Contacts of the strand formed by residues 99 - 104 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  ASP*     4.7     0.3    -      -       -      +
     93A  GLY*     4.7     2.6    -      -       -      -
     94A  HIS      5.3     0.3    +      -       -      -
     98A  THR*     1.3    98.8    +      -       -      +
    100A  TRP*     1.3    61.2    +      -       -      +
    101A  PHE*     3.2    23.2    -      -       +      -
    111A  LYS*     4.0    30.7    -      -       +      +
    112A  THR      3.4    19.7    -      -       -      +
    113A  ASN*     4.2     6.5    -      -       -      +
    114A  THR      3.3    21.5    -      -       -      +
    115A  ALA*     4.2     3.4    -      -       +      -
    116A  VAL*     3.6    15.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 100 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77A  THR*     3.2    37.7    -      -       +      -
     91A  ILE*     3.6    20.2    -      -       +      -
     92A  ALA      3.8     2.9    -      -       -      -
     93A  GLY*     3.6    26.0    -      -       -      -
     99A  VAL*     1.3    76.8    -      -       -      +
    101A  PHE*     1.3    59.9    +      -       -      +
    111A  LYS*     3.7     2.3    -      -       -      -
    112A  THR*     3.0    41.8    +      -       +      +
    114A  THR*     3.2    13.8    +      -       +      -
    115A  ALA      2.9    30.6    +      -       -      -
    116A  VAL*     3.7    14.3    -      -       +      +
    118A  SER      3.5    12.2    +      -       -      -
    119A  SER      3.6     3.4    +      -       -      -
    120A  GLN*     3.7    41.1    -      -       +      -
    121A  PRO*     3.6    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 101 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  ASP*     3.8    42.2    -      -       +      -
     36A  VAL*     3.6    17.3    -      -       +      -
     37A  THR*     3.3    24.2    -      -       +      -
     40A  LEU*     3.3    24.1    -      -       +      +
     91A  ILE*     3.5     3.6    -      -       -      -
     92A  ALA      2.8    37.0    +      -       -      +
     98A  THR*     4.5     2.9    -      -       -      -
     99A  VAL*     3.2    23.3    -      -       +      -
    100A  TRP*     1.3    72.7    -      -       -      +
    102A  ALA*     1.3    60.0    +      -       -      +
    109A  VAL*     4.8     5.6    -      -       +      -
    110A  TYR*     3.4    13.0    -      -       -      +
    111A  LYS*     3.7    31.2    -      -       +      -
    112A  THR*     5.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 102 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  LEU*     3.9     0.3    -      -       -      +
     90A  MET      3.4     6.7    -      -       -      -
     91A  ILE*     3.8    10.7    -      -       +      +
    100A  TRP      4.2     1.0    +      -       -      -
    101A  PHE*     1.3    74.2    -      -       -      +
    103A  ALA*     1.3    65.6    +      -       -      +
    108A  GLY      4.6     0.9    -      -       -      -
    109A  VAL*     3.6     6.8    -      -       -      +
    110A  TYR*     2.8    57.9    +      -       +      +
    111A  LYS*     4.7     0.4    -      -       -      +
    112A  THR*     5.0     4.7    -      -       -      +
    124A  CYS*     3.7    21.3    -      -       +      -
    125A  PRO*     4.4     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 103 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  LEU*     3.8    17.5    -      -       +      -
     44A  VAL*     4.3     3.6    -      -       +      -
     88A  TYR*     3.3    13.0    -      -       -      -
     89A  CYS*     3.8     0.5    -      -       -      -
     90A  MET*     2.9    48.0    +      -       +      +
    102A  ALA*     1.3    79.2    -      -       -      +
    104A  THR*     1.3    62.9    +      -       -      +
    108A  GLY      3.5     7.6    -      -       -      -
    109A  VAL*     4.1    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 104 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  VAL*     5.3     1.0    -      -       -      +
     88A  TYR*     3.7    14.9    +      -       -      +
    103A  ALA*     1.3    78.3    -      -       -      +
    105A  PRO*     1.4    71.8    -      -       -      +
    106A  ASP*     2.7    23.0    +      -       -      +
    107A  LYS*     3.2    18.0    +      -       +      +
    108A  GLY*     2.9    30.1    +      -       -      -
    110A  TYR*     4.2    11.0    -      -       +      +
    124A  CYS*     3.5    36.6    -      -       +      -
    125A  PRO*     5.1     1.8    -      -       -      +
     24E  LEU*     5.3     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