Contacts of the strand formed by residues 60 - 67 (chain Q) in PDB entry 1VQ7


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 THR 60 (chain Q).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   10180    A      2.8    35.8    +      -       -      -
   10190    C      3.4    38.2    -      -       -      +
     38Q  LYS*     4.5     5.1    +      -       +      +
     39Q  VAL      3.3    11.9    -      -       -      +
     40Q  HIS*     3.0    28.8    -      -       +      +
     58Q  GLY      4.4     0.3    +      -       -      -
     59Q  GLN*     1.3    73.7    -      -       -      +
     61Q  GLY*     1.3    62.9    +      -       -      +
     75Q  ILE*     4.9     1.9    -      -       -      +
     94Q  GLN*     3.7    27.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 61 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38Q  LYS*     3.3     7.7    -      -       -      +
     39Q  VAL      2.8    33.4    +      -       -      -
     41Q  LEU*     3.8     4.2    -      -       -      +
     59Q  GLN      3.8     2.4    -      -       -      -
     60Q  THR*     1.3    75.7    -      -       -      +
     62Q  THR*     1.3    63.4    +      -       -      -
     73Q  VAL*     3.5    16.8    -      -       -      -
     74Q  ASP      3.3    13.5    -      -       -      -
     75Q  ILE*     3.8     7.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 62 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36Q  GLY*     3.7    31.2    -      -       -      +
     37Q  GLU      3.5     3.1    -      -       -      -
     38Q  LYS*     3.2    32.2    +      -       +      -
     61Q  GLY*     1.3    71.4    -      -       -      -
     63Q  VAL*     1.3    67.7    +      -       -      +
     64Q  GLU*     3.4    14.6    +      -       +      +
     73Q  VAL*     3.5     1.9    -      -       -      +
     74Q  ASP*     2.9    36.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 63 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33Q  PHE*     4.0    15.5    -      -       +      -
     34Q  ASP      3.7    26.0    -      -       -      +
     35Q  ASP*     4.1     4.5    -      -       -      +
     36Q  GLY      2.7    28.9    +      -       -      -
     37Q  GLU      2.9    18.3    +      -       -      +
     39Q  VAL*     3.8    29.6    -      -       +      -
     61Q  GLY      4.2     0.8    -      -       -      -
     62Q  THR*     1.3    70.8    -      -       -      +
     64Q  GLU*     1.3    66.2    +      -       -      +
     65Q  GLY      4.1     8.5    -      -       -      +
     71Q  TYR*     3.9    26.7    -      -       +      -
     72Q  LYS      3.8     5.8    -      -       -      +
     73Q  VAL*     4.3     9.2    -      -       +      +
     91Q  LEU*     5.3     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 64 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35Q  ASP*     3.8     8.3    -      -       -      +
     36Q  GLY*     3.5    11.4    +      -       -      -
     62Q  THR*     3.5    15.6    -      -       +      +
     63Q  VAL*     1.3    90.5    -      -       -      +
     65Q  GLY*     1.3    66.3    +      -       -      +
     72Q  LYS*     2.8    32.9    +      -       +      +
     74Q  ASP*     2.9    31.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 65 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35Q  ASP*     2.8    30.9    +      -       -      -
     63Q  VAL*     4.1     6.1    -      -       -      +
     64Q  GLU*     1.3    76.8    +      -       -      +
     66Q  LYS*     1.3    64.5    +      -       -      +
     71Q  TYR*     4.0     3.0    -      -       -      -
     72Q  LYS*     3.0    22.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 66 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32Q  GLU*     3.7    15.5    +      -       -      -
     33Q  PHE      5.4     0.4    -      -       -      -
     65Q  GLY*     1.3    76.7    -      -       -      +
     67Q  GLN*     1.3    62.9    +      -       -      +
     68Q  GLY      3.7    14.1    +      -       -      +
     69Q  ASP*     3.8    16.0    +      -       -      +
     70Q  ALA      3.0    13.0    -      -       -      +
     71Q  TYR*     3.3    43.6    +      -       +      -
     72Q  LYS*     4.0    17.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 67 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   23850    G      3.1     9.2    -      -       -      +
   23860    U      2.8    42.3    +      -       -      +
   24030    C      2.5    59.4    +      -       -      +
   24040    G      3.7    18.4    -      -       -      +
     66Q  LYS*     1.3    75.4    -      -       -      +
     68Q  GLY*     1.3    64.7    +      -       -      +
     69Q  ASP      3.4     0.2    +      -       -      -
     70Q  ALA*     2.9    19.8    +      -       -      +
     72Q  LYS*     3.8    20.3    +      -       +      +
     85Q  ILE*     4.2    10.5    -      -       +      +
----------------------------------------------------------
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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