Contacts of the strand formed by residues 483 - 495 (chain B) in PDB entry 4RYD


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 483 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    395B  HIS*     4.0    19.3    +      -       -      -
    399B  GLN*     4.3    14.3    -      -       -      +
    441B  TRP*     5.7     3.0    -      -       -      -
    444B  VAL*     5.3     5.9    -      -       -      +
    481B  ILE*     3.8     2.5    -      -       -      -
    482B  THR*     1.3    81.6    -      -       -      +
    484B  LEU*     1.3    64.9    +      -       -      +
    485B  GLU*     4.6     1.9    -      -       -      +
    540B  ASP*     3.0    47.6    +      -       -      +
    541B  GLU      3.7     1.8    -      -       -      -
    572B  GLY*     3.4     1.6    -      -       -      -
    573B  THR*     2.9    47.3    +      -       -      +
    574B  ALA      5.1     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 484 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    481B  ILE*     4.0     3.9    -      -       +      +
    483B  ARG*     1.3    73.3    -      -       -      +
    485B  GLU*     1.3    69.8    +      -       -      +
    486B  HIS      3.6    11.2    -      -       -      +
    487B  ALA*     4.1    14.8    -      -       +      -
    538B  SER*     3.7    36.6    -      -       -      +
    539B  TRP*     3.6     1.7    -      -       -      -
    540B  ASP*     2.6    29.5    +      -       -      +
    541B  GLU*     2.9    22.8    +      -       +      +
    543B  PRO*     4.3    13.0    -      -       +      -
    547B  TRP*     4.1    15.3    -      -       +      -
    570B  LEU*     3.7    29.8    -      -       +      -
    571B  TYR      3.4    18.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 485 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    391B  ARG*     2.9    48.5    +      -       -      +
    395B  HIS*     2.8    35.9    +      -       +      +
    447B  GLN*     4.5     3.3    +      -       -      +
    483B  ARG      4.6     2.0    -      -       -      +
    484B  LEU*     1.3    85.6    -      -       -      +
    486B  HIS*     1.3    71.6    +      -       -      +
    487B  ALA      4.0     0.2    +      -       -      -
    535B  THR      4.5     3.6    -      -       -      +
    536B  THR*     5.0     0.2    -      -       -      -
    538B  SER      4.5     0.3    +      -       -      -
    539B  TRP*     3.6    45.5    +      -       +      -
    571B  TYR*     2.8    15.4    +      -       -      +
    572B  GLY*     4.0    15.7    +      -       -      -
    573B  THR*     4.0     6.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 486 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    312B  ILE*     3.4    57.9    +      -       +      +
    390B  TRP*     4.4    12.1    -      +       -      -
    391B  ARG*     5.3     2.2    -      -       +      -
    394B  GLN*     2.8    30.4    +      -       -      -
    447B  GLN*     5.3     0.8    +      -       -      -
    484B  LEU*     3.6     3.3    -      -       -      +
    485B  GLU*     1.3    92.5    +      -       +      +
    487B  ALA*     1.3    61.3    +      -       -      +
    534B  MET*     4.1    20.2    -      -       +      -
    535B  THR      3.9     5.8    -      -       -      -
    536B  THR*     4.8     4.3    -      -       +      -
    539B  TRP*     3.6    22.8    -      +       -      -
    571B  TYR*     3.1    37.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 487 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    484B  LEU*     4.1    14.6    -      -       +      -
    486B  HIS*     1.3    75.6    -      -       -      +
    488B  GLN*     1.3    63.8    -      -       -      +
    505B  LEU*     5.4     1.3    -      -       +      -
    533B  PHE      4.0     0.2    -      -       -      +
    534B  MET*     3.4     4.4    -      -       -      +
    535B  THR*     3.0    49.3    +      -       +      +
    547B  TRP*     4.5     9.2    -      -       +      -
    568B  LEU*     5.1     2.9    -      -       +      -
    569B  VAL      3.3     9.4    -      -       -      +
    570B  LEU*     4.1    17.0    -      -       +      -
    571B  TYR*     5.0     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 488 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269A  LEU*     5.6     0.2    -      -       -      +
    272A  GLU*     5.3     3.1    +      -       -      +
    310B  ASN      5.3     1.8    +      -       -      -
    311B  SER*     6.0     0.6    -      -       -      +
    312B  ILE*     4.2    15.9    -      -       +      +
    487B  ALA*     1.3    79.1    -      -       -      +
    489B  ALA*     1.3    60.9    +      -       -      +
    490B  ARG*     3.8    17.9    +      -       +      +
    505B  LEU*     5.5     0.7    -      -       -      -
    532B  ALA*     3.9    27.4    +      -       +      +
    533B  PHE      3.2     8.3    -      -       -      +
    534B  MET*     4.2    15.9    -      -       +      +
    567B  THR      4.3     0.2    -      -       -      -
    568B  LEU*     3.5     8.9    -      -       -      +
    569B  VAL*     2.8    47.7    +      -       +      +
    571B  TYR*     3.4    34.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 489 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    488B  GLN*     1.3    73.0    -      -       -      +
    490B  ARG*     1.3    63.4    +      -       -      +
    491B  LEU*     3.3    11.1    +      -       +      +
    505B  LEU*     4.3    11.0    -      -       +      +
    515B  LEU*     3.7    29.4    -      -       +      -
    531B  TRP      3.4     0.7    -      -       -      +
    533B  PHE*     2.8    32.9    +      -       -      +
    549B  LEU*     5.0     0.9    -      -       +      -
    566B  PHE*     4.0    20.6    -      -       +      -
    567B  THR      3.5     5.2    -      -       -      -
    568B  LEU*     4.7     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 490 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    268A  ARG*     3.1    43.7    -      -       -      +
    269A  LEU*     3.8    35.5    -      -       -      +
    272A  GLU*     4.4    14.3    +      -       -      -
    488B  GLN*     3.8    16.4    +      -       +      +
    489B  ALA*     1.3    68.7    -      -       -      +
    491B  LEU*     1.3    60.7    +      -       -      +
    530B  ASP*     3.1    33.1    +      -       -      +
    531B  TRP      3.4     6.3    -      -       -      +
    532B  ALA*     3.5    30.9    -      -       +      +
    565B  LYS*     3.2     9.0    +      -       -      -
    566B  PHE*     3.4     3.1    -      -       -      -
    567B  THR*     2.8    45.1    +      -       -      +
    569B  VAL*     3.9    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 491 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    489B  ALA*     3.7    12.1    -      -       +      +
    490B  ARG*     1.3    77.5    -      -       -      +
    492B  THR*     1.3    62.4    +      -       -      +
    493B  LEU*     4.2    10.1    -      -       +      -
    503B  ILE*     4.0    32.5    -      -       +      -
    515B  LEU*     5.1     1.3    -      -       +      -
    528B  PHE*     3.8     8.3    -      -       +      +
    530B  ASP      3.0     2.6    +      -       -      -
    531B  TRP      2.9    29.4    +      -       -      +
    533B  PHE*     3.8    27.6    -      -       +      -
    549B  LEU*     3.8    20.0    -      -       +      -
    551B  ILE*     4.9     0.7    -      -       +      -
    563B  LEU*     4.4     9.6    -      -       +      -
    565B  LYS*     3.4     2.9    -      -       -      +
    566B  PHE*     3.5    37.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 492 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    491B  LEU*     1.3    69.8    -      -       -      +
    493B  LEU*     1.3    65.3    +      -       -      +
    528B  PHE      3.2    10.5    -      -       -      +
    529B  ASN*     4.2    10.9    +      -       -      +
    530B  ASP*     2.9    18.0    +      -       -      +
    563B  LEU*     3.5     2.6    -      -       -      +
    564B  THR*     2.9    36.6    +      -       -      +
    565B  LYS*     2.7    47.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 493 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461B  ILE*     4.4     7.2    -      -       +      -
    491B  LEU*     4.6     8.3    -      -       +      -
    492B  THR*     1.3    77.6    -      -       -      +
    494B  SER*     1.3    75.4    +      -       -      +
    495B  TYR*     4.1     2.7    -      -       +      -
    501B  LEU*     4.0    22.7    -      -       +      -
    503B  ILE*     4.3    19.5    -      -       +      -
    526B  ASP      4.4     1.4    -      -       -      +
    527B  GLY*     3.4     5.8    -      -       -      -
    528B  PHE*     2.9    57.8    +      -       +      +
    551B  ILE*     4.4     9.6    -      -       +      -
    562B  THR      3.1    14.8    -      -       -      +
    563B  LEU*     3.8    22.2    -      -       +      -
    564B  THR*     4.4     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 494 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461B  ILE*     3.9     0.7    -      -       -      +
    493B  LEU*     1.3    79.5    -      -       -      +
    495B  TYR*     1.3    65.0    +      -       -      +
    525B  ALA      5.7     1.1    -      -       -      -
    526B  ASP      5.5     1.3    -      -       -      -
    527B  GLY*     4.5     3.1    -      -       -      +
    561B  GLY*     3.0     6.0    -      -       -      -
    562B  THR*     2.9    46.2    +      -       -      +
    564B  THR*     5.7     1.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 495 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461B  ILE*     3.8    20.6    -      -       +      -
    462B  GLY      3.6     6.4    +      -       -      -
    493B  LEU*     4.1     3.7    -      -       +      +
    494B  SER*     1.3    75.9    -      -       -      +
    496B  ASN*     1.3    62.5    +      -       -      +
    497B  ARG      3.3    34.5    -      -       -      +
    498B  ARG*     4.8     4.7    +      -       -      +
    500B  ASP*     4.5     2.9    -      -       +      -
    501B  LEU*     3.5    46.2    -      -       +      +
    524B  SER      4.3     0.9    -      -       -      +
    525B  ALA*     3.4    24.4    +      -       -      +
    527B  GLY*     4.4     7.0    +      -       -      +
    553B  ASN*     3.2    24.4    -      -       -      +
    559B  ASN*     2.9    36.4    -      -       +      +
    560B  TYR*     3.4    29.2    -      -       -      -
    561B  GLY*     3.8     6.1    -      -       -      -
----------------------------------------------------------
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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