Contacts of the strand formed by residues 289 - 295 (chain B) in PDB entry 6W01


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 SER 289 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244B  SER      3.0    11.5    +      -       -      +
    245B  GLN*     3.2    11.4    -      -       -      +
    246B  LEU*     2.8    22.4    +      -       -      -
    280B  PHE*     4.6     9.3    -      -       -      -
    281B  ILE      3.2    14.6    -      -       -      -
    282B  THR*     4.0    16.2    -      -       -      -
    287B  GLY      4.2     6.6    +      -       -      -
    288B  SER*     1.3    76.7    +      -       -      +
    290B  LYS*     1.3    62.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 290 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245B  GLN*     4.2    24.0    -      -       -      +
    246B  LEU*     2.8    30.8    +      -       +      +
    248B  GLY      2.9    28.9    +      -       -      +
    250B  HIS*     4.4     1.3    -      -       -      -
    279B  TYR      3.7     1.0    -      -       -      +
    280B  PHE*     3.4     4.1    -      -       -      -
    281B  ILE*     3.0    41.6    +      -       +      +
    289B  SER*     1.3    77.3    -      -       -      +
    291B  CYS*     1.3    63.6    -      -       -      +
    292B  VAL      3.5    19.6    +      -       -      +
    293B  CYS*     3.6    28.0    -      -       -      +
    408B  CIT      3.0    30.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 291 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245B  GLN*     5.0     3.3    +      -       -      -
    269B  PHE*     3.5     7.4    -      -       -      -
    279B  TYR      3.4     0.9    -      -       -      +
    280B  PHE*     3.3    56.2    -      -       +      +
    290B  LYS*     1.3    76.0    -      -       -      +
    292B  VAL*     1.3    71.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 292 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250B  HIS*     5.6     0.3    -      -       -      -
    269B  PHE*     4.1    13.2    -      -       +      -
    278B  ASN*     3.8    30.7    -      -       +      +
    279B  TYR      3.7     1.8    -      -       -      -
    290B  LYS*     3.7    16.5    -      -       -      +
    291B  CYS*     1.3    89.8    -      -       +      +
    293B  CYS*     1.3    59.4    +      -       -      +
    294B  SER      3.9     1.4    +      -       -      -
    346B  LEU*     3.5    34.1    -      -       +      +
    408B  CIT      4.3     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 293 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246B  LEU*     5.3     0.4    -      -       -      -
    248B  GLY      3.8     5.4    -      -       -      -
    249B  LEU*     3.3    33.0    -      -       -      -
    250B  HIS*     4.3     1.8    -      -       -      -
    255B  LEU*     6.3     0.2    -      -       -      -
    266B  LEU*     6.2     0.2    -      -       +      -
    277B  LYS      3.7     0.3    -      -       -      +
    278B  ASN*     3.5     2.2    -      -       -      -
    279B  TYR*     2.7    42.7    +      -       +      +
    281B  ILE*     3.7    24.0    -      -       +      -
    290B  LYS*     3.6    27.4    -      -       +      +
    292B  VAL*     1.3    71.6    -      -       -      +
    294B  SER*     1.3    67.8    +      -       -      +
    295B  VAL*     3.6    13.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 294 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250B  HIS*     2.7    51.1    +      -       -      +
    276B  VAL*     3.9    15.0    -      -       -      -
    277B  LYS      3.3     6.5    -      -       -      -
    278B  ASN*     3.2    16.7    +      -       -      -
    292B  VAL*     3.9     3.6    +      -       -      +
    293B  CYS*     1.3    73.0    -      -       -      +
    295B  VAL*     1.3    60.6    +      -       -      +
    343B  TYR*     5.3     0.3    -      -       -      -
    344B  PRO*     3.7    24.6    +      -       -      +
    346B  LEU*     4.0    15.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 295 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    249B  LEU      4.0    14.4    -      -       -      +
    250B  HIS      3.4     4.0    -      -       -      +
    252B  LEU*     4.0    38.4    -      -       +      +
    255B  LEU*     4.1    19.5    -      -       +      -
    266B  LEU*     5.7     0.7    -      -       +      -
    275B  THR      4.4     0.3    -      -       -      +
    276B  VAL*     3.7     3.0    -      -       -      +
    277B  LYS*     2.7    37.9    +      -       +      +
    279B  TYR*     3.8    24.2    -      -       +      -
    293B  CYS*     3.7    15.9    -      -       +      +
    294B  SER*     1.3    80.3    -      -       -      +
    296B  ILE*     1.3    65.8    +      -       -      +
    344B  PRO*     5.5     0.2    -      -       -      -
----------------------------------------------------------
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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