Contacts of the strand formed by residues 267 - 280 (chain A) in PDB entry 1AF6


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 GLY 267 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236A  THR*     3.6     2.9    +      -       -      -
    237A  ASP*     2.8    32.1    +      -       -      +
    240A  THR*     4.3     2.9    -      -       -      -
    265A  ASN      3.3     1.4    +      -       -      -
    266A  ASN*     1.3    75.6    -      -       -      +
    268A  HIS*     1.3    66.5    +      -       -      +
    296A  ASN      3.3    10.5    -      -       -      -
    297A  TRP*     4.3     0.7    -      -       -      -
    298A  ASP*     3.8    11.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 268 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234A  TYR*     3.6    36.6    +      +       +      +
    235A  ALA      3.1    13.5    -      -       -      +
    236A  THR*     4.7     2.0    -      -       -      +
    240A  THR*     3.8     8.9    -      -       -      +
    267A  GLY*     1.3    77.9    -      -       -      +
    269A  MET*     1.3    69.5    +      -       -      +
    270A  LEU*     4.3     6.3    -      -       +      +
    294A  ASP*     4.4    10.1    +      -       -      -
    295A  ILE*     3.7     1.9    -      -       -      +
    296A  ASN*     2.9    63.0    +      -       +      +
    297A  TRP*     4.9     0.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 269 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  GLN*     6.0     0.4    -      -       -      -
    214A  LEU*     4.6     7.2    -      -       +      -
    233A  GLN*     4.0     2.4    -      -       +      +
    234A  TYR*     3.3     8.5    -      -       -      -
    235A  ALA*     2.7    53.4    +      -       +      +
    239A  MET      4.9     0.2    -      -       -      +
    240A  THR*     3.8    14.5    -      -       +      +
    243A  GLY*     3.6    31.9    -      -       -      +
    268A  HIS*     1.3    78.5    -      -       -      +
    270A  LEU*     1.3    70.8    +      -       -      +
    271A  ARG*     3.6    33.0    -      -       +      +
    293A  GLN*     3.9    15.9    -      -       +      +
    294A  ASP      3.1    11.7    -      -       -      +
    295A  ILE*     3.8    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 270 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  VAL*     4.5    10.5    -      -       +      -
    233A  GLN      3.6    12.8    -      -       -      +
    234A  TYR*     4.5    16.4    -      -       +      -
    268A  HIS*     4.3     8.4    -      -       +      +
    269A  MET*     1.3    76.2    -      -       -      +
    271A  ARG*     1.3    62.5    +      -       -      +
    272A  ILE*     4.2    30.7    -      -       +      -
    292A  TYR*     3.9    14.0    -      -       +      +
    293A  GLN*     3.5     2.1    -      -       -      -
    294A  ASP*     2.8    41.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 271 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  GLN*     4.3     5.1    -      -       -      +
    117A  PHE*     3.8    20.2    -      -       -      -
    119A  TYR*     3.2    22.6    +      -       -      +
    231A  VAL*     3.9     1.4    -      -       +      +
    232A  VAL*     3.3     4.5    -      -       -      +
    233A  GLN*     2.8    75.5    +      -       +      +
    243A  GLY*     2.9    32.9    +      -       -      -
    244A  LYS*     5.1     1.6    -      -       -      +
    269A  MET*     3.6    22.9    -      -       +      +
    270A  LEU*     1.3    73.9    -      -       -      +
    272A  ILE*     1.3    66.7    -      -       -      +
    273A  LEU*     4.6     6.7    -      -       +      -
    291A  MET*     3.8    26.9    -      -       +      -
    292A  TYR      3.5     3.6    -      -       -      +
    293A  GLN*     2.7    33.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 272 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230A  PHE*     4.0    27.6    -      -       +      -
    231A  VAL      3.5     4.7    -      -       -      +
    232A  VAL*     4.6    10.1    -      -       +      -
    270A  LEU*     4.2    30.3    -      -       +      -
    271A  ARG*     1.3    76.8    -      -       -      +
    273A  LEU*     1.3    63.4    +      -       -      +
    290A  GLY      4.8     0.2    -      -       -      -
    291A  MET*     3.3     3.0    -      -       -      +
    292A  TYR*     2.9    53.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 273 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  VAL*     4.0     5.8    -      -       +      -
    117A  PHE*     5.6     0.2    -      -       +      -
    119A  TYR*     3.6    47.6    -      -       +      -
    229A  LYS      3.9     0.3    -      -       -      +
    230A  PHE*     3.5     4.2    -      -       -      -
    231A  VAL*     2.6    56.1    +      -       +      +
    271A  ARG*     4.6     5.2    -      -       +      -
    272A  ILE*     1.3    77.2    -      -       -      +
    274A  ASP*     1.3    82.5    +      -       -      +
    275A  HIS*     3.9    13.2    -      -       +      -
    289A  VAL*     3.9    17.0    -      -       +      -
    290A  GLY      3.6    11.4    -      -       -      +
    291A  MET*     3.9    23.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 274 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228A  ASN*     2.6    41.5    +      -       -      +
    229A  LYS      3.2    10.9    -      -       -      +
    230A  PHE*     3.3    23.0    -      -       +      +
    273A  LEU*     1.3    77.0    -      -       -      +
    275A  HIS*     1.3    63.3    +      -       -      +
    288A  TYR*     3.6    10.0    -      -       -      -
    289A  VAL*     3.5     0.9    -      -       -      -
    290A  GLY*     2.9    36.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 275 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111A  ASP      3.5    21.5    -      -       -      -
    112A  VAL*     3.9    23.8    -      -       +      +
    113A  HIS      5.5     0.6    +      -       -      -
    119A  TYR*     3.1    24.2    +      -       -      -
    227A  PHE*     4.4    10.3    -      +       -      -
    228A  ASN*     3.5     0.7    +      -       -      -
    229A  LYS*     2.6    72.6    +      -       +      +
    231A  VAL*     4.8     0.9    -      -       +      -
    273A  LEU*     3.9    14.6    -      -       +      -
    274A  ASP*     1.3    78.0    +      -       -      +
    276A  GLY*     1.3    56.5    +      -       -      +
    288A  TYR*     3.3    22.4    -      -       -      +
    289A  VAL*     3.8    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 276 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    227A  PHE*     3.1    27.6    -      -       -      -
    275A  HIS*     1.3    80.1    +      -       -      +
    277A  ALA*     1.3    65.2    +      -       -      +
    287A  MET*     3.4     4.3    -      -       -      +
    288A  TYR*     3.2    40.6    +      -       -      +
    358A  TRP*     5.6     0.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 277 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226A  GLY*     3.2     6.5    -      -       -      -
    227A  PHE*     2.9    34.2    +      -       +      -
    276A  GLY*     1.3    76.1    -      -       -      +
    278A  ILE*     1.3    60.6    +      -       -      +
    286A  MET      3.1    11.2    -      -       -      +
    287A  MET*     4.0     9.4    -      -       +      -
    288A  TYR*     3.9     1.2    -      -       -      -
    357A  ILE*     4.7     5.4    -      -       +      -
    358A  TRP*     3.5    39.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 278 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223A  VAL*     4.0    22.0    -      -       +      +
    224A  LEU*     3.9    33.0    -      -       +      -
    226A  GLY*     4.6     1.3    -      -       -      -
    227A  PHE      4.2     9.6    -      -       -      +
    277A  ALA*     1.3    80.2    -      -       -      +
    279A  SER*     1.3    61.6    +      -       -      +
    280A  MET*     4.4    19.6    -      -       +      +
    285A  ASP*     3.4     4.6    -      -       -      +
    286A  MET*     2.8    53.6    +      -       +      +
    288A  TYR*     4.3    19.3    -      -       +      +
    357A  ILE*     5.8     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 279 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224A  LEU*     2.9    38.7    +      -       -      +
    225A  LYS*     3.9    31.6    +      -       -      +
    226A  GLY      4.9     0.4    -      -       -      +
    278A  ILE*     1.3    74.2    -      -       -      +
    280A  MET*     1.3    64.3    +      -       -      +
    281A  GLY      3.8     4.4    +      -       -      -
    284A  TRP      3.4     4.9    -      -       -      -
    285A  ASP*     2.5    24.6    +      -       -      -
    315A  LYS*     4.7     2.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 280 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224A  LEU*     5.4     5.6    -      -       +      -
    278A  ILE*     4.4    19.3    -      -       +      +
    279A  SER*     1.3    76.8    -      -       -      +
    281A  GLY*     1.3    61.6    +      -       -      +
    282A  ASP      3.9     0.2    +      -       -      -
    283A  ASN      4.4     0.2    +      -       -      -
    284A  TRP*     2.9    62.5    +      -       +      +
    285A  ASP      5.7     0.2    -      -       -      -
    286A  MET*     4.4    33.7    -      -       +      -
    312A  PRO*     6.3     0.9    -      -       +      -
----------------------------------------------------------
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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