Contacts of the strand formed by residues 107 - 113 (chain B) in PDB entry 3FA6


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 THR 107 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  LEU*     3.8    28.0    -      -       +      -
     75B  THR*     3.9    16.4    -      -       +      +
     76B  VAL*     5.7     3.6    -      -       +      -
     79B  ARG*     4.6     5.6    -      -       -      +
     97B  GLN*     2.7    52.4    +      -       -      +
     99B  LEU*     6.1     0.5    -      -       -      +
    105B  PRO*     3.3    12.5    +      -       +      +
    106B  LYS*     1.3    85.2    +      -       -      +
    108B  SER*     1.3    65.4    +      -       -      +
    124B  THR*     3.2    13.7    -      -       -      +
    125B  ALA*     4.3     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 108 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94B  VAL*     5.6     4.7    -      -       -      +
     95B  CYS      3.3    16.4    -      -       -      -
     96B  GLU*     4.8     2.9    -      -       -      -
     97B  GLN*     4.1     6.2    -      -       -      +
    106B  LYS*     6.1     4.5    -      -       -      -
    107B  THR*     1.3    78.3    -      -       -      +
    109B  TRP*     1.3    69.2    +      -       -      +
    110B  THR*     4.9     4.9    -      -       -      +
    123B  MET*     3.5     3.6    -      -       -      +
    124B  THR*     2.7    49.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 109 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65B  PHE*     3.8    25.6    -      +       -      -
     71B  PHE*     4.6     2.5    -      +       -      -
     73B  GLU*     3.0    25.3    +      -       -      -
     85B  VAL*     3.7    23.1    -      -       +      -
     93B  MET*     3.9    19.5    -      -       +      -
     94B  VAL*     4.2     0.2    -      -       -      +
     95B  CYS*     2.8    50.3    +      -       +      +
     97B  GLN*     3.5    21.8    -      -       -      -
    108B  SER*     1.3    77.1    -      -       -      +
    110B  THR*     1.3    75.9    +      -       -      +
    111B  LEU*     3.8    24.9    -      -       +      -
    121B  ASP*     4.5     0.4    -      -       -      +
    122B  THR      3.1    11.7    -      -       -      +
    123B  MET*     4.0     3.1    -      -       +      -
    138B  LSR      3.5    51.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 110 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92B  LYS*     4.5    14.9    -      -       -      -
     93B  MET      3.3    12.8    -      -       -      -
     94B  VAL*     4.0    25.4    -      -       +      -
    108B  SER*     4.9     6.3    -      -       -      +
    109B  TRP*     1.3    85.2    -      -       -      +
    111B  LEU*     1.3    62.8    +      -       -      +
    112B  GLU*     5.2     1.2    +      -       -      +
    120B  ILE      3.5     1.6    +      -       -      +
    121B  ASP*     3.3     9.0    -      -       -      +
    122B  THR*     2.8    53.0    +      -       +      +
    124B  THR*     6.1     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 111 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3B  PHE*     3.7    15.5    -      -       +      -
     43B  ILE*     4.3    14.4    -      -       +      -
     50B  PHE*     5.8     0.7    -      -       +      -
     52B  ILE*     4.2    14.6    -      -       +      -
     92B  LYS*     3.3     3.8    -      -       -      -
     93B  MET*     2.9    52.6    +      -       +      +
    109B  TRP*     3.8    22.2    -      -       +      -
    110B  THR*     1.3    81.1    -      -       -      +
    112B  GLU*     1.3    60.2    +      -       -      +
    119B  LEU*     4.3    16.8    -      -       +      -
    120B  ILE      3.3     2.2    -      -       -      +
    121B  ASP*     3.7    30.3    -      -       +      +
    138B  LSR      4.1    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 112 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3B  PHE*     4.1     5.4    -      -       -      -
     91B  ASN*     3.2    14.0    -      -       +      +
     92B  LYS*     4.0    32.8    +      -       +      +
    110B  THR*     5.7     1.3    -      -       -      +
    111B  LEU*     1.3    75.1    -      -       -      +
    113B  LEU*     1.3    73.2    +      -       -      +
    114B  THR*     3.9     6.1    +      -       +      +
    118B  GLU      3.7     0.5    -      -       -      +
    119B  LEU*     3.4     5.2    -      -       -      +
    120B  ILE*     2.9    56.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 113 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  PRO*     3.9    21.3    -      -       +      -
      2B  ASN      3.6    29.2    -      -       -      +
      3B  PHE*     3.8    22.0    -      -       +      -
      7B  TRP*     3.7    35.9    -      -       +      -
     91B  ASN*     2.8    35.9    +      -       -      +
    112B  GLU*     1.3    78.0    -      -       -      +
    114B  THR*     1.3    67.1    +      -       -      +
    117B  GLY*     5.6     2.0    -      -       -      -
    118B  GLU      3.4     7.2    -      -       -      +
    119B  LEU*     4.1     8.3    -      -       +      -
    136B  ARG*     4.5     4.9    -      -       -      +
----------------------------------------------------------
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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