Contacts of the strand formed by residues 5 - 13 (chain B) 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 GLY 5 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3B  PHE      3.4     0.6    +      -       -      -
      4B  SER*     1.3    76.1    -      -       -      +
      6B  ASN*     1.3    68.3    +      -       -      -
      7B  TRP*     3.6     9.5    -      -       -      -
     42B  GLU*     3.5     3.0    -      -       -      +
     43B  ILE      2.8    34.0    +      -       -      +
    136B  ARG*     4.2     9.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 6 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  GLY*     1.3    78.1    +      -       -      -
      7B  TRP*     1.3    61.1    +      -       -      +
     40B  ALA*     6.0     1.6    -      -       -      +
     41B  VAL      3.6     3.1    -      -       -      +
     42B  GLU*     3.5    34.0    +      -       -      +
    136B  ARG*     3.6     5.1    -      -       -      +
    137B  GLU*     2.9    45.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 7 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3B  PHE*     2.8    31.2    +      -       -      -
      5B  GLY      3.6    14.7    +      -       -      -
      6B  ASN*     1.3    72.6    -      -       -      +
      8B  LYS*     1.3    60.2    +      -       -      +
     40B  ALA*     3.6     9.2    -      -       -      +
     41B  VAL*     2.7    45.3    +      -       +      +
     43B  ILE*     3.9    16.5    -      -       +      +
    113B  LEU*     3.6    27.4    -      -       +      -
    117B  GLY      3.6    15.5    -      -       -      -
    119B  LEU*     3.7    34.8    -      -       +      -
    134B  PHE*     3.7    18.0    -      -       +      -
    135B  VAL*     3.4     9.4    -      -       -      -
    136B  ARG*     3.4    65.3    -      -       +      -
    137B  GLU*     5.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 8 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  ASN      4.1     0.4    +      -       -      -
      7B  TRP*     1.3    75.2    -      -       -      +
      9B  ILE*     1.3    66.5    +      -       -      +
     10B  ILE*     5.5     1.8    -      -       +      -
     39B  PRO      4.8     2.5    -      -       -      -
     40B  ALA*     5.3     2.7    -      -       +      +
    134B  PHE*     3.1     2.8    -      -       -      -
    135B  VAL*     2.8    59.6    +      -       +      +
    136B  ARG      4.6     1.6    -      -       -      -
    137B  GLU*     4.2    42.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 9 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  LYS*     1.3    77.5    -      -       -      +
     10B  ILE*     1.3    66.2    +      -       -      +
     11B  ARG      3.4    25.4    -      -       -      +
     12B  SER*     3.9    17.3    -      -       -      -
     38B  LYS*     5.0     4.7    -      -       -      -
     39B  PRO*     3.9    40.8    +      -       +      +
    132B  LYS*     4.0    19.3    -      -       +      -
    133B  VAL      3.6     4.9    -      -       -      +
    134B  PHE*     3.5    20.8    -      -       +      -
    138B  ACT      4.3     4.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 10 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  LYS*     4.1     2.7    -      -       +      +
      9B  ILE*     1.3    79.1    -      -       -      +
     11B  ARG*     1.3    70.7    +      -       +      +
    118B  GLU*     3.8    11.9    -      -       -      +
    133B  VAL*     2.7    42.9    +      -       +      +
    135B  VAL*     3.4    46.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 11 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  ILE*     3.4    11.9    -      -       -      +
     10B  ILE*     1.3    89.9    -      -       +      +
     12B  SER*     1.3    64.7    +      -       -      +
     13B  GLU*     4.2    18.0    +      -       -      +
    131B  THR      4.5     1.6    -      -       -      +
    132B  LYS*     3.4     1.0    -      -       -      -
    133B  VAL*     2.9    44.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with SER 12 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  ILE*     3.9    17.3    -      -       -      -
     11B  ARG*     1.3    82.2    +      -       -      +
     13B  GLU*     1.3    64.0    +      -       -      +
     15B  PHE*     4.5     8.7    +      -       -      +
    130B  CYS*     5.0     0.2    -      -       -      -
    131B  THR      3.4     7.0    -      -       -      -
    132B  LYS*     4.2     6.9    -      -       -      +
    138B  ACT      3.1    25.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 13 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  ARG*     4.2    19.3    +      -       -      +
     12B  SER*     1.3    78.9    +      -       -      +
     14B  ASN*     1.3    84.3    +      -       -      +
     15B  PHE      3.3     2.7    -      -       -      -
    129B  VAL      5.4     0.4    -      -       -      +
    130B  CYS*     3.2     6.4    -      -       -      -
    131B  THR*     2.9    44.8    +      -       -      +
----------------------------------------------------------
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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