Contacts of the strand formed by residues 268 - 276 (chain F) in PDB entry 1F1H


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 MET 268 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128F  PRO*     3.8    25.8    -      -       +      -
    129F  GLU      3.4     4.3    -      -       -      -
    130F  PRO*     3.8    24.7    -      -       +      -
    235F  ILE*     4.2    13.9    -      -       +      -
    239F  LYS*     6.4     0.4    -      -       -      -
    267F  GLY*     1.3    73.7    -      -       -      +
    269F  HIS*     1.3    67.3    +      -       -      +
    270F  CYS*     3.4     5.9    -      -       -      -
    321F  ARG*     4.4     0.2    -      -       -      +
    361F  PRO*     2.7    34.5    +      -       +      +
    362F  ASP      3.6    28.3    -      -       -      +
    363F  PRO*     3.7    11.4    -      -       +      +
    365F  ALA*     4.3    18.6    -      -       +      +
    367F  PRO*     5.2     4.9    -      -       +      -
    370F  CYS*     4.9     1.8    -      -       -      -
    371F  PHE*     4.3    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 269 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  ASP*     5.6     4.5    -      -       -      -
    127F  GLY      3.7     1.4    -      -       -      +
    128F  PRO*     3.1     4.3    -      -       -      +
    129F  GLU*     2.7    46.3    +      -       +      +
    131F  GLU*     5.7     7.2    +      -       -      -
    267F  GLY*     5.1     2.6    -      -       -      -
    268F  MET*     1.3    75.6    -      -       -      +
    270F  CYS*     1.3    60.1    +      -       -      +
    271F  HIS      4.0     0.4    -      -       -      -
    321F  ARG*     4.5     9.2    +      -       -      -
    329F  PRO*     5.6     1.2    -      -       -      +
    357F  GLU*     3.0    16.6    +      -       +      +
    358F  VAL      3.5     7.0    -      -       -      +
    359F  ARG*     3.4    61.4    +      -       +      +
    470F   MN      2.3    32.6    +      -       -      -
   1476F  ADP      4.8     3.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 270 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126F  PHE*     4.7    11.7    -      -       +      -
    127F  GLY      4.0     2.9    -      -       -      -
    128F  PRO*     4.4     7.2    -      -       -      -
    268F  MET*     3.4    18.4    -      -       -      -
    269F  HIS*     1.3    75.3    -      -       -      +
    271F  HIS*     1.3    61.8    +      -       -      +
    272F  MET*     3.7     9.1    +      -       +      +
    356F  ILE      3.6     1.4    -      -       -      +
    357F  GLU*     3.4     1.6    -      -       -      -
    358F  VAL*     2.8    39.8    +      -       +      +
    361F  PRO*     4.3    13.9    -      -       -      -
    370F  CYS*     5.0     0.9    -      -       -      -
    371F  PHE*     4.0    27.1    -      -       -      -
    374F  LEU*     4.5    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 271 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126F  PHE*     3.5     1.7    -      -       -      +
    127F  GLY      2.9    45.8    +      -       -      +
    129F  GLU*     3.1    21.6    +      -       -      -
    269F  HIS*     5.1     0.4    -      -       +      -
    270F  CYS*     1.3    72.8    -      -       -      +
    272F  MET*     1.3    63.5    +      -       -      +
    344F  ARG*     4.8     3.4    -      -       -      -
    346F  PRO*     4.1     9.6    -      -       +      +
    355F  ARG*     2.9    30.2    +      -       -      -
    356F  ILE      3.2     5.6    -      -       -      +
    357F  GLU*     3.0    42.6    +      -       +      +
   1476F  ADP      3.2    48.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with MET 272 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124F  VAL*     6.0     1.1    -      -       +      -
    125F  LEU      3.2     8.5    -      -       -      +
    126F  PHE*     3.5    42.8    -      -       +      -
    270F  CYS*     3.9     9.9    -      -       +      +
    271F  HIS*     1.3    79.2    -      -       -      +
    273F  SER*     1.3    61.7    +      -       -      +
    282F  PHE*     4.0     2.3    -      -       -      -
    297F  TYR*     3.6    26.9    -      -       +      +
    301F  VAL*     5.2     0.2    -      -       +      -
    355F  ARG*     3.0    21.6    -      -       -      +
    356F  ILE*     2.8    35.0    +      -       +      +
    358F  VAL*     3.2    36.3    -      -       +      -
    374F  LEU*     3.9    17.9    -      -       +      -
   1476F  ADP      4.5     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 273 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124F  VAL*     3.9     2.9    -      -       -      +
    125F  LEU*     2.9    40.8    +      -       -      +
    272F  MET*     1.3    78.8    -      -       -      +
    274F  LEU*     1.3    65.7    +      -       -      +
    275F  ALA*     5.7     0.2    -      -       -      +
    280F  ASN*     3.9    11.9    +      -       -      -
    282F  PHE*     3.8    11.9    -      -       -      -
    297F  TYR*     6.1     0.4    -      -       -      -
    354F  ARG      3.7    17.5    -      -       -      -
    355F  ARG*     3.9     0.7    -      -       -      -
   1476F  ADP      2.9    29.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 274 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115F  LEU*     3.9    17.9    -      -       +      -
    120F  ILE*     4.8     3.4    -      -       +      -
    121F  ALA*     4.0    14.1    -      -       +      -
    123F  THR      3.7     8.7    -      -       -      +
    124F  VAL*     3.3    32.5    -      -       +      -
    273F  SER*     1.3    76.1    +      -       -      +
    275F  ALA*     1.3    63.5    +      -       -      +
    280F  ASN*     3.4     8.0    -      -       -      +
    281F  LEU*     3.1    26.6    +      -       +      +
    282F  PHE*     3.5    29.5    -      -       +      -
    293F  GLN*     5.1     2.0    -      -       -      +
    297F  TYR*     3.8    22.0    -      -       +      -
    375F  LEU*     4.4     3.8    -      -       +      -
    379F  LEU*     4.3     9.6    -      -       +      -
    382F  ILE*     4.1    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 275 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121F  ALA*     3.2     4.4    -      -       -      +
    122F  ASP*     2.8    30.1    +      -       -      +
    123F  THR*     3.1    25.2    +      -       -      +
    125F  LEU*     5.0    13.7    -      -       +      -
    273F  SER*     5.7     0.2    -      -       -      +
    274F  LEU*     1.3    78.3    -      -       -      +
    276F  LYS*     1.3    61.4    +      -       -      +
    278F  GLY*     5.2     4.7    -      -       -      +
    279F  THR      3.2    19.7    -      -       -      +
    280F  ASN*     4.7     1.8    -      -       -      -
    281F  LEU*     4.0     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 276 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119F  GLY*     2.9    35.7    +      -       -      +
    120F  ILE      4.6     3.6    -      -       -      +
    121F  ALA*     4.3    11.8    -      -       -      +
    122F  ASP*     3.2    17.0    +      -       -      +
    275F  ALA*     1.3    74.3    -      -       -      +
    277F  ASN*     1.3    89.6    +      -       -      +
    278F  GLY      3.2     0.9    -      -       -      -
    279F  THR*     2.8    25.5    +      -       -      -
    281F  LEU*     3.5    18.4    -      -       +      +
----------------------------------------------------------
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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