Contacts of the strand formed by residues 48 - 51 (chain F) in PDB entry 1VQN


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 48 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36F  THR*     4.0     7.6    -      -       +      -
     40F  ILE*     3.8    34.5    -      -       +      -
     45F  ALA*     4.3     3.1    -      -       +      -
     47F  LEU*     1.3    76.5    -      -       -      +
     49F  PHE*     1.3    63.4    +      -       -      +
     50F  VAL*     5.2     0.7    -      -       +      -
     63F  ILE*     4.3     9.6    -      -       +      -
     67F  ALA*     4.9     1.6    -      -       +      -
     72F  VAL*     4.1    11.7    -      -       +      -
     73F  PRO      3.1     7.4    +      -       -      +
     74F  PHE*     3.1    25.1    -      -       +      +
     75F  ILE*     2.9    27.7    +      -       -      +
     96F  ALA      3.1     6.7    -      -       -      +
     97F  ALA*     3.4    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 49 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16F  ALA*     3.6    43.5    -      -       +      -
     17F  LEU*     4.2     2.7    -      -       +      -
     19F  ALA*     5.7     1.3    -      -       +      -
     20F  LEU*     3.7    22.4    -      -       +      -
     47F  LEU*     4.0    22.0    -      -       +      -
     48F  VAL*     1.3    78.0    -      -       -      +
     50F  VAL*     1.3    67.5    +      -       -      +
     75F  ILE*     3.4    15.7    -      -       +      +
     77F  VAL*     4.0    10.1    -      -       +      -
     83F  LEU*     3.4    37.0    -      -       +      -
     95F  ALA*     3.1     5.5    -      -       -      +
     96F  ALA*     2.4    47.9    +      -       +      +
     98F  VAL*     3.2    31.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 50 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3F  TYR*     3.7    12.1    -      -       +      -
     48F  VAL*     5.2     3.1    -      -       +      +
     49F  PHE*     1.3    81.1    -      -       -      +
     51F  ALA*     1.3    77.2    +      -       -      +
     60F  VAL*     3.2    27.6    -      -       +      -
     63F  ILE*     3.3    39.9    -      -       +      -
     64F  PRO*     5.8     0.4    -      -       +      -
     74F  PHE*     5.5     2.7    -      -       +      -
     75F  ILE      3.0     9.1    +      -       -      +
     76F  PHE*     3.3    24.2    -      -       +      -
     77F  VAL      3.1    18.9    +      -       -      +
     83F  LEU*     4.3     1.1    -      -       -      -
     94F  ALA      3.6     3.6    -      -       -      +
     95F  ALA*     4.2     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 51 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3F  TYR*     3.0    15.2    +      -       -      -
     50F  VAL*     1.3    87.4    -      -       -      +
     52F  GLU*     1.3    59.7    +      -       -      +
     53F  ASP*     3.5    18.2    -      -       -      +
     54F  VAL*     3.7    11.4    -      -       +      +
     77F  VAL*     3.4    10.8    -      -       -      +
     79F  GLN      4.0     3.8    -      -       -      +
     80F  GLN*     3.7    20.4    -      -       +      -
     83F  LEU*     3.8     5.4    -      -       +      +
     93F  SER      4.1     4.9    -      -       -      +
     94F  ALA      2.8    18.9    +      -       -      +
----------------------------------------------------------
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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