Contacts of the strand formed by residues 340 - 349 (chain A) in PDB entry 5VLR


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 340 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    338A  ARG      5.3     1.1    -      -       -      +
    339A  MET*     1.3    77.7    -      -       -      +
    341A  LEU*     1.3    59.8    +      -       -      +
    362A  GLU*     3.8    30.7    -      -       +      -
    363A  VAL*     3.4    28.0    -      -       -      +
    364A  SER*     3.9    11.0    -      -       -      +
    365A  VAL*     3.9     4.5    -      -       -      -
    396A  ALA*     3.5     2.8    -      -       -      -
    397A  VAL*     2.8    40.8    +      -       +      +
    399A  GLU*     3.8    30.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 341 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    333A  VAL*     4.5    22.0    -      -       +      -
    335A  ALA*     4.9     2.9    -      -       +      -
    340A  LYS*     1.3    71.7    -      -       -      +
    342A  VAL*     1.3    60.5    +      -       -      +
    361A  SER      3.6     6.9    -      -       -      +
    362A  GLU*     3.6     2.1    -      -       -      -
    363A  VAL      2.8    35.1    +      -       -      +
    365A  VAL*     3.8    25.7    -      -       +      +
    369A  PRO*     4.9    10.5    -      -       +      -
    371A  TRP*     3.8    23.8    +      -       +      -
    394A  LEU*     4.9     7.6    -      -       +      -
    395A  TYR      3.4     8.1    -      -       -      +
    396A  ALA*     4.9     4.3    -      -       +      -
    418A  ILE*     5.7     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 342 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    340A  LYS      4.0     0.6    +      -       -      -
    341A  LEU*     1.3    73.4    -      -       -      +
    343A  VAL*     1.3    60.4    +      -       -      +
    344A  GLN*     4.1     1.1    -      -       +      +
    359A  SER*     6.2     2.2    -      -       -      -
    360A  SER*     3.8    15.3    -      -       -      +
    361A  SER      4.4     1.8    -      -       -      +
    362A  GLU*     5.2     8.3    -      -       +      -
    371A  TRP*     4.8     2.9    -      -       -      -
    394A  LEU*     3.5     5.4    -      -       -      +
    395A  TYR*     2.8    38.7    +      -       +      +
    397A  VAL*     3.8    25.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 343 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    327A  LEU*     3.7    32.2    -      -       +      +
    342A  VAL*     1.3    73.6    -      -       -      +
    344A  GLN*     1.4    61.2    +      -       -      +
    345A  ALA*     3.9     2.5    +      -       -      +
    359A  SER*     3.9     2.2    -      -       -      -
    360A  SER*     2.8    33.1    +      -       -      +
    371A  TRP*     4.8     9.8    -      -       +      -
    375A  LEU*     5.0     2.5    -      -       +      +
    392A  PHE*     5.7     8.3    -      -       +      -
    393A  ALA      3.4     8.3    -      -       -      +
    394A  LEU*     4.5     5.6    -      -       +      +
    471A  LEU*     5.3     7.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 344 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    342A  VAL*     4.1     2.4    -      -       +      +
    343A  VAL*     1.4    72.2    -      -       -      +
    345A  ALA*     1.3    62.2    +      -       -      +
    357A  THR*     4.8    15.0    -      -       -      +
    358A  VAL      4.2     3.4    -      -       -      +
    359A  SER*     3.6    21.5    -      -       -      +
    392A  PHE*     3.5     3.7    -      -       -      +
    393A  ALA*     2.9    35.5    +      -       +      +
    395A  TYR*     4.6    18.5    -      -       +      -
    452A  LEU*     4.3    19.7    -      -       +      -
    453A  LEU*     3.3    10.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 345 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343A  VAL      3.9     0.9    +      -       -      +
    344A  GLN*     1.3    75.6    -      -       -      +
    346A  GLY*     1.3    58.2    +      -       -      +
    357A  THR*     3.3     4.5    -      -       -      -
    358A  VAL      2.9    38.9    +      -       -      +
    375A  LEU*     4.3    12.6    -      -       +      -
    377A  PHE*     3.6    20.4    -      -       +      -
    390A  LEU*     4.2     1.6    -      -       +      -
    391A  CYS      3.3     9.2    -      -       -      +
    392A  PHE*     3.9    22.7    -      -       +      -
    453A  LEU*     4.0     4.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 346 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    345A  ALA*     1.3    74.5    -      -       -      +
    347A  LEU*     1.3    64.2    +      -       -      -
    348A  PHE*     4.0     6.1    -      -       -      -
    356A  LYS      5.2     0.2    -      -       -      -
    357A  THR*     3.9    12.8    -      -       -      -
    377A  PHE*     4.3     6.1    -      -       -      -
    390A  LEU*     3.7     6.1    -      -       -      +
    391A  CYS*     3.0    32.7    +      -       -      +
    453A  LEU*     3.4    17.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 347 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323A  PHE*     4.4    22.9    -      -       +      -
    346A  GLY*     1.3    77.5    -      -       -      +
    348A  PHE*     1.4    66.9    +      -       -      +
    353A  MET*     3.6     7.3    -      -       -      +
    354A  LEU*     3.0    36.4    +      -       +      -
    355A  CYS*     4.2    18.3    +      -       -      -
    356A  LYS      5.4     0.2    +      -       -      -
    377A  PHE*     4.4    20.3    -      -       +      -
    379A  ILE*     4.7     7.0    -      -       +      -
    384A  LEU*     5.0     6.7    -      -       +      -
    388A  ALA*     6.3     1.1    -      -       +      -
    389A  ARG      3.7     6.3    -      -       -      +
    390A  LEU*     4.7     8.3    -      -       +      -
    425A  LEU*     5.4     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 348 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    346A  GLY*     4.0     5.4    -      -       -      -
    347A  LEU*     1.4    85.2    -      -       -      +
    349A  HIS*     1.3    58.5    +      -       -      +
    350A  GLY      4.1     6.3    -      -       -      +
    351A  ASN      3.5    20.0    -      -       -      -
    352A  GLU      3.2    21.5    -      -       -      -
    353A  MET*     3.6    38.4    -      -       +      -
    354A  LEU*     3.4    12.6    -      -       -      +
    388A  ALA*     3.4     1.0    -      -       -      -
    389A  ARG*     2.9    47.9    +      -       +      +
    391A  CYS*     3.5    17.5    -      -       -      -
    453A  LEU*     3.6    34.5    -      -       +      -
    455A  PRO*     3.7    26.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 349 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    348A  PHE*     1.3    72.9    -      -       -      +
    350A  GLY*     1.3    61.5    +      -       -      +
    351A  ASN      3.4     0.5    +      -       -      -
    352A  GLU*     3.0    28.3    +      -       +      +
    354A  LEU*     3.7    23.5    -      -       +      +
    385A  PRO*     3.7    21.4    -      -       +      +
    387A  MET*     3.5    35.8    -      -       +      +
    555A  TRP*     3.4    48.4    -      +       +      -
    586A  SER      5.2     1.4    -      -       -      +
    588A  PRO*     3.4    26.3    -      -       +      +
    589A  ASP*     4.0    15.1    +      -       +      -
----------------------------------------------------------
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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