Contacts of the strand formed by residues 62 - 68 (chain S) in PDB entry 1VQM


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 LYS 62 (chain S).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   16740    C      4.3     7.9    +      -       -      -
   16750    C      2.9    35.1    +      -       -      -
     27S  ALA*     3.5     4.0    -      -       -      +
     28S  VAL*     2.8    59.8    +      -       +      +
     30S  ASP*     3.3    26.3    +      -       -      +
     31S  ARG      4.7     0.4    -      -       -      -
     32S  ALA      2.8    29.1    +      -       -      +
     33S  SER*     4.9     0.2    -      -       -      +
     54S  THR*     4.1    18.0    -      -       +      +
     55S  GLN      3.3    13.2    -      -       -      +
     56S  ASN*     3.4    15.3    -      -       -      +
     61S  GLU*     1.3    77.3    -      -       -      +
     63S  LYS*     1.3    68.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 63 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   14450    G      4.1    23.2    +      -       -      -
   14460    U      2.7    28.3    +      -       -      -
      9S  HIS*     3.9    28.0    +      -       +      +
     13S  LYS*     5.8     1.6    -      -       -      +
     25S  GLN*     3.8    21.6    +      -       -      +
     26S  PHE      3.4     9.4    -      -       -      +
     27S  ALA*     4.7     1.3    -      -       -      +
     53S  ASN      3.9     0.2    -      -       -      +
     54S  THR*     3.4     3.6    -      -       -      -
     55S  GLN*     2.7    56.0    +      -       +      +
     57S  THR*     4.0    16.0    +      -       -      +
     61S  GLU      4.2     0.4    +      -       -      -
     62S  LYS*     1.3    77.1    -      -       -      +
     64S  ALA*     1.3    69.3    +      -       -      +
     65S  VAL*     5.1     9.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 64 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24S  LEU      3.8     0.5    -      -       -      +
     25S  GLN*     3.1     7.3    -      -       -      +
     26S  PHE*     2.8    42.0    +      -       +      +
     28S  VAL*     4.1    15.7    -      -       +      -
     37S  VAL*     3.9    28.3    -      -       +      -
     52S  VAL*     4.6     1.3    -      -       +      -
     53S  ASN      3.4     7.4    -      -       -      +
     54S  THR*     4.6     7.4    -      -       +      -
     63S  LYS*     1.3    76.3    -      -       -      +
     65S  VAL*     1.3    62.4    +      -       -      +
     66S  VAL*     3.8     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 65 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   14470    U      3.6    32.3    -      -       +      +
     17S  ASP*     3.6    21.8    -      -       -      +
     23S  LYS*     3.8    25.6    -      -       +      +
     24S  LEU      3.7     2.2    -      -       -      -
     25S  GLN*     3.9    21.5    -      -       +      +
     51S  GLN      3.8     1.2    -      -       -      +
     52S  VAL*     3.5     3.6    -      -       -      -
     53S  ASN*     2.9    39.7    +      -       +      +
     54S  THR      6.4     0.4    -      -       -      -
     63S  LYS*     5.1    11.2    -      -       +      +
     64S  ALA*     1.3    76.0    -      -       -      +
     66S  VAL*     1.3    60.6    +      -       -      +
     67S  ARG      3.9     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 66 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23S  LYS*     3.3     2.8    -      -       -      -
     24S  LEU*     2.6    44.3    +      -       +      +
     26S  PHE*     3.9    27.8    -      -       +      -
     37S  VAL*     3.9    24.9    -      -       +      -
     41S  VAL*     4.2    12.3    -      -       +      -
     49S  VAL*     3.5    42.6    -      -       +      -
     51S  GLN      3.6     2.7    -      -       -      +
     52S  VAL*     4.2     4.7    -      -       +      -
     64S  ALA*     4.3     5.2    -      -       +      -
     65S  VAL*     1.3    74.3    -      -       -      +
     67S  ARG*     1.3    61.0    +      -       -      +
     68S  LEU*     3.8     6.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 67 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   15080    C      3.0    28.9    +      -       -      -
     21S  GLN      3.8    21.8    -      -       -      +
     22S  ASN*     3.7     3.8    -      -       +      +
     23S  LYS*     3.8    17.0    -      -       +      +
     49S  VAL*     3.7     4.3    -      -       -      +
     50S  GLU*     2.9    54.7    +      -       -      +
     51S  GLN*     3.0    57.0    +      -       +      +
     65S  VAL      3.9     1.6    +      -       -      +
     66S  VAL*     1.3    73.3    -      -       -      +
     68S  LEU*     1.3    72.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 68 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22S  ASN*     3.0    28.6    +      -       -      +
     24S  LEU*     3.8    29.4    -      -       +      -
     41S  VAL*     4.8     1.1    -      -       +      -
     47S  VAL*     3.6    27.1    -      -       +      -
     48S  THR      3.4     7.4    -      -       -      +
     49S  VAL*     4.4     1.8    -      -       +      -
     50S  GLU*     4.0     4.9    -      -       -      +
     66S  VAL*     4.3    20.6    -      -       +      +
     67S  ARG*     1.3    90.0    +      -       -      +
     69S  SER*     1.3    67.5    +      -       -      +
     70S  GLU*     5.6     0.5    -      -       -      +
     72S  ASP*     4.1    16.6    -      -       +      -
     74S  ALA*     3.9    27.6    -      -       +      +
     77S  VAL*     4.3     7.4    -      -       +      -
----------------------------------------------------------
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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