -       +      -
    188G  LEU*     3.8    11.4    -      -       +      -
    191G  ILE*     4.7    12.8    -      -       +      -
    192G  GLN*     2.7    41.7    -      -       -      +
    195G  ILE*     3.4    21.2    -      -       +      +
    200G  PHE      4.6     0.5    -      -       -      +
    201G  PRO*     3.7     0.5    -      -       -      +
    202G  PHE*     2.8    49.6    +      -       +      +
    204G  MET*     4.1    13.1    -      -       +      +
    245G  TYR*     1.3    73.1    -      -       -      +
    247G  GLN*     1.3    64.0    +      -       -      +
    249G  GLY      4.2     0.2    -      -       -      -
    250G  ALA*     3.5    26.2    -      -       -      +
    251G  VAL*     3.7    14.4    -      -       +      +
    263G  ILE*     5.0     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 247 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195G  ILE*     4.9     4.7    -      -       -      -
    199G  SER      2.7    29.0    +      -       -      +
    200G  PHE      3.3     3.1    -      -       -      +
    201G  PRO*     3.2    29.9    -      -       +      +
    245G  TYR*     3.7    28.5    +      -       +      -
    246G  ILE*     1.3    81.0    -      -       -      +
    248G  ARG*     1.3    84.8    +      -       +      +
    249G  GLY      3.0     5.4    -      -       -      +
    250G  ALA      2.9    21.0    +      -       -      +
    252G  TYR*     3.2    11.3    -      -       +      -
----------------------------------------------------------
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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