Contacts of the strand formed by residues 389 - 397 (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 ARG 389 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    347A  LEU*     3.7     3.6    -      -       -      -
    348A  PHE*     2.9    55.4    +      -       +      +
    349A  HIS      4.7     0.2    -      -       -      +
    350A  GLY*     4.7    11.1    -      -       -      +
    387A  MET      4.1     5.8    +      -       -      +
    388A  ALA*     1.3    74.3    -      -       -      +
    390A  LEU*     1.3    61.0    +      -       -      +
    391A  CYS*     3.7    13.9    +      -       -      -
    422A  ASN*     3.9     5.0    -      -       +      +
    423A  LEU      3.2    12.1    -      -       -      +
    424A  MET*     4.1    16.4    -      -       -      -
    425A  LEU*     4.7     2.5    -      -       -      -
    455A  PRO      2.8    35.1    +      -       -      -
    456A  THR      4.4     1.0    +      -       -      -
    457A  GLY      2.8    24.0    +      -       -      -
    458A  THR*     5.6     0.2    -      -       -      +
    459A  VAL*     3.4    34.8    -      -       +      +
    588A  PRO*     6.2     1.8    -      -       -      +
    621A  TYR      4.8     9.5    +      -       -      -
    622A  GLU      4.8     1.6    +      -       -      -
    623A  SER*     4.7     9.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 390 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323A  PHE*     3.7    34.8    -      -       +      -
    325A  ILE*     3.7    23.1    -      -       +      -
    345A  ALA*     4.2     8.3    -      -       +      -
    346A  GLY      3.7    12.1    -      -       -      +
    347A  LEU*     4.7     6.1    -      -       +      +
    377A  PHE*     4.5     7.2    -      -       +      -
    389A  ARG*     1.3    70.1    -      -       -      +
    391A  CYS*     1.3    66.9    +      -       -      +
    392A  PHE*     3.5    37.3    -      -       +      -
    421A  ALA      4.1     0.9    -      -       -      +
    422A  ASN*     3.3     1.7    -      -       -      -
    423A  LEU*     2.7    56.2    +      -       +      +
    425A  LEU*     4.3    11.3    -      -       +      +
    475A  LEU*     5.4     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 391 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    345A  ALA*     3.3     5.5    -      -       -      -
    346A  GLY      3.0    35.4    +      -       -      +
    348A  PHE*     3.5    31.0    -      -       +      -
    389A  ARG*     3.8    15.0    -      -       -      -
    390A  LEU*     1.3    79.6    -      -       -      +
    392A  PHE*     1.3    60.1    +      -       -      +
    422A  ASN*     3.2    26.0    -      -       -      +
    453A  LEU*     3.4    18.1    -      -       +      +
    454A  ASN      5.1     0.2    -      -       -      +
    455A  PRO*     3.8    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 392 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    325A  ILE*     4.6     9.6    -      -       +      -
    327A  LEU*     5.8     5.2    -      -       +      -
    343A  VAL*     5.7     8.3    -      -       +      -
    344A  GLN      3.5     4.7    -      -       -      -
    345A  ALA*     3.9    20.2    -      -       +      -
    375A  LEU*     5.4     3.1    -      -       +      -
    390A  LEU*     3.5    45.1    -      -       +      -
    391A  CYS*     1.3    73.8    -      -       -      +
    393A  ALA*     1.3    61.4    +      -       -      +
    420A  TRP*     3.1     7.6    -      -       -      +
    421A  ALA*     2.8    47.1    +      -       +      +
    422A  ASN*     4.7     0.9    -      -       -      +
    423A  LEU*     4.8     3.1    -      -       +      -
    439A  LEU*     3.5    33.7    -      -       +      -
    441A  MET*     5.6     5.8    -      -       -      -
    453A  LEU*     3.7     3.4    -      -       -      +
    454A  ASN      5.6     0.9    +      -       -      -
    471A  LEU*     5.8    11.4    -      -       +      -
    473A  ILE*     3.7    31.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 393 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    342A  VAL      4.0     0.2    -      -       -      +
    343A  VAL*     3.4     4.5    -      -       -      +
    344A  GLN*     2.9    34.7    +      -       +      +
    392A  PHE*     1.3    75.3    -      -       -      +
    394A  LEU*     1.3    59.9    +      -       -      +
    395A  TYR*     3.8    14.7    +      -       +      -
    417A  PRO*     6.5     0.2    -      -       +      -
    419A  ALA      3.3     9.9    -      -       -      +
    420A  TRP*     4.7     4.7    -      -       +      -
    441A  MET*     5.8     0.7    -      -       -      -
    444A  SER*     5.3     3.1    -      -       -      +
    452A  LEU      3.3    26.7    -      -       -      +
    453A  LEU*     3.8    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 394 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    333A  VAL*     5.1    11.7    -      -       +      -
    341A  LEU*     4.9    12.6    -      -       +      -
    342A  VAL      3.5     9.4    -      -       -      +
    343A  VAL*     4.5     5.2    -      -       +      +
    371A  TRP*     5.1    11.0    -      -       +      -
    393A  ALA*     1.3    72.4    -      -       -      +
    395A  TYR*     1.3    60.4    +      -       -      +
    417A  PRO*     3.9     0.9    -      -       -      +
    418A  ILE*     2.8    50.7    +      -       +      +
    419A  ALA      2.8    13.5    +      -       -      +
    441A  MET*     4.3    25.3    -      -       +      -
    444A  SER*     5.1     0.2    +      -       -      -
    471A  LEU*     5.8     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 395 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341A  LEU*     3.4     5.9    -      -       -      +
    342A  VAL*     2.8    40.4    +      -       +      +
    344A  GLN*     4.6    11.2    -      -       +      -
    393A  ALA*     3.8    17.5    -      -       +      -
    394A  LEU*     1.3    79.1    -      -       -      +
    396A  ALA*     1.3    57.1    +      -       -      +
    397A  VAL*     3.7    15.6    +      -       +      -
    415A  ASP*     3.7    27.4    -      -       +      -
    416A  CYS      3.1    22.2    -      -       -      -
    417A  PRO*     3.6    25.0    -      -       +      +
    418A  ILE*     3.9     4.5    -      -       -      -
    450A  GLY      4.2     3.6    +      -       -      -
    451A  GLU      3.3     8.3    +      -       -      -
    452A  LEU*     3.1    47.3    +      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 396 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    335A  ALA*     4.3    17.0    -      -       +      -
    336A  ASP*     5.6     1.1    -      -       +      +
    339A  MET*     3.7    23.2    -      -       +      +
    340A  LYS      3.5     6.5    -      -       -      -
    341A  LEU*     4.7     3.6    -      -       +      +
    395A  TYR*     1.3    69.7    -      -       -      +
    397A  VAL*     1.3    61.0    +      -       -      +
    398A  ILE*     4.1     3.8    +      -       -      +
    415A  ASP*     4.4     0.9    -      -       -      -
    416A  CYS*     2.9    46.6    +      -       +      +
    418A  ILE*     3.7    12.5    -      -       +      +
    564B  ASN      5.5     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 397 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    339A  MET*     3.4     2.6    -      -       -      +
    340A  LYS*     2.8    39.9    +      -       +      +
    342A  VAL*     3.8    27.6    -      -       +      -
    362A  GLU*     3.7    21.5    -      -       +      +
    395A  TYR*     4.1    11.9    -      -       +      -
    396A  ALA*     1.3    72.8    -      -       -      +
    398A  ILE*     1.3    75.2    +      -       -      +
    399A  GLU      3.3     1.6    +      -       -      -
    400A  LYS*     5.6     0.9    -      -       +      +
    415A  ASP*     3.4    28.7    -      -       -      +
----------------------------------------------------------
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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