Contacts of the strand formed by residues 199 - 203 (chain B) in PDB entry 6A5T


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 199 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108B  ASN*     4.8     1.0    +      -       -      -
    195B  VAL*     3.2     3.8    -      -       -      +
    196B  ILE      2.9    33.2    +      -       -      -
    197B  ASN      3.4     3.6    +      -       -      -
    198B  GLY*     1.3    78.5    -      -       -      +
    200B  GLU*     1.3    78.3    +      -       -      +
    201B  LYS*     4.1    17.2    +      -       -      -
    475B  VAL*     4.3    10.4    -      -       -      +
     41T    A      4.8    11.1    +      -       -      -
     42T    C      4.4    10.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 200 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105B  ARG*     2.5    33.8    +      -       +      +
    193B  TYR*     3.0    35.8    +      -       +      -
    194B  PHE      3.7     4.7    -      -       -      -
    195B  VAL*     4.6     2.0    -      -       +      +
    198B  GLY      4.7     1.8    -      -       -      +
    199B  SER*     1.3    87.7    +      -       -      +
    201B  LYS*     1.3    77.1    +      -       -      +
    475B  VAL*     3.8    14.1    -      -       +      +
    476B  LEU*     3.8    17.7    +      -       +      +
    478B  ARG*     3.5    17.7    +      -       -      +
    788B  ARG*     3.0    25.4    +      -       -      +
    790B  ASP*     6.0     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 201 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193B  TYR*     3.0     5.9    -      -       -      +
    194B  PHE*     2.8    42.2    +      -       +      +
    196B  ILE*     4.3    31.2    -      -       +      -
    199B  SER*     4.1    14.6    +      -       -      -
    200B  GLU*     1.3    86.6    -      -       -      +
    202B  VAL*     1.3    61.7    +      -       -      +
    454B  LEU*     4.0    19.5    -      -       +      +
    455B  ALA*     3.9    15.1    +      -       -      +
    473B  SER*     3.4    19.3    -      -       -      +
    474B  GLN      3.5    11.0    -      -       -      +
    475B  VAL*     3.4    24.2    -      -       -      +
    476B  LEU*     4.8     0.9    -      -       -      +
     41T    A      3.9    21.0    +      -       -      -
     42T    C      4.1     6.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 202 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34B  GLN*     5.7     2.2    -      -       -      +
    192B  GLY      5.0     3.6    -      -       -      +
    193B  TYR*     4.1     8.5    -      -       +      +
    194B  PHE*     5.9     1.3    -      -       -      -
    201B  LYS*     1.3    73.8    -      -       -      +
    203B  LEU*     1.3    81.4    +      -       -      +
    204B  ILE*     4.2    12.1    -      -       +      -
    473B  SER*     3.0    25.1    +      -       -      -
    474B  GLN*     3.1    32.4    +      -       +      +
    476B  LEU*     4.2    15.9    -      -       +      +
    487B  HIS*     4.0    15.5    -      -       -      +
    488B  LEU*     3.9    31.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 203 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34B  GLN*     4.2    21.2    +      -       -      +
    164B  MET*     5.6     1.1    -      -       +      -
    192B  GLY      5.4     1.6    +      -       -      -
    194B  PHE*     3.7    27.1    -      -       +      -
    202B  VAL*     1.3    90.2    -      -       -      +
    204B  ILE*     1.3    62.4    +      -       -      +
    205B  ALA*     3.1     7.9    +      -       -      +
    401B  LEU      5.2     0.9    -      -       -      -
    402B  ALA*     3.5    45.1    -      -       +      +
    405B  LEU*     5.1    10.5    -      -       +      -
    406B  LEU*     5.0     7.6    -      -       +      -
    454B  LEU*     4.6    11.7    -      -       +      -
    459B  TRP*     4.8     9.6    -      -       +      -
    472B  VAL*     3.6    19.3    -      -       +      +
    473B  SER*     4.3     8.5    -      -       -      -
    488B  LEU      4.8     3.3    -      -       -      +
    490B  ARG      5.1     0.3    -      -       -      +
----------------------------------------------------------
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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