Contacts of the helix formed by residues 308 - 319 (chain 2) in PDB entry 1O1F


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 308 (chain 2).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2192  VAL*     3.0    19.2    -      -       -      +
    2212  LEU*     4.7     5.4    -      -       -      +
    3072  PRO*     1.3    72.2    -      -       -      +
    3092  ILE*     1.3    63.1    +      -       -      +
    3102  ALA*     3.3     4.2    -      -       -      +
    3112  ASP*     4.0    21.4    -      -       -      +
    3122  ARG*     3.3    21.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 309 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1532  LEU*     5.7     4.3    -      -       +      -
    2192  VAL*     3.9    15.7    -      -       +      -
    2612  LEU*     4.3    14.1    -      -       +      -
    2622  PHE*     4.6     8.1    -      -       +      -
    2742  ILE*     6.2     2.7    -      -       +      -
    2992  MET*     4.3    14.4    -      -       +      -
    3032  THR      3.9     7.0    -      -       -      +
    3042  THR*     3.2    50.9    -      -       +      +
    3062  TYR*     3.2    26.5    -      -       +      +
    3072  PRO      3.2     1.0    -      -       -      -
    3082  GLY*     1.3    77.6    -      -       -      +
    3102  ALA*     1.3    74.8    +      -       +      +
    3122  ARG*     3.8     2.6    +      -       -      +
    3132  MET*     3.0    33.2    +      -       +      +
    3352  ARG*     3.5    13.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 310 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2992  MET*     4.0    22.9    -      -       +      -
    3082  GLY*     5.2     1.3    -      -       -      +
    3092  ILE*     1.3    81.3    -      -       +      +
    3112  ASP*     1.4    54.4    +      -       -      +
    3132  MET*     3.1     4.0    +      -       -      +
    3142  GLN*     2.8    38.5    +      -       +      +
    3292  ILE*     4.1    15.3    -      -       +      +
    3312  ALA*     4.1    13.7    -      -       +      -
    3352  ARG*     5.5     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 311 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2212  LEU*     3.8    32.4    -      -       +      +
    3082  GLY*     3.8    16.3    +      -       -      +
    3102  ALA*     1.4    72.8    -      -       -      +
    3122  ARG*     1.3    65.5    +      -       -      +
    3142  GLN*     3.2    11.3    -      -       -      +
    3152  LYS*     3.0    27.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 312 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2192  VAL*     3.6    12.8    -      -       +      -
    2202  ALA      3.0    24.0    +      -       -      +
    2212  LEU*     3.8    11.7    -      -       -      +
    2222  ASP      4.9     2.7    -      -       -      +
    2232  PHE*     2.9    40.8    -      -       -      +
    2622  PHE*     3.3    26.2    -      -       +      +
    2632  GLN*     3.4    26.7    +      -       -      +
    3082  GLY      3.3    15.4    +      -       -      +
    3092  ILE      3.9     2.9    -      -       -      +
    3112  ASP*     1.3    78.2    -      -       -      +
    3132  MET*     1.3    51.6    +      -       -      +
    3152  LYS*     3.3     4.1    +      -       -      +
    3162  GLU*     2.7    76.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 313 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1532  LEU*     4.5     8.7    -      -       +      -
    2622  PHE*     4.2    11.0    -      -       +      -
    2742  ILE*     3.9    17.7    -      -       +      -
    2752  HIS*     3.4    33.7    -      -       -      -
    2782  THR*     3.0    36.6    -      -       +      +
    2972  ASN*     4.4    11.0    -      -       -      +
    2992  MET*     4.8    10.1    -      -       -      -
    3092  ILE*     3.0    25.1    +      -       +      +
    3102  ALA*     3.1     4.9    +      -       -      +
    3122  ARG*     1.3    72.7    -      -       -      +
    3142  GLN*     1.3    59.2    +      -       -      +
    3162  GLU*     3.6     1.5    -      -       -      +
    3172  ILE*     2.9    39.5    +      -       +      +
    3292  ILE*     4.1    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 314 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    3102  ALA*     2.8    12.5    +      -       +      +
    3112  ASP*     3.2    16.8    -      -       -      +
    3132  MET*     1.3    76.1    -      -       -      +
    3152  LYS*     1.3    61.3    +      -       +      +
    3182  THR*     2.8    34.8    +      -       -      +
    3272  ILE*     3.5    32.3    +      -       -      +
    3282  LYS*     4.3     2.0    -      -       -      +
    3292  ILE*     3.5    31.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 315 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2212  LEU*     6.3     4.0    -      -       +      -
    3112  ASP      3.0    11.9    +      -       -      +
    3122  ARG*     4.0     3.4    -      -       -      +
    3142  GLN*     1.3    82.7    -      -       +      +
    3162  GLU*     1.3    66.8    +      -       +      +
    3182  THR*     3.1    34.7    +      -       +      +
    3192  ALA*     3.5    30.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 316 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2622  PHE*     4.6     2.5    -      -       +      -
    2752  HIS*     3.2    56.7    +      -       +      -
    3122  ARG*     2.7    60.5    +      -       -      +
    3132  MET*     3.2     8.3    +      -       -      +
    3152  LYS*     1.3    81.1    -      -       -      +
    3172  ILE*     1.3    61.6    +      -       -      +
    3192  ALA*     3.9     3.9    +      -       -      +
    3202  LEU*     3.8    16.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 317 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2752  HIS*     3.8    22.4    -      -       +      +
    2782  THR*     4.1    15.7    -      -       +      -
    2792  TYR*     5.1     5.6    -      -       +      +
    2942  TYR*     4.0    25.6    -      -       +      +
    2972  ASN*     3.9    13.7    -      -       -      +
    3132  MET*     2.9    28.1    +      -       +      +
    3162  GLU*     1.3    77.4    -      -       -      +
    3182  THR*     1.3    66.7    +      -       -      +
    3192  ALA      3.2     1.8    -      -       -      -
    3202  LEU*     3.0     5.9    +      -       +      +
    3212  ALA*     2.9    25.1    +      -       -      +
    3272  ILE*     3.7    26.0    -      -       +      -
    3292  ILE*     3.6    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 318 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    3142  GLN*     2.8    31.1    +      -       -      +
    3152  LYS*     3.1    31.0    +      -       +      +
    3172  ILE*     1.3    72.7    -      -       -      +
    3192  ALA*     1.3    60.9    +      -       -      +
    3202  LEU      3.1     5.7    +      -       -      -
    3212  ALA*     3.1    20.4    +      -       -      +
    3232  SER*     5.8     0.9    -      -       -      -
    3252  MET      6.1     0.4    -      -       -      +
    3272  ILE*     3.7    29.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 319 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    3152  LYS*     3.5    28.2    +      -       -      +
    3162  GLU      4.0     4.7    -      -       -      +
    3172  ILE      3.2     0.2    -      -       -      -
    3182  THR*     1.3    79.7    +      -       -      +
    3202  LEU*     1.3    59.1    +      -       -      +
    3212  ALA      4.8     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