Contacts of the strand formed by residues 188 - 196 (chain D) 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 188 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91D  THR*     5.3     2.4    +      -       -      -
    122D  THR*     4.7    13.5    -      -       -      +
    156D  ASP*     3.0    21.1    +      -       -      -
    157D  TYR*     2.9    43.1    +      -       +      +
    158D  PHE*     3.7    28.4    -      +       -      -
    159D  PRO*     4.4     7.0    -      -       +      -
    160D  GLU*     3.6    40.5    -      -       +      +
    180D  ALA*     4.4     3.6    -      -       +      -
    181D  VAL      3.4    15.0    -      -       -      -
    182D  LEU*     3.6    41.5    -      -       +      +
    187D  LEU*     1.3    74.0    -      -       -      +
    189D  SER*     1.3    67.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 189 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179C  THR*     5.2     8.1    +      -       -      +
    153D  LEU*     4.7     6.8    -      -       -      +
    154D  VAL      3.2    12.8    +      -       -      -
    155D  LYS*     3.9    21.9    -      -       -      +
    157D  TYR*     3.6     3.3    -      -       -      -
    179D  PRO      4.9     0.2    -      -       -      +
    180D  ALA*     4.3     0.7    -      -       -      -
    181D  VAL*     2.8    40.9    +      -       -      +
    183D  GLN*     4.0    19.7    +      -       -      -
    188D  TYR*     1.3    82.9    -      -       -      +
    190D  LEU*     1.3    62.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 190 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153D  LEU*     3.5     6.4    -      -       -      +
    154D  VAL*     2.7    56.5    +      -       +      +
    157D  TYR*     3.9     7.6    -      -       -      +
    160D  GLU*     5.7     0.2    -      -       -      +
    162D  VAL*     3.5    31.9    -      -       +      +
    164D  VAL*     3.8    11.0    -      -       +      -
    177D  THR*     4.4    11.2    -      -       +      -
    178D  PHE*     3.8    18.4    -      -       -      +
    179D  PRO      5.2     0.9    -      -       -      -
    180D  ALA*     3.6    20.0    -      -       +      +
    189D  SER*     1.3    75.9    -      -       -      +
    191D  SER*     1.3    78.7    -      -       -      +
    192D  SER*     3.7     3.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 191 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134C  VAL*     4.9     6.5    -      -       -      -
    177C  SER*     2.7    35.6    +      -       -      -
    179C  THR*     5.5     2.1    +      -       -      -
    136D  LEU*     5.3     2.2    -      -       -      -
    152D  CYS      3.4     9.9    -      -       -      -
    153D  LEU*     4.1    17.9    -      -       -      -
    178D  PHE*     3.0    31.1    +      -       -      +
    190D  LEU*     1.3    81.5    -      -       -      +
    192D  SER*     1.3    61.1    +      -       -      +
    193D  VAL*     5.0     4.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 192 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151D  GLY*     3.1     1.4    -      -       -      -
    152D  CYS*     2.9    35.4    +      -       -      +
    154D  VAL*     5.8     0.2    -      -       -      -
    164D  VAL*     3.2    33.8    -      -       -      +
    166D  TRP*     3.2    20.8    +      -       -      -
    175D  VAL*     4.5     0.9    -      -       -      +
    176D  HIS      3.5     4.8    +      -       -      -
    177D  THR*     2.6    28.3    +      -       -      +
    190D  LEU*     3.7     2.4    -      -       -      +
    191D  SER*     1.3    75.4    -      -       -      +
    193D  VAL*     1.3    63.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 193 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119C  PHE*     4.9     3.8    -      -       +      -
    134C  VAL*     5.8     0.7    -      -       +      -
    136C  LEU*     3.9    29.6    -      -       +      -
    138C  ASN*     5.6     0.2    -      -       -      +
    177C  SER*     4.7     5.2    -      -       -      +
    136D  LEU*     4.3    13.7    -      -       +      -
    150D  LEU      3.3    18.4    -      -       -      +
    151D  GLY*     3.7     1.1    -      -       -      -
    166D  TRP*     3.8    10.1    +      -       -      -
    174D  GLY      5.0     0.2    -      -       -      +
    175D  VAL*     3.8     1.7    -      -       -      -
    176D  HIS*     3.0    48.7    +      -       +      +
    178D  PHE*     4.0    17.3    -      -       +      -
    191D  SER*     4.6     4.5    -      -       -      +
    192D  SER*     1.3    81.9    +      -       -      +
    194D  VAL*     1.3    69.7    +      -       -      +
    195D  THR*     5.6     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 194 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149D  ALA*     3.1     3.8    -      -       -      +
    150D  LEU*     2.8    44.4    +      -       +      -
    166D  TRP*     4.6    13.5    -      -       +      -
    171D  LEU*     4.2    17.9    -      -       +      -
    173D  SER      3.8     7.2    -      -       -      +
    174D  GLY      3.5     7.4    -      -       -      -
    175D  VAL*     3.5    41.7    -      -       +      +
    193D  VAL*     1.3    78.8    -      -       -      +
    195D  THR*     1.3    64.5    +      -       -      +
    196D  VAL*     3.4    26.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with THR 195 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117C  PHE*     5.7     4.9    -      -       +      -
    136C  LEU*     5.4     2.7    -      -       +      -
    138C  ASN*     2.9    29.6    -      -       -      +
    139C  ASN*     5.4     0.2    -      -       -      +
    147D  THR*     4.6     8.7    +      -       -      +
    148D  ALA      3.1    11.2    -      -       -      -
    149D  ALA*     4.1     7.9    -      -       +      +
    173D  SER      4.5     4.3    -      -       -      +
    174D  GLY*     3.5    29.1    +      -       -      +
    176D  HIS*     5.5     0.4    -      -       +      +
    193D  VAL*     5.6     1.1    -      -       +      -
    194D  VAL*     1.3    77.1    -      -       -      +
    196D  VAL*     1.3    62.5    +      -       -      +
    197D  PRO*     4.4     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 196 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147D  THR*     2.9    14.8    +      -       -      -
    148D  ALA*     2.6    34.3    +      -       +      +
    150D  LEU*     3.2    38.4    -      -       +      -
    171D  LEU*     4.7     5.6    -      -       +      -
    194D  VAL*     3.4    16.3    +      -       +      -
    195D  THR*     1.3    75.0    -      -       -      +
    197D  PRO*     1.3    70.6    -      -       +      +
    198D  SER      5.2     2.2    -      -       -      +
    206D  TYR*     3.5    38.8    -      -       +      +
----------------------------------------------------------
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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