Contacts of the strand formed by residues 304 - 309 (chain B) in PDB entry 4CY1


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 304 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262B  ILE*     3.4     6.9    -      -       -      +
    277B  GLY*     3.3    36.9    -      -       -      -
    278B  SER      3.1    12.3    +      -       -      +
    281B  ASN      3.5    31.2    -      -       -      +
    282B  LEU      3.9     7.4    -      -       -      +
    283B  VAL*     4.1     3.8    -      -       +      +
    300B  HIS*     3.7    24.5    -      -       +      -
    303B  VAL*     1.3    68.8    -      -       -      +
    305B  ILE*     1.3    61.3    +      -       -      +
    306B  SER      3.7    14.6    -      -       -      +
    307B  THR*     4.0     8.5    -      -       +      -
    318B  SER*     4.0    11.2    -      -       -      -
    319B  ALA      3.4    13.7    -      -       -      +
    320B  ALA*     4.3     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 305 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48B  VAL      3.2    26.5    -      -       -      +
     49B  SER*     3.7    21.3    -      -       -      +
    260B  TYR*     3.7    29.8    -      -       +      -
    261B  CYS      3.6    21.3    -      -       -      +
    262B  ILE*     3.2     9.0    -      -       +      -
    263B  PHE*     3.1    25.5    +      -       -      -
    303B  VAL*     3.2     4.3    +      -       +      -
    304B  VAL*     1.3    73.8    -      -       -      +
    306B  SER*     1.3    63.6    +      -       -      +
    319B  ALA*     3.0    15.5    +      -       +      +
    320B  ALA      4.6     0.4    -      -       -      -
    321B  LEU*     3.6    21.8    -      -       +      -
    592C  ARG*     3.8    24.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 306 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49B  SER      3.9     2.5    -      -       -      -
     50B  SER*     3.8    15.9    -      -       -      -
     51B  VAL*     3.0    33.9    +      -       -      +
    263B  PHE*     3.6    22.6    -      -       -      +
    277B  GLY      5.5     0.2    -      -       -      -
    304B  VAL*     3.4     1.8    -      -       -      +
    305B  ILE*     1.3    87.6    -      -       -      +
    307B  THR*     1.3    69.0    +      -       -      +
    318B  SER*     3.3     3.6    -      -       -      -
    319B  ALA*     2.9    31.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 307 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  VAL*     4.4     1.5    -      -       -      +
     52B  LYS*     6.1     0.3    -      -       -      +
    263B  PHE*     3.3    25.2    +      -       -      +
    265B  ASN*     2.8    37.3    +      -       -      +
    275B  VAL*     3.9    10.4    +      -       -      -
    276B  SER*     3.8    12.3    -      -       -      -
    277B  GLY      3.8    17.3    -      -       -      +
    283B  VAL*     4.1    14.1    -      -       +      -
    304B  VAL*     4.0    12.3    -      -       +      -
    306B  SER*     1.3    85.1    +      -       -      +
    308B  ALA*     1.3    63.6    +      -       -      +
    316B  ILE*     4.6     1.8    -      -       +      -
    317B  ALA      3.1     6.3    -      -       -      +
    318B  SER*     4.1    10.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 308 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  VAL*     3.5    31.2    -      -       +      +
     52B  LYS*     4.3     7.4    -      -       +      -
     53B  PHE*     3.6    21.1    -      -       +      +
    265B  ASN*     3.7     7.0    -      -       -      +
    307B  THR*     1.3    74.4    -      -       -      +
    309B  CYS*     1.3    64.5    +      -       -      +
    316B  ILE*     3.3     7.5    -      -       -      +
    317B  ALA*     2.8    31.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 309 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53B  PHE*     3.6     7.5    -      -       -      +
    265B  ASN*     3.6    29.8    +      -       +      -
    266B  PHE      4.1    12.1    -      -       -      +
    267B  SER*     3.8    29.8    -      -       -      +
    275B  VAL*     3.9    15.7    -      -       -      -
    308B  ALA*     1.3    76.5    -      -       -      +
    310B  HIS*     1.3    68.5    +      -       -      +
    311B  PRO*     3.6     3.5    -      -       -      +
    315B  ILE      3.7     4.0    -      -       -      +
    316B  ILE*     4.4     8.1    -      -       -      -
----------------------------------------------------------
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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