Contacts of the strand formed by residues 70 - 75 (chain D) 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 GLY 70 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   23460    C      4.7     1.1    -      -       -      -
     25D  MET      3.4    14.6    -      -       -      -
     26D  GLY*     4.7     2.5    -      -       -      -
     27D  ILE*     4.3     1.6    -      -       -      -
     35D  ALA      4.6    12.1    +      -       -      +
     51D  ARG*     3.5     7.8    -      -       -      +
     52D  THR*     2.8    35.6    +      -       -      -
     68D  PRO*     5.6     0.2    -      -       -      +
     69D  ILE*     1.3    83.2    +      -       -      +
     71D  ALA*     1.3    63.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 71 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24D  HIS*     3.1     8.3    -      -       -      +
     25D  MET*     2.9    34.3    +      -       +      +
     35D  ALA      4.8     4.5    -      -       -      +
     37D  ALA*     6.3     0.2    -      -       +      -
     38D  GLU*     4.1    28.3    -      -       +      +
     41D  LEU*     4.0    10.3    -      -       +      +
     49D  PRO*     4.5     8.5    -      -       +      -
     50D  VAL      2.9    15.0    -      -       -      +
     51D  ARG*     4.8     0.4    -      -       -      -
     52D  THR*     3.5     4.4    +      -       -      -
     70D  GLY*     1.3    75.8    -      -       -      +
     72D  LYS*     1.3    60.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 72 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   23470    C      3.3    33.6    +      -       -      +
   23480    C      2.7    29.6    +      -       -      +
   30419    C      4.1    22.2    -      -       -      +
     22D  VAL*     4.2    11.2    -      -       +      -
     23D  VAL      3.1     7.4    -      -       -      +
     24D  HIS*     3.3    22.2    -      -       +      -
     41D  LEU*     4.8     0.4    -      -       -      -
     49D  PRO*     3.3     0.3    -      -       -      +
     50D  VAL*     2.8    45.6    +      -       +      +
     51D  ARG      5.7     2.2    -      -       -      -
     52D  THR*     4.9     4.3    -      -       -      +
     71D  ALA*     1.3    71.9    -      -       -      +
     73D  VAL*     1.3    68.5    +      -       -      +
     74D  THR*     4.8     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 73 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   30419    C      3.7     3.6    -      -       -      -
     21D  VAL      3.2     4.0    -      -       -      +
     22D  VAL*     3.3     2.0    -      -       -      -
     23D  VAL*     2.7    51.8    +      -       +      +
     41D  LEU*     4.3    12.3    -      -       +      +
     45D  THR*     3.9    10.3    -      -       -      +
     47D  GLN*     3.3    39.5    -      -       +      +
     48D  MET      3.9     4.7    -      -       -      +
     49D  PRO*     3.5    24.7    -      -       +      -
     72D  LYS*     1.3    81.9    -      -       -      +
     74D  THR*     1.3    64.8    +      -       -      +
     75D  LEU*     3.8    10.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 74 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   23480    C      5.4     2.2    -      -       -      +
   30419    C      2.7    45.2    +      -       -      +
   30429    C      3.3    30.9    +      -       +      +
     20D  LYS*     5.2     3.8    -      -       +      +
     21D  VAL      3.4     3.6    -      -       -      -
     22D  VAL*     3.7    28.9    -      -       +      -
     47D  GLN*     2.5    23.1    -      -       -      +
     72D  LYS*     4.8     8.5    -      -       +      -
     73D  VAL*     1.3    74.1    -      -       -      +
     75D  LEU*     1.3    56.7    +      -       -      +
     76D  ARG*     4.3     8.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 75 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20D  LYS*     3.2     6.6    -      -       -      -
     21D  VAL*     2.7    44.5    +      -       +      +
     23D  VAL*     5.0     0.7    -      -       +      -
     45D  THR*     3.8    29.8    -      -       +      +
     47D  GLN*     3.4    36.8    -      -       +      +
     73D  VAL*     3.8     9.9    -      -       +      +
     74D  THR*     1.3    73.4    -      -       -      +
     76D  ARG*     1.3    60.7    +      -       -      +
     79D  MET*     3.2    34.5    -      -       +      +
     80D  ALA*     3.7    17.3    -      -       +      +
     83D  PHE*     3.7    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