Contacts of the strand formed by residues 38 - 45 (chain B) in PDB entry 1F3F


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 38 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36B  GLY      4.3     7.9    -      -       -      +
     37B  PHE*     1.3    75.8    -      -       -      +
     39B  LEU*     1.3    75.2    +      -       -      +
     40B  VAL*     3.2    14.5    +      -       +      +
     82B  PHE*     3.2     5.7    -      -       -      -
     83B  GLU*     2.8    39.9    +      -       +      +
    144B  LEU*     4.8     4.9    -      -       +      -
    147B  VAL*     4.1    27.1    -      -       +      -
    148B  LYS      6.1     0.4    -      -       -      +
    150B  ASN*     6.3     3.4    -      -       +      +
    153B  LEU*     5.7     3.1    -      -       +      -
    154B  TYR*     6.3     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 39 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  ILE*     4.8    13.9    -      -       +      -
     33B  GLU*     5.8     6.9    -      -       +      +
     37B  PHE      4.0     0.6    +      -       -      -
     38B  VAL*     1.3    74.9    -      -       -      +
     40B  VAL*     1.3    59.1    +      -       -      +
     41B  GLY      3.4    24.7    -      -       -      +
     42B  LEU*     3.8    32.1    -      -       +      -
     80B  MET*     4.2     7.6    -      -       +      -
     81B  VAL      3.6     4.9    -      -       -      +
     82B  PHE*     3.6    36.7    -      -       +      -
    144B  LEU*     3.3    18.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 40 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  ARG*     3.6    26.5    -      -       -      +
     38B  VAL*     3.7    13.0    -      -       +      +
     39B  LEU*     1.3    77.5    -      -       -      +
     41B  GLY*     1.3    56.9    +      -       -      +
     81B  VAL*     2.8    42.4    +      -       +      +
     82B  PHE      4.3     1.1    -      -       -      +
     83B  GLU*     3.7    25.8    -      -       +      +
    142B  GLU      3.6     1.4    -      -       -      +
    143B  LEU*     3.0     9.1    -      -       +      -
    144B  LEU*     2.8    39.5    +      -       +      +
    147B  VAL*     3.8    20.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 41 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  LEU*     3.4     9.2    -      -       -      +
     40B  VAL*     1.3    82.3    -      -       -      +
     42B  LEU*     1.3    64.3    +      -       -      +
     80B  MET*     3.3     3.5    -      -       -      -
     81B  VAL      2.9    24.1    +      -       -      -
    138B  PHE*     3.7     9.4    -      -       -      -
    142B  GLU      3.8     7.6    -      -       -      -
    143B  LEU*     3.8    16.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 42 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25B  VAL*     6.0     0.2    -      -       +      -
     29B  ILE*     4.1    23.1    -      -       +      -
     39B  LEU*     3.8    26.7    -      -       +      -
     41B  GLY*     1.3    75.6    -      -       -      +
     43B  LYS*     1.3    72.9    +      -       -      +
     78B  VAL*     5.1     7.6    -      -       +      -
     79B  ALA      3.4     7.6    -      -       -      +
     80B  MET*     3.7    28.9    -      -       +      -
    138B  PHE*     3.4     6.4    -      -       -      -
    142B  GLU      4.7     1.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 43 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42B  LEU*     1.3    84.6    -      -       -      +
     44B  GLN*     1.3    62.8    +      -       -      +
     45B  LEU*     4.1    29.1    +      -       +      +
     78B  VAL*     3.4     4.4    -      -       -      -
     79B  ALA*     2.9    34.3    +      -       +      +
    137B  TRP*     2.7    30.2    +      -       -      -
    138B  PHE*     4.0    18.4    -      -       +      -
    139B  LYS*     5.7     2.2    -      -       -      +
    142B  GLU*     2.9    36.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 44 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20B  VAL*     3.7    17.5    -      -       -      +
     43B  LYS*     1.3    78.9    -      -       -      +
     45B  LEU*     1.3    67.4    +      -       -      +
     76B  PRO*     3.6    28.7    -      -       +      +
     77B  VAL      3.2    11.9    -      -       -      +
     78B  VAL*     3.9    16.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 45 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43B  LYS*     4.1    21.8    -      -       +      +
     44B  GLN*     1.3    79.0    -      -       -      +
     46B  VAL*     1.3    72.8    +      -       -      +
     47B  PRO*     3.5     4.4    -      -       +      +
     48B  THR      5.7     0.2    -      -       -      +
     51B  LEU*     4.0    26.2    -      -       +      -
     76B  PRO*     3.3     2.3    -      -       -      +
     77B  VAL*     2.8    42.1    +      -       +      +
     79B  ALA*     4.0    16.2    -      -       +      -
    137B  TRP*     3.9    22.7    -      -       +      +
----------------------------------------------------------
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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