Contacts of the strand formed by residues 99 - 104 (chain J) in PDB entry 6XXD


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 99 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33J  ASP*     4.7     0.5    -      -       -      +
     93J  GLY*     4.7     2.6    -      -       -      -
     94J  HIS      5.3     0.3    +      -       -      -
     98J  THR*     1.3    98.5    +      -       -      +
    100J  TRP*     1.3    61.5    +      -       -      +
    101J  PHE*     3.2    24.2    -      -       +      -
    111J  LYS*     4.0    30.5    -      -       +      -
    112J  THR      3.4    20.4    -      -       -      +
    113J  ASN*     4.2     6.5    -      -       -      +
    114J  THR      3.3    20.9    -      -       -      +
    115J  ALA*     4.2     3.4    -      -       +      -
    116J  VAL*     3.6    15.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 100 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77J  THR*     3.2    36.3    -      -       +      -
     91J  ILE*     3.6    20.4    -      -       +      -
     92J  ALA      3.8     2.7    -      -       -      -
     93J  GLY*     3.6    25.4    -      -       -      -
     99J  VAL*     1.3    76.3    -      -       -      +
    101J  PHE*     1.3    59.7    +      -       -      +
    111J  LYS*     3.7     2.6    -      -       -      -
    112J  THR*     3.0    41.6    +      -       +      +
    114J  THR*     3.2    13.2    +      -       +      -
    115J  ALA      2.9    29.0    +      -       -      -
    116J  VAL*     3.7    14.7    -      -       +      +
    118J  SER      3.5    12.1    +      -       -      -
    119J  SER*     3.6     4.0    +      -       -      -
    120J  GLN*     3.7    42.8    -      -       +      -
    121J  PRO*     3.6    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 101 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33J  ASP*     3.8    41.7    -      -       +      -
     36J  VAL*     3.6    18.2    -      -       +      -
     37J  THR*     3.3    23.3    -      -       +      -
     40J  LEU*     3.3    24.7    -      -       +      +
     91J  ILE*     3.5     3.9    -      -       -      -
     92J  ALA      2.8    36.0    +      -       -      +
     98J  THR*     4.5     2.7    -      -       -      -
     99J  VAL*     3.2    23.6    -      -       +      -
    100J  TRP*     1.3    74.1    -      -       -      +
    102J  ALA*     1.3    58.9    +      -       -      +
    109J  VAL*     4.8     6.7    -      -       +      -
    110J  TYR*     3.4    12.8    -      -       -      +
    111J  LYS*     3.7    30.3    -      -       +      -
    112J  THR*     5.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 102 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40J  LEU*     3.9     0.2    -      -       -      +
     90J  MET      3.4     6.3    -      -       -      -
     91J  ILE*     3.8     9.4    -      -       +      -
    100J  TRP      4.2     0.8    +      -       -      -
    101J  PHE*     1.3    75.1    -      -       -      +
    103J  ALA*     1.3    64.9    +      -       -      +
    108J  GLY      4.6     0.7    -      -       -      -
    109J  VAL*     3.6     6.2    -      -       -      +
    110J  TYR*     2.8    58.0    +      -       +      +
    111J  LYS*     4.7     0.4    -      -       -      +
    112J  THR*     5.0     4.7    -      -       -      +
    124J  CYS*     3.7    21.5    -      -       +      -
    125J  PRO*     4.4     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 103 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40J  LEU*     3.8    17.3    -      -       +      -
     44J  VAL*     4.3     3.6    -      -       +      -
     88J  TYR*     3.3    13.5    -      -       -      -
     89J  CYS*     3.8     0.3    -      -       -      -
     90J  MET*     2.9    49.2    +      -       +      +
    102J  ALA*     1.3    79.8    -      -       -      +
    104J  THR*     1.3    61.8    +      -       -      +
    108J  GLY      3.5     7.4    -      -       -      -
    109J  VAL*     4.1    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 104 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44J  VAL*     5.3     1.0    -      -       -      +
     88J  TYR*     3.7    16.2    +      -       -      +
    103J  ALA*     1.3    77.4    -      -       -      +
    105J  PRO*     1.4    70.4    -      -       -      +
    106J  ASP*     2.7    23.5    +      -       -      -
    107J  LYS*     3.2    17.6    +      -       +      +
    108J  GLY*     2.9    29.9    +      -       -      +
    110J  TYR*     4.2    10.3    -      -       +      +
    124J  CYS*     3.5    36.8    -      -       +      -
    125J  PRO*     5.1     2.0    -      -       -      +
----------------------------------------------------------
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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