Contacts of the strand formed by residues 379 - 387 (chain A) in PDB entry 4RYL


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 ILE 379 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    377A  PRO*     3.6     0.4    -      -       -      +
    378A  ASP*     1.3    90.3    -      -       -      +
    380A  CYS*     1.3    69.7    +      -       -      +
    438A  HIS*     3.5    33.4    -      -       +      +
    439A  ILE      3.3     6.7    -      -       -      +
    440A  ASP*     3.7    20.9    -      -       +      +
    474A  ILE*     4.6     0.5    -      -       -      +
    475A  TYR*     2.8    57.9    +      -       +      +
    477A  GLU*     3.4    43.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 380 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    347A  TRP*     3.5    33.0    -      -       -      -
    352A  LEU*     4.0    22.7    -      -       +      -
    377A  PRO*     4.9     6.1    -      -       -      -
    379A  ILE*     1.3    79.3    -      -       -      +
    381A  THR*     1.3    67.0    +      -       -      +
    439A  ILE*     2.8    42.2    +      -       +      +
    441A  CYS*     4.5    12.3    -      -       -      -
    473A  ASP      3.3    10.1    -      -       -      +
    474A  ILE*     3.9    13.7    -      -       -      -
    475A  TYR*     4.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 381 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    352A  LEU*     5.6     0.2    -      -       -      -
    379A  ILE*     4.9     0.9    -      -       +      -
    380A  CYS*     1.3    79.7    -      -       -      +
    382A  ILE*     1.3    65.8    +      -       -      +
    383A  SER*     4.7     5.6    +      -       -      -
    437A  LYS      3.2    10.5    -      -       -      +
    438A  HIS*     3.9    25.8    -      -       +      -
    439A  ILE*     6.4     0.2    -      -       -      -
    472A  PHE*     3.0    10.2    -      -       -      +
    473A  ASP*     2.9    52.1    +      -       -      +
    475A  TYR*     4.1    16.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 382 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    351A  PHE*     3.5    39.7    -      -       +      +
    352A  LEU*     3.9    35.2    -      -       +      -
    353A  LEU*     4.0    22.7    -      -       +      -
    381A  THR*     1.3    78.9    -      -       -      +
    383A  SER*     1.3    63.6    +      -       -      +
    435A  GLY*     3.5     2.9    -      -       -      -
    436A  ILE*     2.8    46.2    +      -       +      +
    437A  LYS*     3.0    28.2    +      -       +      +
    451A  PHE*     4.2     7.2    -      -       +      -
    471A  TYR      3.4     9.0    -      -       -      +
    472A  PHE*     4.5     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 383 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    381A  THR*     4.7     7.3    +      -       -      -
    382A  ILE*     1.3    79.1    +      -       -      +
    384A  LEU*     1.3    66.8    +      -       -      +
    433A  PRO*     4.4     4.1    -      -       -      +
    434A  CYS      3.3    12.8    -      -       -      -
    435A  GLY*     3.8     9.7    +      -       -      -
    436A  ILE*     4.3     1.1    -      -       -      +
    470A  GLY*     3.2     5.5    -      -       -      -
    471A  TYR*     2.9    63.0    +      -       -      +
    472A  PHE*     4.9     0.5    -      -       -      +
    473A  ASP*     5.1     3.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 384 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    351A  PHE*     4.1    10.8    -      -       +      -
    383A  SER*     1.3    83.2    -      -       -      +
    385A  VAL*     1.3    61.6    +      -       -      +
    433A  PRO*     3.3     5.5    -      -       -      +
    434A  CYS*     2.9    33.7    +      -       +      +
    436A  ILE*     3.9    25.8    -      -       +      -
    455A  PHE*     3.6    40.6    -      -       +      -
    457A  LEU*     3.9    13.3    -      -       +      +
    468A  ILE*     4.1    18.6    -      -       +      -
    469A  ALA      3.2    12.8    -      -       -      +
    470A  GLY*     4.0     7.0    -      -       -      -
    502A  PHE*     4.6     6.3    -      -       +      -
    520A  VAL*     4.3    12.8    -      -       +      -
    536A  LEU*     4.4     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 385 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    384A  LEU*     1.3    77.9    -      -       -      +
    386A  ALA*     1.3    67.6    +      -       -      +
    387A  VAL*     4.0     0.2    -      -       -      +
    429A  LEU*     3.6    35.0    -      -       +      -
    431A  SER*     3.3    31.0    -      -       -      +
    433A  PRO*     4.3    12.6    -      -       +      -
    457A  LEU*     4.5     5.2    -      -       -      -
    468A  ILE*     3.6     3.5    -      -       -      +
    469A  ALA*     2.8    52.0    +      -       +      +
    471A  TYR*     4.1    19.1    -      -       +      -
    490A  PRO*     4.6     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 386 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    385A  VAL*     1.3    75.9    -      -       -      +
    387A  VAL*     1.3    61.9    +      -       -      +
    429A  LEU*     3.5     6.4    -      -       -      -
    430A  ILE*     2.9    42.2    +      -       +      -
    431A  SER*     3.0    24.4    +      -       -      +
    457A  LEU*     4.1    14.4    -      -       +      +
    459A  ILE*     4.4     7.0    -      -       +      -
    465A  CYS*     4.3     5.8    -      -       -      -
    468A  ILE*     3.9    12.8    -      -       +      -
    516A  LEU*     5.0     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 387 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    385A  VAL      4.0     0.4    -      -       -      +
    386A  ALA*     1.3    79.1    -      -       -      +
    388A  SER*     1.3    64.4    +      -       -      +
    389A  ASP*     4.5     0.4    -      -       +      -
    424A  LEU*     4.3    10.3    -      -       +      -
    428A  THR*     3.4    29.6    -      -       -      +
    429A  LEU*     4.1     8.7    -      -       +      -
    430A  ILE*     3.9     4.0    -      -       -      -
    465A  CYS*     3.4     5.2    -      -       -      -
    466A  THR*     2.9    23.3    +      -       -      -
    467A  ALA*     3.0    26.6    +      -       +      +
    468A  ILE      4.3     0.4    -      -       -      -
    469A  ALA*     3.8    32.3    -      -       +      +
    501A  VAL*     5.4     1.3    -      -       +      -
    601A  3ZG      4.0    21.8    -      -       +      -
----------------------------------------------------------
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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