Contacts of the strand formed by residues 116 - 121 (chain L) in PDB entry 1VCB


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 LEU 116 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63L  LEU*     4.3    11.4    -      -       +      -
     64L  ARG      3.9    26.5    -      -       -      +
     65L  SER*     3.0    10.1    +      -       -      +
     66L  VAL*     6.1     0.4    -      -       +      -
     88L  TRP*     3.5     5.2    -      -       -      -
     89L  LEU*     2.8    61.7    +      -       +      +
    114L  GLY      3.6    11.7    -      -       -      +
    115L  HIS*     1.3    82.1    -      -       -      +
    117L  TRP*     1.3    62.0    +      -       -      +
    135L  LEU*     4.2    23.3    -      -       +      -
    136L  PHE      3.7     1.1    -      -       -      -
    137L  VAL*     3.9    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 117 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76L  PHE*     3.8    36.7    -      +       -      -
     86L  PRO*     4.1     3.8    -      -       +      -
     87L  VAL      3.4    13.0    -      -       -      -
     88L  TRP*     3.6    49.5    -      +       +      -
     89L  LEU*     5.7     0.4    -      -       -      -
     98L  TYR*     3.6    44.6    -      +       +      -
    109L  ILE*     4.4    13.5    -      -       +      -
    110L  HIS      5.4     1.3    -      -       -      -
    111L  SER*     3.2    26.1    +      -       -      -
    115L  HIS*     4.6     0.4    -      -       -      -
    116L  LEU*     1.3    79.6    -      -       -      +
    118L  LEU*     1.3    65.5    +      -       -      +
    119L  PHE*     3.9    16.6    -      +       +      -
    135L  LEU*     3.4     9.0    -      -       -      +
    136L  PHE*     2.9    41.0    +      +       +      +
    138L  PRO*     3.9    23.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 118 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87L  VAL*     2.7    64.3    +      -       +      +
     89L  LEU*     4.4    10.5    -      -       +      -
    117L  TRP*     1.3    78.7    -      -       -      +
    119L  PHE*     1.3    66.7    +      -       -      +
    120L  ARG*     4.0    29.4    -      -       +      +
    134L  GLU      4.3     5.6    -      -       -      +
    135L  LEU*     3.7    18.4    -      -       +      -
    194L  VAL*     4.0    24.0    -      -       +      +
    197L  ASP*     6.1     1.1    -      -       +      -
    198L  LEU*     3.9    28.3    -      -       +      -
    201L  LEU*     5.4     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 119 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76L  PHE*     3.6    34.3    -      +       -      -
     84L  VAL*     4.0    13.2    -      -       +      -
     85L  LEU      3.7     2.0    -      -       -      -
     86L  PRO*     3.6    34.3    -      -       +      -
    117L  TRP*     3.9    23.6    -      +       +      -
    118L  LEU*     1.3    78.2    -      -       -      +
    120L  ARG*     1.3    80.5    +      -       -      +
    128L  LEU*     3.3    22.5    +      -       +      +
    129L  LEU      5.3     0.4    -      -       -      +
    130L  VAL*     3.5    44.4    -      -       +      +
    134L  GLU      4.9     2.0    +      -       -      -
    136L  PHE*     4.1     2.5    -      +       +      -
    149L  ALA*     4.7     0.9    -      -       +      -
    151L  ILE*     3.7    37.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 120 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84L  VAL*     3.6     3.6    -      -       -      -
     85L  LEU*     2.8    41.7    +      -       +      +
     87L  VAL*     4.8     4.9    -      -       +      -
    118L  LEU*     4.0    31.8    -      -       +      +
    119L  PHE*     1.3    94.4    +      -       -      +
    121L  ASP*     1.3    66.2    +      -       -      +
    125L  HIS*     3.4    24.7    -      -       +      +
    126L  ASP      3.3    10.8    -      -       -      +
    127L  GLY*     3.5    13.4    -      -       -      -
    128L  LEU*     3.5    20.9    +      -       -      +
    134L  GLU*     4.0    25.3    +      -       -      +
    194L  VAL*     4.0    28.3    -      -       +      +
    197L  ASP*     2.9    35.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 121 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82L  ARG*     3.3    46.1    +      -       +      +
     83L  VAL*     3.7     8.0    +      -       -      +
     85L  LEU*     4.6     0.3    -      -       -      +
    120L  ARG*     1.3    72.9    -      -       -      +
    122L  ALA*     1.3    61.0    +      -       -      +
    123L  GLY*     2.8    26.9    +      -       -      -
    124L  THR*     2.9    32.4    +      -       -      +
    125L  HIS*     2.9    28.6    +      -       -      -
    126L  ASP*     2.9    16.5    +      -       +      +
    128L  LEU*     3.6     8.5    -      -       +      +
----------------------------------------------------------
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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