Contacts of the strand formed by residues 217 - 222 (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 217 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175B  SER*     2.6    23.7    +      -       -      -
    189B  SER*     3.5    24.7    -      -       -      -
    190B  SER      3.0    21.3    +      -       -      +
    191B  TYR*     4.0     3.0    +      -       -      -
    193B  GLY      3.5    31.0    -      -       -      +
    194B  LEU      3.9     7.2    -      -       -      +
    195B  CYS*     3.8    15.5    -      -       -      -
    215B  PRO      3.8     5.8    -      -       -      +
    216B  PRO*     1.3    70.7    -      -       -      +
    218B  SER*     1.3    53.6    +      -       -      +
    219B  PHE      3.7     9.9    -      -       -      +
    231B  ALA*     4.3     6.1    -      -       +      -
    232B  ALA      3.3    16.6    -      -       -      +
    233B  THR*     3.9     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 218 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175B  SER*     3.5    13.5    -      -       -      +
    191B  TYR*     4.7     1.3    -      -       -      -
    216B  PRO      3.7     1.0    +      -       -      -
    217B  VAL*     1.3    72.3    -      -       -      +
    219B  PHE*     1.3    62.4    +      -       -      +
    232B  ALA*     2.8    24.6    +      -       -      +
    233B  THR      4.0     0.7    +      -       -      -
    234B  LEU*     3.5    36.1    -      -       -      +
    257B  ASN*     3.8     5.7    +      -       -      -
    260B  TYR      3.9     5.4    -      -       -      -
    261B  CYS*     3.2    40.7    -      -       -      +
    262B  ILE      4.9     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 219 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175B  SER*     3.9     0.6    +      -       -      -
    176B  ALA*     4.0    11.9    -      -       +      -
    189B  SER*     3.8     7.2    -      -       -      -
    217B  VAL*     3.6     4.4    -      -       -      +
    218B  SER*     1.3    81.6    +      -       -      +
    220B  VAL*     1.3    92.7    +      -       -      +
    221B  LYS*     3.8    24.5    -      -       +      -
    230B  LEU*     4.5     4.9    -      -       +      -
    231B  ALA*     3.3     1.7    -      -       -      -
    232B  ALA*     2.8    33.8    +      -       +      +
    262B  ILE      3.5    18.6    -      -       -      +
    263B  PHE*     3.4    37.7    -      +       -      -
    264B  ALA*     3.3    44.9    -      -       +      -
    592C  ARG*     5.1     5.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 220 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176B  ALA*     3.5    17.2    -      -       +      +
    177B  VAL      5.2     0.2    -      -       -      +
    178B  HIS*     4.3     7.4    -      -       -      +
    187B  VAL*     3.8    31.6    -      -       +      +
    188B  SER      3.8     7.4    -      -       -      -
    189B  SER*     3.4    35.0    -      -       -      +
    195B  CYS*     4.0     9.6    -      -       -      -
    219B  PHE*     1.3    85.7    -      -       -      +
    221B  LYS*     1.3    68.3    +      -       -      +
    229B  ILE*     3.8    21.5    -      -       +      -
    230B  LEU      3.1    13.7    -      -       -      +
    231B  ALA*     4.1     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 221 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178B  HIS*     3.8    34.3    -      -       +      +
    187B  VAL*     4.2     2.0    -      -       -      -
    219B  PHE*     3.8    16.5    -      -       +      -
    220B  VAL*     1.3    77.3    -      -       -      +
    222B  PHE*     1.3    71.4    +      -       -      +
    229B  ILE*     3.2     6.2    -      -       -      -
    230B  LEU*     2.8    37.0    +      -       +      +
    264B  ALA      3.4    22.4    +      -       -      +
    265B  ASN*     3.7    26.6    +      -       -      +
    266B  PHE*     4.4    14.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 222 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178B  HIS*     3.1    41.8    +      -       +      +
    179B  PHE      3.6     4.7    -      -       -      -
    180B  ASN*     3.5    44.0    -      -       +      -
    185B  LEU*     3.9    17.0    -      -       +      -
    187B  VAL*     3.6    24.9    -      -       +      -
    197B  ILE*     4.0     9.0    -      -       +      -
    221B  LYS*     1.3    88.4    -      -       -      +
    223B  SER*     1.3    69.8    +      -       -      +
    224B  PRO*     3.9     1.2    -      -       -      +
    226B  GLY*     4.8     4.3    -      -       -      -
    228B  TYR      3.4     3.6    -      -       -      -
    229B  ILE*     3.5    18.6    -      -       +      -
    243B  TYR*     3.6    37.5    -      +       -      -
    266B  PHE*     4.0     2.8    -      -       -      -
----------------------------------------------------------
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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