Contacts of the strand formed by residues 148 - 153 (chain A) in PDB entry 6Y2E


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 148 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  VAL*     3.8    28.0    -      -       +      -
     17A  MET*     4.5     6.0    -      -       +      +
     30A  LEU*     4.2    22.2    -      -       +      -
    113A  SER      3.9     0.5    -      -       -      +
    114A  VAL*     3.5     6.0    -      -       -      +
    115A  LEU*     3.2    28.2    +      -       +      +
    146A  GLY      3.4    17.5    -      -       -      +
    147A  SER*     1.3    75.0    -      -       -      +
    149A  GLY*     1.3    62.1    +      -       -      +
    150A  PHE*     4.0     3.5    -      -       +      -
    159A  PHE*     3.9    20.4    -      -       +      -
    161A  TYR*     3.1    13.2    -      -       -      +
    162A  MET*     3.9    19.5    -      -       +      -
    177A  LEU*     5.0     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 149 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  PHE*     3.5    20.9    -      -       -      -
    113A  SER      3.1    10.8    -      -       -      -
    114A  VAL*     4.4     1.6    -      -       -      -
    148A  VAL*     1.3    73.5    -      -       -      +
    150A  PHE*     1.3    63.7    +      -       -      +
    159A  PHE*     3.6     6.1    -      -       -      +
    160A  CYS*     3.0    27.4    +      -       -      -
    161A  TYR*     2.8    18.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  PHE*     3.9    24.2    -      -       +      -
      9A  PRO      4.1     2.5    -      -       -      -
     10A  SER*     4.3    19.3    -      -       -      -
     13A  VAL*     3.7    34.1    -      -       +      -
    112A  PHE*     3.5     2.2    -      -       -      +
    113A  SER*     2.9    57.7    +      -       -      -
    114A  VAL      4.5     0.2    -      -       -      -
    115A  LEU*     4.1    20.9    -      -       +      -
    125A  VAL*     4.6     1.6    -      -       +      -
    148A  VAL*     4.0     7.0    -      -       +      -
    149A  GLY*     1.3    77.4    -      -       -      +
    151A  ASN*     1.3    66.7    +      -       -      +
    152A  ILE*     3.9    21.5    -      -       +      -
    157A  VAL*     3.8    13.5    -      -       +      -
    158A  SER      3.2    13.7    -      -       -      +
    159A  PHE*     4.1     6.1    -      -       +      -
    160A  CYS*     3.9     4.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 151 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  PHE*     3.1    28.7    -      -       +      -
    104A  VAL*     5.9     1.4    -      -       -      +
    106A  ILE*     4.7     8.7    -      -       -      +
    110A  GLN*     5.8     1.6    -      -       -      +
    111A  THR*     3.1    29.4    +      -       -      +
    112A  PHE*     3.5    11.9    -      -       -      +
    150A  PHE*     1.3    73.9    -      -       -      +
    152A  ILE*     1.3    66.6    +      -       -      +
    157A  VAL*     3.5     4.9    -      -       -      +
    158A  SER*     2.9    42.0    +      -       -      +
    160A  CYS*     4.2     8.5    -      -       -      -
    295A  ASP*     5.6     0.9    -      -       -      +
    298A  ARG*     5.4     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 152 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  PHE*     3.4    34.5    -      -       +      -
      9A  PRO*     3.3    31.2    -      -       +      +
     12A  LYS*     4.7    15.0    -      -       +      -
     13A  VAL*     5.6     0.7    -      -       +      -
    150A  PHE*     3.9    13.5    -      -       +      -
    151A  ASN*     1.3    82.6    -      -       -      +
    153A  ASP*     1.3    61.3    +      -       -      +
    154A  TYR      3.6    22.2    -      -       -      +
    155A  ASP      4.7     1.8    -      -       -      -
    156A  CYS      3.4    15.0    -      -       -      +
    157A  VAL*     4.4    15.7    -      -       +      +
    294A  PHE*     6.0     1.2    -      -       -      -
    298A  ARG*     5.8     0.5    -      -       -      -
    305A  PHE*     3.0    32.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 153 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152A  ILE*     1.3    71.0    -      -       -      +
    154A  TYR*     1.3    63.4    +      -       -      +
    155A  ASP*     2.8    17.3    +      -       -      +
    156A  CYS*     2.9    29.8    +      -       +      +
    158A  SER*     6.0     1.8    -      -       -      +
    294A  PHE*     6.6     0.2    -      -       -      -
    305A  PHE*     4.3     1.8    -      -       -      -
----------------------------------------------------------
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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