Contacts of the strand formed by residues 173 - 179 (chain D) 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 GLN 173 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162D  ALA*     3.6    24.5    -      -       +      +
    165D  PHE*     3.6     9.3    +      -       -      +
    166D  MET*     3.6    14.1    -      -       -      +
    169D  ASP*     5.2     0.7    -      -       -      +
    171D  GLU*     2.9    30.9    +      -       -      +
    172D  ASN*     1.3    79.6    +      -       -      +
    174D  SER*     1.3    58.4    +      -       -      +
    458D  PHE*     3.2     7.8    +      -       -      +
    459D  ILE*     3.6    23.6    -      -       +      -
    460D  GLY*     3.0    20.6    +      -       -      -
    667D  THR*     3.0    16.7    +      -       -      +
    668D  HIS*     2.6    38.9    +      -       -      +
    670D  HIS*     3.2    25.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with SER 174 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173D  GLN*     1.3    73.5    -      -       -      +
    175D  ILE*     1.3    61.3    +      -       -      +
    176D  LEU*     3.3    13.3    -      -       -      +
    249D  PHE*     5.5     1.1    -      -       -      -
    460D  GLY*     3.0    14.8    -      -       -      -
    462D  LEU*     6.3     0.4    -      -       -      -
    490D  PHE*     5.1     0.3    -      -       -      -
    664D  LEU*     4.7    14.9    +      -       -      +
    667D  THR*     2.9    27.7    -      -       -      +
    668D  HIS      3.2     2.8    +      -       -      -
    669D  PRO*     3.1    16.5    -      -       -      +
    670D  HIS*     2.7    38.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 175 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158D  ILE*     4.0    21.3    -      -       +      -
    159D  SER*     4.8     1.6    -      -       -      -
    162D  ALA*     4.5     9.9    -      -       +      -
    174D  SER*     1.3    79.7    -      -       -      +
    176D  LEU*     1.3    64.9    +      -       -      +
    177D  ILE*     3.5    26.5    -      -       +      -
    192D  VAL*     4.7    10.5    -      -       +      -
    196D  PHE*     4.2    18.6    -      -       +      -
    459D  ILE*     4.2    22.7    -      -       +      -
    460D  GLY      2.7     9.7    +      -       -      +
    461D  VAL*     4.3     9.6    -      -       +      +
    462D  LEU*     3.0    26.2    +      -       -      +
    670D  HIS*     2.9     7.6    -      -       +      +
    672D  VAL*     3.8    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 176 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174D  SER*     3.3    25.1    -      -       -      +
    175D  ILE*     1.3    79.5    -      -       -      +
    177D  ILE*     1.4    62.9    -      -       -      +
    178D  THR*     5.9     0.7    -      -       -      +
    462D  LEU*     3.6    32.8    -      -       +      -
    487D  LEU*     4.6    10.3    -      -       +      -
    490D  PHE*     4.5    10.5    -      -       +      -
    664D  LEU*     4.4    16.6    -      -       +      -
    669D  PRO*     4.5     2.9    -      -       +      -
    670D  HIS      2.7    29.0    +      -       -      +
    671D  PHE*     4.2    21.8    -      -       +      -
    672D  VAL      2.8    25.9    +      -       -      +
    673D  ARG*     3.0    17.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 177 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155D  ILE*     6.2     0.2    -      -       +      -
    175D  ILE*     3.5    23.8    -      -       +      -
    176D  LEU*     1.4    70.6    -      -       -      +
    178D  THR*     1.3    70.0    +      -       -      +
    185D  LYS*     3.6    22.1    -      -       +      +
    188D  ASN*     4.8     4.0    -      -       +      -
    189D  THR*     4.4    23.1    -      -       +      +
    192D  VAL*     4.4    10.5    -      -       +      -
    461D  VAL*     4.0    20.6    -      -       +      -
    462D  LEU*     2.9    22.7    +      -       -      +
    463D  ASP*     4.0     2.5    -      -       -      -
    464D  ILE      3.7    12.6    +      -       -      +
    672D  VAL*     3.4    24.7    -      -       +      +
    674D  CYS*     3.5    27.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 178 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176D  LEU*     5.4     0.3    -      -       -      +
    177D  ILE*     1.3    81.5    +      -       -      +
    179D  GLY*     1.4    61.3    +      -       -      +
    185D  LYS*     4.3     3.8    -      -       -      -
    462D  LEU*     5.7     3.1    -      -       -      +
    464D  ILE*     3.5    16.7    +      -       -      +
    465D  ALA      4.2     2.8    +      -       -      -
    466D  GLY*     4.6    11.0    -      -       -      -
    484D  ASN*     4.0    14.2    +      -       -      +
    487D  LEU*     5.4     4.0    -      -       -      +
    672D  VAL      3.3     4.9    +      -       -      -
    673D  ARG*     3.6    39.7    +      -       -      +
    674D  CYS*     2.9    26.2    +      -       -      +
    697D  CYS      5.8     1.1    -      -       -      +
    698D  ASN*     4.8    12.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 179 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178D  THR*     1.4    78.9    -      -       -      +
    180D  GLU*     1.3    63.2    +      -       -      -
    183D  ALA*     4.1     4.7    -      -       -      -
    185D  LYS*     2.9    25.5    -      -       -      +
    464D  ILE      4.3     1.0    +      -       -      -
    465D  ALA*     4.2     1.4    -      -       -      +
    466D  GLY*     3.8    17.9    +      -       -      +
    674D  CYS*     3.7    15.3    -      -       -      -
    698D  ASN*     5.4     3.8    -      -       -      -
----------------------------------------------------------
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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