Contacts of the strand formed by residues 45 - 51 (chain H) in PDB entry 1VQ4


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 45 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43H  TYR*     4.2     3.4    -      -       -      +
     44H  PRO*     1.3    82.4    -      -       -      +
     46H  GLN*     1.3    63.9    +      -       -      +
     47H  ILE*     3.8    28.7    +      -       +      -
    136H  ALA      4.0     0.2    -      -       -      +
    137H  TYR*     3.3     6.1    -      -       -      +
    138H  CYS*     3.0    46.6    +      -       -      +
    140H  VAL*     3.6    42.2    -      -       +      +
    143H  ALA*     4.4     8.5    -      -       +      -
    165H  SER*     4.6     0.9    -      -       -      +
    167H  PRO      2.9     1.8    -      -       -      -
    168H  ALA*     3.7    22.4    -      -       +      -
    170H  ASN*     5.0     2.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 46 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43H  TYR      5.9     0.9    -      -       -      +
     45H  VAL*     1.3    74.2    -      -       -      +
     47H  ILE*     1.3    58.1    +      -       -      +
     48H  SER*     4.9     4.0    +      -       -      +
     88H  ARG*     5.7     1.7    -      -       -      +
    132H  GLN*     5.6     1.0    -      -       -      +
    135H  THR*     4.0    10.3    -      -       +      +
    136H  ALA      3.5     4.7    -      -       -      +
    137H  TYR*     2.9    43.8    +      -       +      -
    165H  SER*     3.6     0.7    +      -       -      -
    166H  SER*     2.6    47.3    +      -       -      +
    167H  PRO*     3.0    40.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 47 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45H  VAL*     3.8    23.5    -      -       +      -
     46H  GLN*     1.3    78.8    -      -       -      +
     48H  SER*     1.3    61.1    +      -       -      +
    135H  THR*     3.4     0.8    -      -       -      -
    136H  ALA      2.8    37.4    +      -       -      -
    138H  CYS*     4.8     1.3    -      -       -      -
    143H  ALA*     4.0    11.7    -      -       +      +
    146H  VAL*     3.5    34.8    -      -       +      -
    147H  LYS*     4.2    14.1    -      -       +      -
    150H  PHE*     3.3    15.1    -      -       +      -
    163H  ILE*     3.7    28.5    -      -       +      -
    164H  ASP      3.2    18.2    -      -       -      +
    165H  SER*     4.0    11.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 48 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46H  GLN*     4.3     4.5    +      -       -      +
     47H  ILE*     1.3    76.8    -      -       -      +
     49H  LEU*     1.3    61.5    +      -       -      +
     50H  ILE*     3.8     8.0    +      -       -      -
     88H  ARG*     4.3     0.2    +      -       -      -
    132H  GLN*     3.2    28.6    +      -       -      -
    134H  PHE      3.1    11.0    -      -       -      -
    135H  THR*     2.7    23.5    +      -       -      +
    150H  PHE*     3.7     4.2    -      -       -      -
    162H  ARG      3.7     0.5    -      -       -      +
    163H  ILE*     3.7     3.5    -      -       -      -
    164H  ASP*     2.8    35.8    +      -       -      +
    166H  SER*     4.7     7.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 49 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48H  SER*     1.3    71.6    -      -       -      +
     50H  ILE*     1.3    59.4    +      -       -      +
     51H  VAL*     5.5     0.4    -      -       +      +
    132H  GLN*     3.4     1.3    -      -       -      -
    133H  LEU*     2.8    32.9    +      -       +      +
    134H  PHE*     2.7    46.1    +      -       +      +
    150H  PHE*     3.8    13.9    -      -       +      +
    153H  ALA*     4.2    18.4    -      -       +      -
    154H  TYR*     4.2    19.7    -      -       +      +
    157H  ILE*     4.6     9.4    -      -       +      -
    161H  CYS*     3.5    30.1    -      -       +      -
    162H  ARG      3.6     7.0    -      -       -      +
    163H  ILE*     4.1    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 50 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48H  SER*     4.5     6.3    -      -       -      +
     49H  LEU*     1.3    75.8    -      -       -      +
     51H  VAL*     1.3    61.8    +      -       -      +
     52H  GLU*     3.5     0.7    +      -       +      +
    130H  GLY*     3.0    45.3    -      -       -      +
    131H  GLU      3.2     5.2    -      -       -      +
    132H  GLN*     4.3    14.6    -      -       +      +
    161H  CYS*     3.1     9.0    -      -       -      -
    162H  ARG*     2.9    62.0    +      -       +      +
    164H  ASP*     3.6    36.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 51 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49H  LEU*     3.9     0.6    +      -       +      -
     50H  ILE*     1.3    74.0    -      -       -      +
     52H  GLU*     1.3    54.1    +      -       -      +
     53H  GLU      2.8    31.0    -      -       -      +
     55H  VAL*     4.5     2.5    -      -       +      -
     57H  LEU*     4.7     3.6    -      -       +      -
    127H  VAL*     3.7    34.3    -      -       +      -
    129H  ALA*     4.4     1.8    -      -       -      -
    130H  GLY*     2.6    34.3    +      -       -      -
    131H  GLU      2.9     7.7    +      -       -      +
    133H  LEU*     4.3    26.9    -      -       +      -
    157H  ILE*     4.5     1.1    -      -       +      -
    159H  PRO*     3.8    23.6    -      -       +      -
    160H  SER      4.2     3.6    -      -       -      -
    161H  CYS*     4.3     7.0    -      -       -      -
----------------------------------------------------------
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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