Contacts of the strand formed by residues 267 - 273 (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 VAL 267 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79B  PHE*     3.9    18.2    -      -       +      -
    104B  GLN*     5.8     0.7    -      -       +      -
    105B  THR      4.1     0.4    -      -       -      -
    107B  GLY*     3.7     5.9    -      -       -      +
    255B  SER*     3.8     4.7    +      -       -      -
    256B  TYR*     2.8    40.5    +      -       +      -
    257B  SER*     3.8     6.6    +      -       -      -
    262B  LEU*     4.0    23.1    +      -       +      +
    265B  GLU*     4.0     4.9    -      -       +      +
    266B  ARG*     1.3    78.1    -      -       -      +
    268B  GLY*     1.3    59.7    +      -       -      +
    302B  GLY*     3.7    30.1    -      -       -      +
    303B  ALA*     3.8    28.0    -      -       +      +
    306B  VAL*     4.0     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 268 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79B  PHE*     3.6    13.0    -      -       -      -
    104B  GLN*     3.6     0.7    -      -       -      +
    105B  THR*     2.8    31.4    +      -       -      -
    107B  GLY      3.6    11.0    -      -       -      +
    254B  SER      3.2    14.6    -      -       -      -
    255B  SER*     4.0     2.5    -      -       -      -
    256B  TYR*     4.2     5.4    -      -       -      -
    267B  VAL*     1.3    76.5    -      -       -      +
    269B  ALA*     1.3    64.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 269 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79B  PHE*     3.9    12.3    -      -       +      -
     83B  THR*     4.2     7.6    -      -       +      -
    102B  THR*     3.6    20.6    -      -       +      -
    103B  ALA      3.2    11.7    -      -       -      +
    105B  THR*     3.5     3.6    +      -       -      -
    111B  ALA*     3.5     7.0    -      -       -      +
    252B  VAL      3.3     2.6    -      -       -      +
    253B  ALA*     3.4     2.9    -      -       -      -
    254B  SER*     2.8    49.2    +      -       -      +
    256B  TYR*     5.0     0.9    -      -       +      -
    268B  GLY*     1.3    77.4    -      -       -      +
    270B  CYS*     1.3    60.3    -      -       -      +
    271B  THR*     4.0     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 270 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101B  ARG      3.8     1.6    -      -       -      +
    102B  THR*     3.3     1.4    -      -       -      -
    103B  ALA*     2.8    39.4    +      -       +      +
    105B  THR*     3.9    14.7    -      -       +      +
    111B  ALA*     3.4    25.8    -      -       -      +
    114B  VAL*     4.7     2.2    -      -       +      -
    115B  ALA*     4.0    16.8    -      -       -      -
    251B  ILE*     4.0    13.7    -      -       -      -
    252B  VAL      3.3     3.8    -      -       -      -
    253B  ALA*     5.3     0.2    -      -       -      -
    269B  ALA*     1.3    72.6    -      -       -      +
    271B  THR*     1.3    64.8    +      -       -      +
    272B  LEU      4.0     0.3    +      -       -      -
    287B  MET*     3.8    30.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 271 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83B  THR*     4.4     1.2    -      -       -      +
     84B  GLN*     4.5     0.7    -      -       +      -
     87B  LEU*     3.8    14.5    -      -       +      +
     88B  PHE*     3.9    32.3    -      -       +      -
    100B  ALA*     4.3     6.5    -      -       +      -
    101B  ARG      3.6     4.0    -      -       -      +
    102B  THR*     2.8    34.1    +      -       -      +
    250B  LEU      3.9     0.5    -      -       -      +
    251B  ILE*     3.3     8.5    -      -       -      +
    252B  VAL*     2.7    52.6    +      -       +      +
    254B  SER*     5.3     0.7    +      -       -      -
    269B  ALA*     4.7     1.0    -      -       -      +
    270B  CYS*     1.3    75.0    +      -       -      +
    272B  LEU*     1.3    67.3    +      -       -      +
    273B  VAL*     4.6     2.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 272 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  PHE*     3.7    16.2    -      -       +      -
    100B  ALA*     3.3     6.2    -      -       -      +
    101B  ARG      3.0    30.8    +      -       -      +
    118B  PHE*     3.7    23.8    -      -       +      -
    250B  LEU      3.8     0.2    -      -       -      -
    251B  ILE*     3.6    27.4    -      -       +      -
    270B  CYS      4.0     0.2    +      -       -      -
    271B  THR*     1.3    72.1    -      -       -      +
    273B  VAL*     1.3    64.4    +      -       -      +
    280B  VAL*     3.5    10.7    -      -       +      +
    283B  ALA*     3.7    28.0    -      -       +      -
    284B  PHE*     3.7    15.0    -      -       +      +
    287B  MET*     3.0    33.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 273 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  PHE*     4.3     4.4    -      -       -      -
     88B  PHE*     4.2    18.8    -      -       +      -
     94B  LEU*     4.0    18.4    -      -       +      -
     99B  ARG*     3.3    28.5    -      -       -      +
    100B  ALA*     4.4     2.0    -      -       +      -
    244B  ALA*     6.0     0.4    -      -       -      +
    247B  HIS      5.3     0.9    -      -       -      +
    248B  LYS      3.6    12.6    -      -       -      +
    249B  GLU*     2.8    34.1    -      -       -      +
    250B  LEU*     2.8    49.5    +      -       +      +
    271B  THR*     4.6     5.2    -      -       +      +
    272B  LEU*     1.3    79.3    -      -       -      +
    274B  ALA*     1.4    53.3    +      -       -      +
    280B  VAL*     4.2     0.4    -      -       -      -
----------------------------------------------------------
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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