Contacts of the strand formed by residues 27 - 34 (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 ALA 27 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  ALA*     4.4     1.3    -      -       -      -
     26A  ASP*     1.3    74.4    -      -       -      +
     28A  ILE*     1.3    64.9    +      -       -      +
     29A  VAL*     4.2    15.7    +      -       +      -
     65A  VAL*     4.3     5.8    -      -       +      -
     67A  GLU      3.2    11.7    -      -       -      +
     68A  VAL*     4.1    10.5    -      -       +      -
     75A  PHE*     5.9     0.2    -      -       +      -
    125A  HIS*     3.5     4.9    -      -       -      -
    126A  VAL*     2.8    36.2    +      -       +      +
    129A  ALA*     3.7    20.1    -      -       +      +
    133A  LEU*     4.3     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 28 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  ARG*     4.7     3.6    -      -       -      +
     20A  PRO*     3.3    33.2    -      -       +      +
     21A  VAL      3.8     2.0    -      -       -      -
     22A  ALA*     3.7    17.5    -      -       +      +
     27A  ALA*     1.3    80.0    -      -       -      +
     29A  VAL*     1.3    65.9    +      -       -      +
     65A  VAL*     3.7     1.4    -      -       -      +
     66A  VAL*     2.9    39.0    +      -       +      -
     67A  GLU*     2.8    40.1    +      -       +      +
    123A  TYR*     3.7    28.5    -      -       +      -
    124A  PHE      3.5     3.8    -      -       -      +
    125A  HIS*     3.9    19.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 29 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  ALA*     4.2    13.5    -      -       +      -
     28A  ILE*     1.3    80.2    -      -       -      +
     30A  ARG*     1.3    63.2    +      -       -      +
     63A  GLY*     3.7    22.2    -      -       -      -
     64A  GLU      3.4    13.7    -      -       -      +
     65A  VAL*     4.3    12.6    -      -       +      -
     66A  VAL*     4.7     0.2    -      -       -      -
     81A  VAL*     4.1    10.5    -      -       +      -
     83A  VAL*     4.7     0.9    -      -       +      -
    123A  TYR*     3.3     6.2    -      -       -      -
    124A  PHE*     2.9    60.8    +      -       +      +
    126A  VAL*     3.9    22.9    -      -       +      -
    133A  LEU*     4.9     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 30 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  VAL*     1.3    76.7    -      -       -      +
     31A  PRO*     1.3    74.9    +      -       +      +
     32A  LEU*     3.5    23.0    -      -       -      +
     63A  GLY*     3.2     0.7    -      -       -      -
     64A  GLU*     2.6    72.1    +      -       +      +
     66A  VAL*     3.6    24.0    -      -       +      +
    122A  GLU      3.5    16.2    -      -       -      +
    123A  TYR*     3.6    17.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 31 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  VAL      4.0     0.7    -      -       -      +
     30A  ARG*     1.3    93.1    +      -       +      +
     32A  LEU*     1.3    62.5    +      -       -      +
     34A  VAL*     3.7    26.7    -      -       +      -
     61A  ALA*     4.9     0.2    -      -       +      -
     62A  VAL      3.7     5.8    -      -       -      +
    119A  VAL      3.7    10.1    -      -       -      +
    121A  GLY      3.2    20.4    -      -       -      +
    122A  GLU      3.3    18.2    -      -       -      +
    124A  PHE*     4.0    19.3    -      -       +      -
    327A  PHE*     5.0     1.3    -      -       +      -
    351A  LEU*     3.5    33.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 32 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  ARG*     3.4    35.0    +      -       -      +
     31A  PRO*     1.3    74.1    -      -       -      +
     33A  ALA*     1.3    60.4    +      -       -      +
     62A  VAL*     2.7    21.3    +      -       +      +
     63A  GLY*     3.7    20.4    -      -       -      +
     64A  GLU*     3.9    16.8    -      -       +      +
     80A  ARG*     3.6    38.4    -      -       +      +
    142A  LEU*     4.1    15.4    -      -       +      +
    350A  ILE*     3.7     7.8    -      -       -      +
    351A  LEU*     3.0    28.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 33 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  PRO      3.8     0.4    -      -       -      -
     32A  LEU*     1.3    78.7    -      -       -      +
     34A  VAL*     1.3    63.6    +      -       -      +
     61A  ALA*     3.3     3.3    -      -       -      -
     62A  VAL*     3.0    33.0    +      -       +      +
    142A  LEU*     4.0    23.8    -      -       +      -
    146A  VAL*     3.6    19.1    -      -       +      +
    348A  VAL*     3.9    11.2    -      -       +      -
    349A  VAL      3.2    12.1    -      -       -      +
    350A  ILE*     4.3     4.3    -      -       +      -
    351A  LEU*     4.5     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 34 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  PRO*     3.7    25.8    -      -       +      -
     33A  ALA*     1.3    81.1    -      -       -      +
     35A  SER*     1.3    60.3    +      -       -      +
     36A  PRO*     6.1     0.2    -      -       +      -
     60A  GLU      3.1    13.5    -      -       -      +
     61A  ALA*     3.8     8.5    -      -       +      -
    119A  VAL*     3.9    13.5    -      -       +      +
    120A  PHE*     3.6    26.0    -      -       +      -
    146A  VAL*     4.2     4.0    -      -       -      -
    330A  ILE*     4.0    21.5    -      -       +      -
    348A  VAL*     3.2     4.9    -      -       -      -
    349A  VAL*     2.8    44.4    +      -       +      +
    351A  LEU*     4.4     4.7    -      -       +      -
----------------------------------------------------------
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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