Contacts of the strand formed by residues 92 - 95 (chain B) 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 ALA 92 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  ARG*     4.2    16.2    -      -       +      +
     39B  GLN      3.4    16.2    -      -       -      +
     40B  ALA*     3.4    12.8    -      -       +      +
     41B  PRO*     3.4    10.5    -      -       -      +
     89B  GLU      5.4     0.4    -      -       -      +
     90B  ASP      2.8    12.1    +      -       -      +
     91B  THR*     1.3    77.5    -      -       -      +
     93B  VAL*     1.3    60.9    +      -       -      +
     94B  TYR*     3.4    10.8    -      -       +      -
    120B  LEU*     3.6     7.1    -      -       -      +
    121B  VAL      2.8    33.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 93 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  ARG*     3.3     4.0    -      -       -      -
     39B  GLN*     2.9    49.3    +      -       +      +
     41B  PRO*     5.2     6.3    -      -       +      -
     92B  ALA*     1.3    70.6    -      -       -      +
     94B  TYR*     1.3    62.5    +      -       -      +
     95B  TYR*     3.8    26.7    +      -       +      +
    117B  GLN      5.2     0.9    -      -       -      +
    118B  GLY*     4.2     5.2    -      -       -      -
    119B  THR      3.4    21.1    -      -       -      +
    120B  LEU*     3.9    22.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 94 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  GLU*     3.2     7.7    -      -       +      +
     20B  LEU*     3.9    20.4    -      -       +      -
     36B  TRP*     4.5     7.0    -      +       +      -
     37B  VAL      3.7     4.5    -      -       -      -
     38B  ARG*     2.5    59.4    +      -       +      -
     48B  VAL*     4.1     9.6    -      -       +      -
     68B  PHE*     3.9    14.1    -      +       -      -
     81B  LEU*     4.6    11.9    -      -       +      -
     83B  MET*     4.1    10.0    -      -       +      -
     90B  ASP*     3.1    18.3    +      -       -      +
     92B  ALA      3.4    10.5    -      -       -      -
     93B  VAL*     1.3    71.6    -      -       -      +
     95B  TYR*     1.3    61.5    +      -       -      +
    118B  GLY*     3.1     4.2    -      -       -      -
    119B  THR*     2.7    38.7    +      -       +      +
    121B  VAL*     3.3    40.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 95 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  GLN*     3.3    18.2    +      -       -      -
     42A  GLN      3.5     8.4    +      -       -      -
     43A  ALA*     3.7    18.8    -      -       +      -
     44A  PRO*     3.6    15.3    -      -       +      -
      6B  GLU*     3.3     2.5    -      -       -      -
     36B  TRP*     3.0    12.7    -      -       -      -
     37B  VAL      2.8    43.6    +      -       -      +
     38B  ARG*     4.7     0.4    -      -       -      -
     39B  GLN*     3.3    29.1    +      -       +      -
     45B  LEU*     4.5     2.7    -      -       +      -
     93B  VAL*     4.0    24.9    -      -       +      +
     94B  TYR*     1.3    71.3    -      -       -      +
     96B  CYS*     1.3    61.4    +      -       -      +
     97B  ALA      4.1     0.4    -      -       -      -
    115B  TRP*     3.5    34.1    -      +       +      -
    116B  GLY      3.5    17.3    -      -       -      +
    117B  GLN      4.1     2.9    -      -       -      -
    118B  GLY*     3.6    22.4    -      -       -      -
----------------------------------------------------------
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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