Contacts of the strand formed by residues 320 - 325 (chain A) in PDB entry 3FPL


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 VAL 320 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143A  GLU*     3.7    43.1    -      -       +      +
    144A  ASN*     4.5     2.5    -      -       -      +
    147A  MET*     3.9    18.4    -      -       +      -
    316A  LEU      4.3     3.8    -      -       -      +
    317A  SER*     3.1    17.6    +      -       -      +
    318A  LYS      3.3     1.3    -      -       -      +
    319A  LEU*     1.3    77.3    -      -       -      +
    321A  THR*     1.3    62.3    +      -       -      +
    322A  HIS      3.9     7.6    -      -       -      +
    323A  VAL*     3.6    31.0    -      -       +      -
    346A  LYS      3.6     6.1    -      -       -      +
    348A  VAL*     4.3     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 321 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202A  VAL*     4.5     5.8    -      -       +      -
    318A  LYS      4.5     4.5    -      -       -      +
    319A  LEU      4.1     0.7    -      -       -      +
    320A  VAL*     1.3    77.0    -      -       -      +
    322A  HIS*     1.3    87.4    +      -       -      +
    323A  VAL*     5.7     0.4    -      -       -      -
    343A  ASP      3.5    17.3    -      -       -      +
    344A  LEU*     3.7     0.2    -      -       -      +
    345A  ILE*     3.0    46.8    +      -       +      +
    346A  LYS      2.9     8.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 322 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    320A  VAL*     3.7     2.0    -      -       -      +
    321A  THR*     1.3   110.1    +      -       -      +
    323A  VAL*     1.3    65.7    +      -       -      +
    324A  TYR*     4.1    14.4    +      -       +      -
    336A  LEU*     3.7    26.3    -      -       +      +
    341A  PRO*     5.1     1.3    -      -       +      -
    343A  ASP*     3.7    36.8    +      -       -      -
    344A  LEU*     3.7    13.3    -      -       +      -
    346A  LYS      3.4     1.9    +      -       -      +
    347A  ALA*     3.2    18.8    -      -       +      -
    348A  VAL      2.9    24.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 323 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143A  GLU*     4.8    11.4    -      -       +      -
    320A  VAL*     3.6    20.9    -      -       +      -
    321A  THR      5.7     0.4    -      -       -      -
    322A  HIS*     1.3    80.3    -      -       -      +
    324A  TYR*     1.3    78.0    +      -       -      +
    325A  HIS*     4.2    18.2    +      -       +      -
    348A  VAL*     3.2    14.4    -      -       +      +
    350A  ILE*     3.8    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 324 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    322A  HIS*     4.1    14.5    +      -       +      -
    323A  VAL*     1.3    81.0    -      -       -      +
    325A  HIS*     1.3    67.1    +      -       -      +
    329A  HIS*     3.6    37.0    -      +       +      -
    332A  GLU*     3.7    31.1    +      -       +      +
    333A  ALA*     4.1    16.4    -      -       +      -
    336A  LEU*     3.3    28.2    -      -       +      +
    347A  ALA*     4.2    16.2    -      -       +      -
    348A  VAL      2.9     9.1    +      -       -      +
    349A  VAL*     4.1    20.4    -      -       +      -
    350A  ILE*     2.9    25.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 325 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323A  VAL*     4.2    25.7    +      -       +      +
    324A  TYR*     1.3    78.8    -      -       -      +
    326A  GLY*     1.3    60.6    +      -       -      +
    329A  HIS*     3.0    23.0    +      -       +      -
    350A  ILE*     3.3    26.9    -      -       +      +
    351A  LEU      5.9     0.2    -      -       -      -
----------------------------------------------------------
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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