Contacts of the strand formed by residues 100 - 106 (chain B) in PDB entry 1AHF


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 ALA 100 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84B  GLN*     2.4    37.7    +      -       -      +
     88B  PHE*     4.2    21.1    -      -       +      -
     94B  LEU*     3.7    13.3    +      -       +      +
     98B  LYS*     3.5    16.1    +      -       -      -
     99B  ARG*     1.3    77.8    -      -       -      +
    101B  ARG*     1.3    63.0    -      -       -      +
    271B  THR*     4.3     2.9    -      -       +      -
    272B  LEU      3.3    10.5    -      -       -      +
    273B  VAL*     4.4     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 101 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74B  ASP*     4.7     5.7    +      -       -      -
     98B  LYS*     5.4     6.1    -      -       -      +
    100B  ALA*     1.3    77.4    -      -       -      +
    102B  THR*     1.3    60.3    +      -       -      +
    270B  CYS      3.8     1.0    -      -       -      +
    271B  THR*     3.6     0.7    -      -       -      -
    272B  LEU*     3.0    31.9    +      -       -      +
    280B  VAL*     4.0    21.5    -      -       +      +
    281B  ASP*     2.9    46.6    +      -       -      +
    284B  PHE*     3.2    58.0    -      -       +      +
    288B  LYS*     4.2    14.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 102 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74B  ASP*     3.9    11.1    -      -       -      +
     79B  PHE*     5.0     0.9    -      -       +      -
     80B  GLY*     4.2    24.1    -      -       -      -
     83B  THR*     4.3    13.7    -      -       -      +
     84B  GLN*     3.2    25.6    +      -       -      +
    101B  ARG*     1.3    71.2    -      -       -      +
    103B  ALA*     1.3    64.6    +      -       -      +
    104B  GLN      4.1     0.4    +      -       -      +
    269B  ALA*     3.6    24.0    -      -       +      -
    270B  CYS      3.3     3.6    -      -       -      +
    271B  THR*     2.8    28.4    +      -       -      +
    284B  PHE*     3.8     9.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 103 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74B  ASP*     3.6    13.7    -      -       +      -
    102B  THR*     1.3    75.3    -      -       -      +
    104B  GLN*     1.3    65.6    +      -       -      +
    105B  THR*     3.5     5.0    -      -       +      +
    269B  ALA*     3.2     4.7    -      -       -      +
    270B  CYS*     2.8    39.9    +      -       +      +
    284B  PHE*     4.0    19.7    -      -       +      -
    287B  MET*     5.0     1.8    -      -       +      -
    291B  ILE*     4.2    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 104 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71B  LEU*     4.0     5.9    -      -       -      +
     73B  ILE      4.6     2.3    -      -       -      +
     74B  ASP      3.0    15.1    +      -       -      +
     75B  GLY*     3.1     2.7    -      -       -      -
     76B  ILE*     2.8    39.4    +      -       -      +
     79B  PHE*     3.4    28.5    -      -       +      -
    102B  THR      4.1     0.2    -      -       -      -
    103B  ALA*     1.3    77.4    -      -       -      +
    105B  THR*     1.3    65.6    +      -       -      +
    266B  ARG      5.9     0.8    +      -       -      -
    267B  VAL*     5.8     0.4    -      -       +      -
    268B  GLY      3.6     7.4    -      -       -      +
    291B  ILE*     5.7     0.2    -      -       -      +
    295B  TYR*     3.9     4.0    +      -       -      -
    298B  PRO*     3.4    35.3    -      -       +      +
    299B  PRO*     3.0    29.1    +      -       -      +
    303B  ALA*     3.1    23.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 105 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103B  ALA*     3.5    17.5    -      -       +      +
    104B  GLN*     1.3    84.6    -      -       -      +
    106B  PRO*     1.3    70.5    -      -       -      +
    107B  GLY      2.9    26.0    +      -       -      -
    110B  GLY      4.1     2.7    -      -       -      +
    111B  ALA*     3.4    32.0    -      -       -      +
    114B  VAL*     4.8     6.1    -      -       +      -
    266B  ARG      3.4     4.9    -      -       -      +
    267B  VAL*     4.1     0.5    -      -       -      -
    268B  GLY      2.8    24.6    +      -       -      +
    270B  CYS*     3.9    11.2    -      -       +      +
    291B  ILE*     5.4     0.4    -      -       +      -
    295B  TYR*     3.9     8.7    -      -       -      +
    298B  PRO*     4.5     4.3    -      -       -      -
    299B  PRO*     5.1     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 106 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  PRO*     5.4     6.7    -      -       +      -
    295A  TYR*     3.9    24.3    -      -       +      +
    299A  PRO*     6.0     1.8    -      -       +      -
    105B  THR*     1.3    84.3    -      -       -      +
    107B  GLY*     1.3    57.2    +      -       -      +
    110B  GLY*     3.3    20.2    +      -       -      -
    266B  ARG*     3.5    35.2    +      -       +      +
    295B  TYR*     3.3    49.6    -      -       +      +
    298B  PRO*     4.4     5.4    -      -       +      -
    299B  PRO*     4.5    11.9    -      -       +      -
----------------------------------------------------------
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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