Contacts of the strand formed by residues 174 - 180 (chain C) in PDB entry 3F12


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 TYR 174 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10C  THR*     4.4    12.2    +      -       +      +
    139C  ASN*     3.2     5.0    +      -       -      -
    140C  PHE*     2.9    51.7    +      -       +      +
    141C  TYR*     3.6    20.4    -      +       -      -
    143C  ARG*     3.2    63.2    -      -       +      +
    164C  VAL*     3.9    18.8    -      -       +      -
    165C  THR*     3.8     4.0    -      -       -      -
    166C  GLU*     3.9     4.7    -      -       -      -
    167C  GLN*     3.1    57.7    +      -       +      +
    172C  SER      4.2     4.5    -      -       -      -
    173C  THR*     1.3    74.5    -      -       -      +
    175C  SER*     1.3    61.4    +      -       -      +
    176D  HIS*     5.7     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 175 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137C  LEU      3.2     7.4    -      -       -      -
    138C  ASN*     2.4    34.1    +      -       -      -
    139C  ASN      3.4     4.0    +      -       -      -
    140C  PHE*     3.6     2.5    -      -       -      -
    164C  VAL*     3.4     5.7    -      -       -      +
    165C  THR*     2.6    41.3    +      -       -      -
    174C  TYR*     1.3    70.3    -      -       -      +
    176C  LEU*     1.3    62.3    +      -       -      +
    176D  HIS*     3.1    19.8    -      -       -      -
    178D  PHE*     3.2    18.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 176 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135C  CYS      3.3     6.8    -      -       -      +
    136C  LEU*     3.4     3.8    -      -       -      +
    137C  LEU*     2.7    52.6    +      -       +      -
    140C  PHE*     3.8    20.4    -      -       +      -
    143C  ARG      5.4     2.2    -      -       -      +
    145C  ALA*     5.5     8.7    -      -       +      +
    147C  VAL*     4.5     3.4    -      -       +      -
    162C  GLU*     3.6    35.0    -      -       -      +
    163C  SER      3.4    12.1    -      -       -      +
    164C  VAL*     3.5    25.8    -      -       +      -
    175C  SER*     1.3    75.6    -      -       -      +
    177C  SER*     1.3    73.5    +      -       -      +
    178C  SER*     4.1     8.5    -      -       -      -
    178D  PHE*     3.2     6.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 177 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134C  VAL*     4.0    10.9    -      -       -      +
    135C  CYS      3.8     2.9    -      -       -      -
    136C  LEU*     4.5     2.4    -      -       -      +
    161C  GLN      3.9     0.5    -      -       -      +
    162C  GLU*     3.4     3.8    -      -       -      -
    163C  SER*     3.0    33.4    +      -       -      -
    176C  LEU*     1.3    73.4    +      -       -      +
    178C  SER*     1.3    62.0    +      -       -      +
    179C  THR*     4.2     3.8    -      -       -      -
    178D  PHE*     3.1    31.2    -      -       -      -
    191D  SER*     2.7    29.0    +      -       -      -
    193D  VAL*     4.7     2.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 178 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133C  VAL      3.4     5.7    -      -       -      +
    134C  VAL*     3.4     2.0    -      -       -      +
    135C  CYS*     3.0    36.4    +      -       -      +
    147C  VAL*     3.3    27.1    -      -       -      +
    149C  TRP*     3.1    23.8    +      -       -      -
    160C  SER*     4.4     3.8    -      -       -      -
    161C  GLN      3.2    11.1    +      -       -      -
    162C  GLU*     4.2     4.5    -      -       -      +
    176C  LEU*     4.1     9.4    -      -       -      -
    177C  SER*     1.3    75.5    -      -       -      +
    179C  THR*     1.3    61.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 179 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132C  SER*     4.2    22.9    -      -       -      +
    133C  VAL      3.6     6.5    -      -       -      +
    134C  VAL*     4.2     4.7    -      -       +      +
    159C  ASN      3.7     1.6    -      -       -      +
    160C  SER*     3.3     4.4    -      -       -      -
    161C  GLN*     3.0    39.0    +      -       -      +
    177C  SER*     4.2     3.0    -      -       -      -
    178C  SER*     1.3    73.1    +      -       -      +
    180C  LEU*     1.3    69.9    -      -       -      +
    181C  THR*     3.7    14.5    +      -       +      +
    153D  LEU*     4.2    21.3    -      -       +      +
    155D  LYS*     5.7     2.2    -      -       -      -
    181D  VAL*     6.0     2.0    -      -       -      +
    183D  GLN*     5.8     2.5    -      -       -      +
    189D  SER*     5.2     4.2    +      -       -      -
    191D  SER*     5.5     2.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 180 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131C  ALA      4.0     0.3    -      -       -      +
    132C  SER*     3.8     5.2    +      -       -      -
    133C  VAL*     3.2    38.7    +      -       +      +
    149C  TRP*     3.8    51.7    -      -       +      -
    151C  VAL*     4.0    21.8    -      -       +      -
    156C  GLN*     4.3     4.0    -      -       +      -
    159C  ASN*     3.1    35.7    -      -       -      +
    160C  SER*     4.3     4.7    -      -       -      +
    178C  SER      4.0     1.0    +      -       -      -
    179C  THR*     1.3    70.9    -      -       -      +
    181C  THR*     1.3    60.3    -      -       -      +
    182C  LEU*     3.8    31.2    +      -       +      +
    193C  TYR*     4.6     2.7    -      -       +      -
----------------------------------------------------------
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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