Contacts of the strand formed by residues 335 - 342 (chain A) in PDB entry 1Y7V


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 MET 335 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  LYS*     5.3     1.3    -      -       +      -
    228A  TRP*     3.6    34.5    -      -       +      -
    279A  LEU*     4.3     5.8    -      -       +      -
    306A  HIS*     3.4    41.6    +      -       +      +
    307A  GLY*     3.8     8.1    -      -       -      -
    308A  ILE*     2.8    28.5    +      -       -      +
    333A  ASN      3.9     2.6    +      -       -      -
    334A  THR*     1.3    75.7    -      -       -      +
    336A  LEU*     1.3    59.4    +      -       -      +
    337A  PHE*     3.8    20.9    -      -       +      -
    376A  VAL*     4.0    33.0    -      -       +      -
    504A  SO4      5.6     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 336 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288A  LEU*     4.4     2.2    -      -       +      -
    308A  ILE*     3.6    39.7    -      -       +      +
    310A  VAL*     4.6     1.8    -      -       +      -
    324A  LEU*     3.4    46.9    -      -       +      +
    327A  THR*     4.1     8.7    -      -       +      -
    328A  HIS*     4.6    13.2    -      -       +      +
    334A  THR      4.4     5.4    -      -       -      +
    335A  MET*     1.3    75.7    -      -       -      +
    337A  PHE*     1.3    55.9    +      -       -      +
    373A  TYR      4.1    11.4    -      -       -      +
    374A  HIS*     4.3    14.3    +      -       +      +
    375A  VAL*     3.2    19.4    -      -       +      -
    376A  VAL*     2.7    35.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 337 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  LYS*     4.3     3.1    -      -       +      -
    118A  ILE*     3.7    25.8    -      -       +      -
    175A  LEU*     3.7    20.2    -      -       +      -
    228A  TRP*     3.6    29.8    -      +       -      -
    279A  LEU*     4.2    17.7    -      -       +      -
    308A  ILE      3.2     8.6    +      -       -      +
    309A  ALA*     3.3     3.1    -      -       -      -
    310A  VAL*     2.7    36.6    +      -       -      +
    335A  MET*     3.8    16.4    -      -       +      -
    336A  LEU*     1.3    75.6    -      -       -      +
    338A  ALA*     1.3    71.8    +      -       -      +
    339A  SER*     4.0     5.2    -      -       -      -
    375A  VAL*     3.9     2.7    -      -       -      -
    376A  VAL*     4.2     8.3    -      -       +      -
    377A  GLY*     3.8    25.1    -      -       -      -
    379A  THR*     3.1    22.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 338 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    310A  VAL*     3.3    12.6    -      -       +      +
    311A  HIS      6.4     0.2    -      -       -      -
    337A  PHE*     1.3    77.4    -      -       -      +
    339A  SER*     1.3    56.6    +      -       -      +
    340A  GLU      3.7     4.7    -      -       -      +
    370A  ASN*     3.7    23.1    -      -       -      +
    375A  VAL*     3.6     1.2    -      -       -      +
    377A  GLY      2.9    20.8    +      -       -      +
    378A  TRP*     3.5    22.0    -      -       +      +
    379A  THR*     2.7    33.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 339 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  ARG*     3.3    23.2    +      -       -      -
    175A  LEU*     4.1    13.2    -      -       -      -
    231A  THR*     5.2     0.2    -      -       -      -
    282A  ASP*     2.5    29.6    +      -       -      -
    309A  ALA*     3.6    11.0    -      -       -      +
    310A  VAL      2.8    12.2    +      -       -      -
    311A  HIS*     3.0    12.2    -      -       -      -
    337A  PHE*     3.6    14.9    +      -       -      -
    338A  ALA*     1.3    72.0    -      -       -      +
    340A  GLU*     1.3    61.9    +      -       -      +
    379A  THR*     3.6    17.0    -      -       -      +
    380A  ASP      4.6     1.2    -      -       -      +
    381A  TRP*     5.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 340 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  ARG*     3.0    23.1    +      -       -      +
    179A  TRP*     3.9     3.6    -      -       -      -
    234A  ASN*     3.4     2.8    -      -       -      +
    235A  GLU*     3.9     0.3    -      -       -      +
    310A  VAL      4.3     0.3    -      -       -      +
    311A  HIS*     3.4    26.9    +      -       +      +
    312A  TRP*     3.0    25.6    +      -       -      +
    313A  TYR*     4.6     1.7    +      -       -      -
    338A  ALA*     3.7     3.0    -      -       -      +
    339A  SER*     1.3    83.0    +      -       -      +
    341A  ALA*     1.3    65.8    +      -       -      +
    379A  THR      3.3     7.6    +      -       -      -
    380A  ASP      4.9     1.3    -      -       -      -
    381A  TRP*     4.1    21.8    -      -       +      -
    507A  INS      1.4    65.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 341 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    312A  TRP*     3.3     7.2    -      -       +      +
    314A  LEU*     4.8     5.4    -      -       +      -
    340A  GLU*     1.3    76.7    -      -       -      +
    342A  CYS*     1.3    64.4    +      -       -      +
    363A  TYR*     4.0     6.4    +      -       +      +
    378A  TRP*     3.3    45.5    -      -       +      -
    379A  THR      3.5     6.0    +      -       -      +
    380A  ASP*     3.8     8.4    -      -       -      +
    381A  TRP*     3.3    26.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 342 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    312A  TRP      3.2     6.2    +      -       -      +
    313A  TYR*     3.7    17.0    -      -       +      -
    314A  LEU*     2.9    37.5    +      -       -      +
    315A  ASP*     4.0     0.5    -      -       -      +
    340A  GLU*     5.0     0.2    -      -       -      -
    341A  ALA*     1.3    79.1    -      -       -      +
    343A  VAL*     1.3    65.7    +      -       -      +
    345A  SER*     3.7    20.0    -      -       -      +
    363A  TYR*     4.7     0.9    -      -       -      -
    381A  TRP*     4.2     8.3    -      -       -      -
    398A  VAL*     4.1    11.9    -      -       -      -
    507A  INS      3.5    38.8    -      -       -      -
----------------------------------------------------------
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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