Contacts of the strand formed by residues 90 - 95 (chain L) in PDB entry 3V4V


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 MET 90 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9L  LEU      5.1     1.6    -      -       -      +
     41L  TYR      3.8     0.7    -      -       -      +
     42L  LEU*     3.7     2.1    -      -       -      +
     43L  HIS*     2.7    54.7    +      -       +      +
     89L  GLY*     1.3    72.1    -      -       -      -
     91L  TYR*     1.3    59.3    +      -       -      +
     92L  TYR*     3.4    34.7    +      -       +      +
    106L  GLY*     4.1     5.6    -      -       -      -
    107L  THR      3.5    13.7    -      -       -      -
    108L  LYS*     3.4    42.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 91 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6L  GLN*     3.0    10.6    +      -       -      +
     21L  ILE*     3.9    16.6    -      -       +      -
     40L  TRP*     5.3     3.1    -      +       +      -
     41L  TYR      3.3    14.4    -      -       -      +
     42L  LEU*     3.5    24.0    -      -       +      +
     52L  LEU*     3.5    24.0    -      -       +      -
     67L  PHE*     4.0     1.6    -      -       -      -
     78L  LEU*     3.9    22.2    -      -       +      -
     80L  ILE*     3.4    25.0    -      -       +      +
     87L  ASP*     3.6    20.8    +      -       -      +
     89L  GLY      3.6    17.3    -      -       -      -
     90L  MET*     1.3    74.5    -      -       -      +
     92L  TYR*     1.3    63.1    +      -       -      +
    106L  GLY*     3.4     4.2    -      -       -      -
    107L  THR      2.8    40.9    +      -       -      +
    109L  LEU*     3.7    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 92 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39H  GLN*     3.7    16.8    +      -       -      -
     43H  GLN      4.8     4.9    +      -       -      -
     44H  GLY*     5.0     3.6    -      -       -      -
     45H  LEU*     3.9    31.4    -      -       +      -
      6L  GLN*     3.6     5.2    -      -       -      -
     40L  TRP*     3.5     6.0    -      -       -      -
     41L  TYR*     2.9    43.2    +      -       +      +
     43L  HIS*     4.1    30.8    -      +       +      -
     49L  PRO*     6.1     0.9    -      -       +      -
     90L  MET*     3.4    31.4    -      -       +      +
     91L  TYR*     1.3    73.7    -      -       -      +
     93L  CYS*     1.3    60.4    +      -       -      +
    103L  PHE*     4.3    20.0    -      -       +      -
    104L  GLY      3.5    18.2    -      -       -      +
    105L  GLY      3.9     8.3    -      -       -      -
    106L  GLY*     3.8    18.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 93 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4L  VAL*     3.5    16.6    -      -       -      +
      6L  GLN*     3.3    15.3    +      -       -      -
     23L  CYS*     2.0    44.2    -      -       -      -
     38L  LEU*     4.4     5.4    -      -       +      -
     39L  SER      3.3     9.2    -      -       -      +
     40L  TRP*     3.7    20.0    -      -       +      -
     92L  TYR*     1.3    75.3    -      -       -      +
     94L  LEU*     1.3    60.8    +      -       -      +
    102L  THR      4.0     0.2    -      -       -      +
    103L  PHE*     3.3     8.2    -      -       -      -
    104L  GLY*     2.9    26.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 94 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108H  ILE*     4.6    19.1    -      -       +      -
    111H  TRP*     5.8     1.1    -      -       +      -
      4L  VAL*     6.0     0.2    -      -       -      -
     37L  TYR      3.6     0.7    -      -       -      +
     38L  LEU*     3.2    12.2    -      -       -      +
     39L  SER*     2.9    35.2    +      -       -      +
     41L  TYR*     3.9    30.7    -      -       +      +
     93L  CYS*     1.3    77.7    -      -       -      +
     95L  GLN*     1.3    79.2    +      -       -      +
     96L  GLY*     4.1     2.2    +      -       -      +
    101L  TYR*     3.9    15.7    -      -       +      -
    102L  THR      3.3    17.9    -      -       -      +
    103L  PHE*     3.7    38.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 95 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2L  VAL*     3.7    21.9    -      -       +      +
      4L  VAL*     3.8    13.6    -      -       +      +
     29L  LEU*     3.5    31.3    -      -       +      +
     37L  TYR      3.5     4.5    -      -       -      -
     38L  LEU*     5.0     0.4    -      -       +      -
     94L  LEU*     1.3    79.5    -      -       -      +
     96L  GLY*     1.3    58.1    +      -       -      +
     97L  THR*     3.4     6.1    +      -       -      -
     98L  HIS*     3.0    41.9    +      -       -      +
    100L  PRO      3.2    16.4    +      -       -      -
    101L  TYR*     3.2    20.8    -      -       -      +
    102L  THR*     3.3    32.8    +      -       -      +
----------------------------------------------------------
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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