Contacts of the strand formed by residues 107 - 113 (chain A) in PDB entry 3FA9


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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  LEU*     5.8     0.9    -      -       +      -
     75A  THR*     3.6    22.4    -      -       +      +
     76A  VAL*     5.0    10.5    -      -       +      -
     77A  ASP*     5.7     1.1    -      -       -      +
     96A  GLU*     4.5     0.2    -      -       -      -
     97A  GLN*     2.7    57.5    +      -       -      +
     99A  LEU*     6.0     0.3    -      -       -      +
    105A  PRO*     3.4    17.9    +      -       +      +
    106A  LYS*     1.3    81.3    -      -       -      +
    108A  SER*     1.3    64.2    +      -       -      +
    124A  THR      3.2    10.3    -      -       -      +
    125A  ALA*     4.1    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  VAL*     5.4     6.3    -      -       -      -
     95A  CYS      3.1    17.9    -      -       -      -
     96A  GLU*     4.5     4.0    -      -       -      -
     97A  GLN*     4.3     4.3    -      -       -      -
    106A  LYS*     5.5     2.4    +      -       -      -
    107A  THR*     1.3    77.4    -      -       -      +
    109A  TRP*     1.3    67.4    +      -       -      +
    110A  THR*     5.7     2.5    -      -       -      +
    123A  MET*     3.6     2.3    -      -       -      +
    124A  THR*     2.9    45.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52A  ILE*     5.0     1.1    -      -       +      -
     63A  ILE*     4.3    19.7    -      -       +      -
     65A  PHE*     4.0    16.8    -      +       -      -
     71A  PHE*     4.5     1.6    -      +       -      -
     73A  GLU*     3.0    25.0    +      -       -      -
     85A  VAL*     4.0    19.1    -      -       +      -
     93A  MET*     3.9    17.3    -      -       +      -
     94A  VAL*     3.9     1.2    -      -       -      +
     95A  CYS*     2.8    53.8    +      -       +      +
     97A  GLN*     3.5    22.0    -      -       -      -
    108A  SER*     1.3    76.6    -      -       -      +
    110A  THR*     1.3    80.5    +      -       -      +
    111A  LEU*     3.9    25.8    -      -       +      -
    121A  ASP*     5.0     3.1    -      -       -      +
    122A  THR*     3.2    15.5    -      -       -      +
    123A  MET*     4.4     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  LYS*     4.3    15.9    +      -       -      +
     93A  MET      3.3    11.7    -      -       -      -
     94A  VAL*     4.0    21.1    -      -       +      -
    108A  SER*     5.7     2.5    -      -       -      +
    109A  TRP*     1.3    87.8    -      -       -      +
    111A  LEU*     1.3    64.6    +      -       -      +
    112A  GLU*     4.2     9.7    +      -       -      -
    120A  ILE      4.9     0.3    +      -       -      -
    121A  ASP*     3.5     5.4    -      -       -      +
    122A  THR*     2.8    55.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  PHE*     3.8     8.2    -      -       +      -
     41A  VAL*     6.3     0.9    -      -       +      -
     43A  ILE*     4.3    14.8    -      -       +      -
     52A  ILE*     3.8    29.4    -      -       +      -
     92A  LYS*     3.4     1.1    -      -       -      -
     93A  MET*     3.0    56.4    +      -       +      +
    109A  TRP*     3.9    16.2    -      -       +      -
    110A  THR*     1.3    74.9    -      -       -      +
    112A  GLU*     1.3    62.1    +      -       -      +
    119A  LEU*     4.1    20.4    -      -       +      -
    120A  ILE      3.3     6.1    -      -       -      +
    121A  ASP*     3.6    34.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 112 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  PHE*     3.9     6.7    -      -       -      -
     91A  ASN*     3.1    20.4    +      -       -      +
     92A  LYS*     3.7    27.5    +      -       +      +
    110A  THR*     4.2    12.0    +      -       -      -
    111A  LEU*     1.3    74.6    -      -       -      +
    113A  LEU*     1.3    62.2    +      -       -      +
    114A  THR*     4.1     0.4    +      -       +      -
    118A  GLU      3.7     0.9    -      -       -      +
    119A  LEU*     3.4     4.0    -      -       -      +
    120A  ILE*     2.7    66.5    +      -       +      +
    122A  THR*     4.7     0.5    -      -       -      +
     26B  VAL*     4.3     9.3    -      -       +      +
     30B  LYS*     3.5    34.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 113 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  PRO*     4.3     6.3    -      -       +      -
      2A  ASN      3.4    39.0    -      -       -      +
      3A  PHE*     3.9    23.1    -      -       +      -
      7A  TRP*     3.6    36.8    -      -       +      -
     91A  ASN*     2.6    46.6    +      -       +      +
    112A  GLU*     1.3    74.9    -      -       -      +
    114A  THR*     1.3    65.3    +      -       -      +
    117A  GLY*     4.9     6.5    -      -       -      -
    118A  GLU      3.4     7.0    -      -       -      +
    119A  LEU*     4.2     7.6    -      -       +      -
    136A  ARG*     4.8     2.9    -      -       -      +
----------------------------------------------------------
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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