Contacts of the strand formed by residues 119 - 127 (chain H) in PDB entry 1VQ9


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 119 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96H  ARG*     3.1     4.6    -      -       -      -
     97H  GLU      3.0    28.0    +      -       -      +
     99H  LYS*     3.4    43.5    -      -       +      +
    118H  GLY*     1.3    74.1    -      -       -      -
    120H  ILE*     1.3    71.4    +      -       -      +
    121H  VAL*     3.4     6.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 120 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14H  TYR*     4.8     9.9    -      -       +      +
     20H  ILE*     3.1    30.7    -      -       +      -
     21H  THR      2.7    32.1    -      -       -      +
     22H  GLY      3.8    10.6    -      -       -      +
     23H  ILE*     3.8     4.7    -      -       -      -
     24H  PRO*     3.7    25.4    -      -       +      +
     94H  VAL*     3.5    26.5    -      -       +      -
     95H  LEU      3.7     4.3    -      -       -      -
     96H  ARG*     4.5     2.9    -      -       +      +
    117H  PHE*     6.5     0.2    -      -       +      -
    118H  GLY      5.3     2.0    -      -       -      +
    119H  LYS*     1.3    82.3    -      -       -      +
    121H  VAL*     1.3    65.6    +      -       -      +
    122H  GLY      4.4     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 121 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6H  TYR*     3.5    26.7    -      -       +      +
     24H  PRO*     3.7    15.1    -      -       -      +
     59H  HIS*     5.3     1.7    -      -       -      -
     95H  LEU*     2.9    17.9    +      -       +      +
     96H  ARG      3.5     8.1    -      -       -      +
     97H  GLU*     3.9    16.2    -      -       +      +
     99H  LYS*     4.0    14.6    -      -       +      +
    119H  LYS*     3.5    23.3    -      -       +      +
    120H  ILE*     1.3    80.1    -      -       -      +
    122H  GLY*     1.3    59.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 122 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23H  ILE*     4.6     1.0    -      -       -      +
     24H  PRO*     4.0    12.0    -      -       -      +
     58H  ARG*     6.2     1.6    -      -       -      -
     59H  HIS*     4.4    11.7    -      -       -      -
     94H  VAL*     3.5     6.4    -      -       -      +
     95H  LEU*     2.9    33.8    +      -       -      +
    121H  VAL*     1.3    82.3    -      -       -      +
    123H  THR*     1.3    69.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 123 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17H  ARG*     4.4     8.5    -      -       -      +
     23H  ILE*     3.5    27.1    -      -       +      -
     24H  PRO      4.3     9.3    +      -       -      +
     26H  SER*     4.8     3.1    -      -       -      -
     58H  ARG*     3.4     5.9    -      -       -      +
     59H  HIS*     3.0    49.8    +      -       -      +
     91H  PRO*     3.6    26.3    -      -       -      +
     92H  HIS      5.4     0.2    -      -       -      +
     93H  GLN      3.2     9.4    -      -       -      +
     94H  VAL*     4.5     4.7    -      -       +      -
     95H  LEU*     4.1     4.0    -      -       -      +
    122H  GLY*     1.3    79.5    -      -       -      +
    124H  ALA*     1.3    61.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 124 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56H  GLN*     4.5    10.5    -      -       +      -
     57H  LEU      3.3    25.6    -      -       -      +
     58H  ARG*     3.7     2.5    -      -       +      +
     91H  PRO*     3.2     9.9    -      -       -      +
     93H  GLN*     2.7    40.7    +      -       +      +
     95H  LEU*     3.7    27.6    -      -       +      -
    123H  THR*     1.3    76.7    -      -       -      +
    125H  ALA*     1.3    58.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 125 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56H  GLN*     3.4     2.3    -      -       -      -
     57H  LEU*     2.8    37.9    +      -       +      +
     62H  LEU*     4.5    10.5    -      -       +      -
     89H  LYS*     4.1    20.4    -      -       +      -
     90H  PHE*     3.6    25.8    -      -       -      +
     91H  PRO*     3.6     7.0    -      -       +      +
     92H  HIS      4.6     0.2    -      -       -      +
    124H  ALA*     1.3    73.5    -      -       -      +
    126H  ARG*     1.3    63.8    +      -       -      +
    127H  VAL*     3.7     7.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 126 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   10040    C      4.3    13.9    +      -       -      -
   10050    A      5.7     5.3    +      -       -      -
      9H  ILE*     3.5    41.2    -      -       +      +
     11H  LYS*     2.7    32.1    +      -       -      +
     12H  PRO      3.8     0.2    +      -       -      -
     13H  ALA*     4.2    18.1    -      -       -      +
     55H  VAL      3.5     4.0    -      -       -      -
     56H  GLN*     3.0    32.0    -      -       +      +
     89H  LYS*     4.4     5.9    -      -       -      +
     93H  GLN*     2.8    33.9    -      -       +      +
    124H  ALA      4.0     0.4    +      -       -      -
    125H  ALA*     1.3    73.3    -      -       -      +
    127H  VAL*     1.3    63.0    +      -       -      +
    128H  GLN*     4.2     6.6    +      -       -      +
    131H  GLU*     4.5     1.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 127 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51H  VAL*     3.7    28.3    -      -       +      -
     53H  GLU      3.8     1.2    -      -       -      +
     54H  THR*     3.2     1.2    -      -       -      -
     55H  VAL*     2.8    43.9    +      -       +      +
     57H  LEU*     4.1    20.9    -      -       +      -
     89H  LYS*     4.1    24.2    -      -       +      +
    125H  ALA*     4.1     8.5    -      -       +      +
    126H  ARG*     1.3    80.1    -      -       -      +
    128H  GLN*     1.3    76.8    +      -       -      +
    131H  GLU*     3.6    16.6    -      -       +      +
    133H  LEU*     4.2     8.3    -      -       +      -
----------------------------------------------------------
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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