Contacts of the strand formed by residues 267 - 273 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  PHE*     3.9    13.5    -      -       +      -
    104A  GLN*     5.7     1.1    -      -       +      -
    105A  THR      4.0     1.1    -      -       -      -
    107A  GLY*     3.5     7.1    -      -       -      +
    255A  SER*     3.6     4.7    +      -       -      -
    256A  TYR*     2.7    40.5    +      -       +      +
    257A  SER*     3.9     5.8    +      -       -      -
    262A  LEU*     3.9    26.0    +      -       +      +
    265A  GLU      4.1     5.4    -      -       -      -
    266A  ARG*     1.3    78.0    -      -       -      +
    268A  GLY*     1.3    54.4    +      -       -      +
    302A  GLY*     3.7    24.5    -      -       -      -
    303A  ALA*     3.7    29.4    -      -       +      +
    306A  VAL*     3.8    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 268 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  PHE*     3.8     8.6    -      -       -      -
    104A  GLN*     3.6     4.0    -      -       -      +
    105A  THR*     2.7    32.5    +      -       -      +
    107A  GLY      3.6    12.3    -      -       -      +
    254A  SER      2.9    14.8    -      -       -      -
    255A  SER*     3.9     1.3    -      -       -      -
    256A  TYR*     4.3     4.7    -      -       -      -
    267A  VAL*     1.3    76.8    -      -       -      +
    269A  ALA*     1.3    63.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 269 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  PHE*     3.9    14.6    -      -       +      -
     83A  THR*     4.1     9.2    -      -       +      -
    102A  THR*     3.5    19.1    -      -       +      -
    103A  ALA      3.2    12.8    -      -       -      +
    105A  THR*     3.4     1.9    +      -       -      -
    111A  ALA*     3.3    12.8    -      -       -      +
    252A  VAL      3.4     1.2    -      -       -      +
    253A  ALA*     3.3     1.0    -      -       -      -
    254A  SER*     2.7    44.9    +      -       -      +
    256A  TYR*     5.0     0.7    -      -       +      -
    268A  GLY*     1.3    77.3    -      -       -      +
    270A  CYS*     1.3    60.5    +      -       -      +
    271A  THR*     4.0     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 270 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  ARG      3.8     1.4    -      -       -      +
    102A  THR*     3.4     0.9    -      -       -      -
    103A  ALA*     2.8    37.4    +      -       +      +
    105A  THR*     4.1    15.0    -      -       +      +
    111A  ALA*     3.4    26.7    -      -       +      +
    114A  VAL*     4.8     2.5    -      -       +      -
    115A  ALA*     3.9    13.0    -      -       -      -
    251A  ILE*     4.1     9.4    -      -       -      -
    252A  VAL      3.2     4.3    -      -       -      -
    253A  ALA*     5.4     0.2    -      -       -      -
    269A  ALA*     1.3    73.6    -      -       -      +
    271A  THR*     1.3    61.6    +      -       -      +
    272A  LEU      4.1     0.3    +      -       -      -
    287A  MET*     3.5    36.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 271 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83A  THR*     4.5     1.0    -      -       -      +
     84A  GLN*     4.5     0.2    -      -       +      -
     87A  LEU*     3.5    20.6    -      -       +      +
     88A  PHE*     3.7    33.9    -      -       +      -
    100A  ALA*     4.1    11.9    -      -       +      -
    101A  ARG      3.5     6.1    -      -       -      +
    102A  THR*     2.9    32.3    +      -       -      +
    250A  LEU      3.8     0.3    -      -       -      +
    251A  ILE*     3.2     7.6    -      -       -      +
    252A  VAL*     2.7    46.2    +      -       +      +
    254A  SER*     5.4     0.5    +      -       -      -
    269A  ALA*     4.7     1.0    -      -       -      +
    270A  CYS*     1.3    74.5    +      -       -      +
    272A  LEU*     1.3    60.8    +      -       -      +
    273A  VAL*     4.3     1.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 272 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100A  ALA*     3.4     5.9    -      -       -      -
    101A  ARG      3.0    31.8    +      -       -      +
    118A  PHE*     3.8    17.5    -      -       +      -
    250A  LEU      3.6     1.1    -      -       -      +
    251A  ILE*     3.5    27.4    -      -       +      -
    270A  CYS      4.1     1.4    +      -       -      -
    271A  THR*     1.3    71.9    -      -       -      +
    273A  VAL*     1.3    60.9    +      -       -      +
    280A  VAL*     3.6    13.7    -      -       +      +
    283A  ALA*     3.6    31.6    -      -       +      -
    284A  PHE*     4.0    19.1    -      -       +      +
    287A  MET*     3.7    21.3    -      -       +      -
      6B  PHE*     3.8    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 273 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  PHE*     4.0    13.0    -      -       +      -
     94A  LEU*     3.4    36.8    -      -       +      -
     99A  ARG*     3.6    18.2    -      -       -      +
    100A  ALA*     3.8    12.3    -      -       +      -
    244A  ALA*     6.4     0.2    -      -       -      -
    247A  HIS      5.5     1.1    -      -       -      +
    248A  LYS      3.6    13.0    -      -       -      +
    249A  GLU*     3.0     4.7    -      -       -      -
    250A  LEU*     2.6    54.5    +      -       +      +
    252A  VAL*     5.9     0.7    -      -       +      -
    271A  THR*     4.3     3.1    -      -       +      +
    272A  LEU*     1.3    82.1    -      -       -      +
    274A  ALA*     1.3    62.6    +      -       -      +
      6B  PHE*     3.3     9.7    -      -       -      -
----------------------------------------------------------
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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