Contacts of the helix formed by residues 257 - 274 (chain A) in PDB entry 2FW0


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 ASP 257 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  PHE*     4.8     0.2    -      -       -      -
    255A  LEU*     3.6    26.9    +      -       +      +
    256A  ASN*     1.3    73.3    +      -       -      +
    258A  ALA*     1.3    57.0    +      -       -      +
    259A  ASN*     3.6    10.0    +      -       -      +
    260A  ASN*     2.9    40.9    +      -       -      +
    261A  GLN*     3.0    26.4    +      -       -      +
    293A  VAL*     3.7    13.0    +      -       +      +
    294A  PRO      3.8    21.7    +      -       -      +
    296A  VAL*     4.6     8.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 258 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  PHE*     3.7    19.5    -      -       +      -
     19A  VAL*     3.4    31.6    -      -       +      -
     20A  VAL*     3.6    26.2    -      -       +      +
     23A  ALA*     5.0     0.2    -      -       -      -
    255A  LEU*     5.2     1.0    -      -       -      +
    256A  ASN      2.8    10.1    +      -       -      +
    257A  ASP*     1.3    68.5    -      -       -      +
    259A  ASN*     1.3    68.1    +      -       -      +
    261A  GLN*     3.2     1.8    +      -       -      +
    262A  ALA*     2.9    25.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 259 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  VAL*     5.0     7.0    -      -       -      +
     23A  ALA*     3.8    20.9    -      -       -      +
     27A  ASP*     4.7     1.2    -      -       -      +
    257A  ASP*     3.2     8.9    +      -       -      +
    258A  ALA*     1.3    80.0    -      -       -      +
    260A  ASN*     1.3    62.0    +      -       -      +
    262A  ALA*     3.4     2.8    +      -       -      +
    263A  LYS*     2.9    27.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 260 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257A  ASP*     2.9    34.4    +      -       -      +
    259A  ASN*     1.3    80.6    -      -       -      +
    261A  GLN*     1.3    66.6    +      -       -      +
    262A  ALA      3.2     0.2    -      -       -      -
    263A  LYS*     4.1    11.9    -      -       -      +
    264A  ALA*     3.0    25.3    +      -       -      +
    284A  TRP*     3.4    27.2    -      -       +      -
    293A  VAL*     3.7    14.7    -      -       +      +
    315A  MLA      5.1     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 261 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  PHE*     4.0    11.3    -      -       +      -
     17A  MET*     4.0     0.7    -      -       -      +
     20A  VAL*     3.6    16.4    -      -       +      +
     90A  PHE*     3.6    13.8    -      -       +      -
     91A  ASN*     2.9    53.5    +      -       -      +
    108A  VAL*     3.8    22.3    -      -       +      +
    109A  GLY*     4.1    11.9    -      -       -      -
    110A  THR*     5.1     1.6    +      -       -      +
    256A  ASN*     5.3     1.8    +      -       -      -
    257A  ASP      3.0    14.7    +      -       -      +
    258A  ALA*     3.2    10.1    +      -       -      +
    260A  ASN*     1.3    76.8    -      -       -      +
    262A  ALA*     1.3    58.0    +      -       -      +
    265A  THR*     2.8    37.9    +      -       -      +
    293A  VAL*     3.9    10.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 262 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  VAL*     3.7     9.1    -      -       +      +
     23A  ALA*     3.5    26.5    -      -       +      -
     24A  ILE*     3.4    31.1    -      -       +      +
     27A  ASP*     3.8     3.4    -      -       -      +
    258A  ALA      2.9    17.2    +      -       -      +
    259A  ASN      3.5     2.7    -      -       -      +
    261A  GLN*     1.3    75.5    -      -       -      +
    263A  LYS*     1.3    59.4    +      -       -      +
    265A  THR*     3.3     1.9    +      -       -      -
    266A  PHE*     2.9    31.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 263 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  ASP*     3.5    24.9    +      -       -      +
    259A  ASN      2.9    18.3    +      -       -      +
    260A  ASN*     3.4    12.1    +      -       -      +
    261A  GLN      3.3     0.2    -      -       -      -
    262A  ALA*     1.3    76.4    -      -       -      +
    264A  ALA*     1.3    53.2    +      -       -      +
    266A  PHE*     3.4     2.0    +      -       -      +
    267A  ASP*     2.7    59.8    +      -       -      +
    284A  TRP*     3.8    15.3    -      -       +      -
    315A  MLA      3.8    30.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 264 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  VAL*     3.8    21.8    -      -       +      -
    260A  ASN      3.0    17.7    +      -       -      +
    263A  LYS*     1.3    73.5    -      -       -      +
    265A  THR*     1.3    66.7    +      -       -      +
    268A  LEU*     3.0    31.8    +      -       +      +
    284A  TRP*     3.4    38.7    -      -       +      +
    291A  VAL*     4.1     8.5    -      -       +      -
    293A  VAL*     4.8     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 265 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  ILE*     4.4     8.3    -      -       +      -
     64A  ALA*     3.7    18.8    -      -       +      -
     88A  VAL*     4.2    11.0    -      -       +      +
     90A  PHE*     3.4    49.7    -      -       +      +
    108A  VAL*     3.6    13.9    -      -       -      +
    261A  GLN      2.8    23.1    +      -       -      -
    262A  ALA*     3.6     6.3    -      -       -      -
    264A  ALA*     1.3    76.9    -      -       -      +
    266A  PHE*     1.3    58.6    +      -       -      +
    268A  LEU*     4.0     0.9    -      -       -      +
    269A  ALA*     2.9    30.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 266 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  ILE*     4.2    12.1    -      -       +      -
     24A  ILE*     4.5    18.8    -      -       +      +
     27A  ASP*     3.8    31.9    -      -       +      +
     28A  ALA*     3.7    35.9    -      -       +      -
     31A  ALA*     3.8    16.6    -      -       +      -
     34A  VAL*     4.0    15.7    -      -       +      -
     36A  LEU*     4.3     4.7    -      -       +      -
    262A  ALA      2.9    17.2    +      -       -      +
    263A  LYS      3.8     2.0    -      -       -      +
    265A  THR*     1.3    75.6    -      -       -      +
    267A  ASP*     1.3    72.7    +      -       -      +
    269A  ALA*     3.2     3.7    +      -       +      +
    270A  LYS*     2.8    58.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 267 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263A  LYS*     2.7    49.0    +      -       -      +
    264A  ALA      3.9     0.9    -      -       -      +
    266A  PHE*     1.3    84.1    -      -       -      +
    268A  LEU*     1.3    63.9    +      -       -      +
    270A  LYS*     3.5     7.7    +      -       -      +
    271A  ASN*     3.0    28.9    +      -       -      +
    278A  ALA      4.4     1.6    -      -       -      -
    282A  THR*     4.0    16.5    -      -       +      +
    284A  TRP*     2.8    34.9    +      -       +      +
    315A  MLA      4.4     2.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 268 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  VAL*     4.0    12.1    -      -       +      -
    106A  TYR*     4.3    22.2    -      -       +      -
    107A  TYR      5.6     0.4    -      -       -      +
    108A  VAL*     4.4    10.8    -      -       +      -
    264A  ALA      3.0    20.2    +      -       -      +
    265A  THR      4.1     0.4    -      -       -      +
    267A  ASP*     1.3    74.4    -      -       +      +
    269A  ALA*     1.3    61.4    +      -       -      +
    271A  ASN*     3.3     1.6    +      -       -      +
    272A  LEU*     2.9    38.6    +      -       +      +
    278A  ALA*     3.5    29.4    -      -       +      +
    279A  ALA*     4.8     0.9    -      -       -      -
    284A  TRP*     4.0    32.1    -      -       +      -
    286A  ILE*     3.9    15.0    -      -       +      -
    289A  LYS      5.8     0.2    -      -       -      +
    291A  VAL*     3.9    22.2    -      -       +      -
----------------------------------------------------------
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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
----------------------------------------------------------
      5A  ILE*     4.1    19.5    -      -       +      -
     62A  ALA*     3.4    18.9    -      -       +      +
     63A  LEU      5.1     0.7    -      -       -      +
     64A  ALA*     4.8     9.0    -      -       +      -
     88A  VAL*     3.9    18.3    -      -       +      +
    265A  THR      2.9    19.8    +      -       -      +
    266A  PHE*     3.2     5.4    +      -       -      +
    268A  LEU*     1.3    77.2    -      -       -      +
    270A  LYS*     1.3    58.0    +      -       -      +
    272A  LEU*     3.4     1.6    +      -       -      -
    273A  ALA*     2.8    30.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 270 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  THR*     6.3     0.9    -      -       +      -
      5A  ILE*     3.9    12.7    -      -       +      +
     31A  ALA*     4.3     7.7    -      -       +      +
     33A  ASP*     5.0    11.4    +      -       -      +
     34A  VAL*     4.1    18.6    -      -       +      -
    266A  PHE*     2.8    46.9    +      -       +      +
    267A  ASP*     3.9     7.6    -      -       -      +
    269A  ALA*     1.3    75.3    -      -       -      +
    271A  ASN*     1.3    70.1    +      -       -      +
    273A  ALA*     3.2     3.5    +      -       +      +
    274A  ASP*     3.0    46.0    +      -       -      +
    276A  LYS*     5.4     5.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 271 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    267A  ASP      3.0    15.7    +      -       -      +
    268A  LEU      3.7     0.4    -      -       -      +
    270A  LYS*     1.3    81.3    -      -       -      +
    272A  LEU*     1.3    61.6    +      -       -      +
    274A  ASP*     3.1     7.5    +      -       -      +
    275A  GLY      3.1     4.5    +      -       -      -
    276A  LYS*     2.8    54.0    +      -       +      +
    277A  GLY      3.3    20.4    -      -       -      +
    278A  ALA      2.9    24.4    -      -       -      +
    279A  ALA*     3.7     1.0    -      -       -      -
    280A  ASP*     2.9    29.6    +      -       -      +
    282A  THR*     4.1     4.9    -      -       -      +
----------------------------------------------------------
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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
----------------------------------------------------------
     61A  LYS      4.6     0.2    -      -       -      +
     86A  PRO*     3.5    35.2    -      -       +      +
     88A  VAL*     3.8    18.2    -      -       +      -
    104A  LYS*     5.5     4.7    -      -       +      -
    106A  TYR*     3.6    44.6    -      -       +      +
    268A  LEU*     2.9    23.7    +      -       +      +
    269A  ALA*     3.9     3.1    -      -       -      +
    271A  ASN*     1.3    75.7    -      -       -      +
    273A  ALA*     1.3    62.6    -      -       -      +
    275A  GLY*     3.0    13.9    +      -       -      -
    276A  LYS      4.0    13.7    -      -       -      +
    278A  ALA*     4.0    19.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 273 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  THR*     3.8    18.3    -      -       +      +
      5A  ILE*     4.4     3.8    -      -       +      -
     61A  LYS*     3.5    52.9    -      -       +      +
     62A  ALA*     3.9     6.9    -      -       +      +
    269A  ALA      2.8    18.7    +      -       -      +
    270A  LYS*     3.5     9.2    -      -       -      +
    272A  LEU*     1.3    76.4    -      -       -      +
    274A  ASP*     1.3    61.9    +      -       -      +
    275A  GLY      3.2     1.1    +      -       -      -
----------------------------------------------------------
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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
----------------------------------------------------------
      3A  THR*     4.3    17.7    +      -       -      +
     33A  ASP*     4.8     9.0    -      -       -      +
    270A  LYS*     3.0    42.9    +      -       -      +
    271A  ASN*     3.1     6.7    +      -       -      +
    273A  ALA*     1.3    79.0    -      -       -      +
    275A  GLY*     1.3    59.4    +      -       -      +
    276A  LYS*     3.5    32.3    +      -       -      +
----------------------------------------------------------
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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