Contacts of the strand formed by residues 545 - 554 (chain D) in PDB entry 1P8J


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 GLY 545 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    470D  ALA*     4.3     3.4    -      -       -      -
    471D  VAL*     2.7    45.9    +      -       -      +
    508D  PRO*     3.5     8.7    -      -       -      -
    543D  PRO      3.4     0.4    +      -       -      -
    544D  ALA*     1.3    74.5    -      -       -      +
    546D  GLU*     1.3    59.5    +      -       -      -
    547D  TRP*     3.7     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 546 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    468D  ARG*     2.8    52.1    +      -       -      +
    469D  LYS*     3.3    13.4    +      -       -      +
    470D  ALA*     4.2     6.5    +      -       +      +
    506D  ILE*     4.2     0.7    -      -       -      +
    507D  SER      4.1     1.9    -      -       -      +
    508D  PRO*     3.4    24.8    -      -       -      +
    545D  GLY*     1.3    71.2    -      -       -      -
    547D  TRP*     1.3    71.0    +      -       -      +
    548D  VAL*     4.1     6.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 547 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    454D  ILE*     5.7     2.0    -      -       +      -
    467D  VAL      3.7     0.5    -      -       -      +
    468D  ARG*     3.3     4.0    -      -       -      -
    469D  LYS*     2.8    36.9    +      -       +      +
    471D  VAL*     3.5    28.9    -      -       +      +
    484D  LEU*     3.9    27.8    -      -       +      -
    487D  VAL*     4.2    15.9    -      -       +      -
    505D  LEU*     3.7    40.2    -      -       +      -
    506D  ILE      3.5    16.2    -      -       -      -
    507D  SER*     3.7    21.1    -      -       -      -
    508D  PRO*     3.2    23.1    -      -       +      +
    535D  THR*     5.8     1.1    -      -       +      -
    538D  SER*     4.5     3.6    -      -       -      -
    543D  PRO*     2.9    23.8    +      -       +      +
    545D  GLY      3.9     0.2    -      -       -      -
    546D  GLU*     1.3    71.5    -      -       -      +
    548D  VAL*     1.3    65.1    +      -       -      +
    566D  PHE*     5.8     4.9    -      -       +      -
    568D  LEU*     3.8    21.0    -      -       +      +
    570D  LEU*     4.1    10.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 548 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    466D  GLU*     3.7    28.7    -      -       +      +
    467D  VAL      3.2     4.3    -      -       -      +
    468D  ARG*     3.8    37.5    -      -       +      +
    504D  HIS      3.7     0.5    -      -       -      +
    505D  LEU*     3.4     8.0    -      -       -      +
    506D  ILE*     2.8    57.5    +      -       +      +
    546D  GLU*     4.1    10.3    -      -       +      +
    547D  TRP*     1.3    82.0    -      -       -      +
    549D  LEU*     1.3    65.9    +      -       -      +
    550D  GLU*     4.2    10.3    -      -       +      +
    566D  PHE*     5.6     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 549 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    465D  LEU*     3.8     1.3    -      -       +      +
    466D  GLU*     3.3     6.2    -      -       -      +
    467D  VAL*     2.8    42.4    +      -       +      +
    491D  LEU*     3.8    21.8    -      -       +      -
    503D  ILE*     3.8    19.5    -      -       +      -
    504D  HIS      3.4    13.2    -      -       -      +
    505D  LEU*     4.5     4.0    -      -       +      -
    515D  LEU*     4.2    13.9    -      -       +      -
    547D  TRP      4.3     0.2    -      -       -      -
    548D  VAL*     1.3    73.0    -      -       -      +
    550D  GLU*     1.3    60.9    +      -       -      +
    551D  ILE*     4.1    13.7    -      -       +      -
    563D  LEU*     3.9    20.9    -      -       +      -
    566D  PHE*     3.7    44.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 550 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    464D  ARG*     4.7    14.8    +      -       -      +
    465D  LEU      3.6     4.7    -      -       -      +
    466D  GLU*     4.6    15.3    -      -       +      +
    502D  ALA      3.6     1.4    -      -       -      +
    503D  ILE*     3.2     8.5    -      -       -      +
    504D  HIS*     2.7    48.6    +      -       +      +
    506D  ILE*     3.8    17.9    -      -       +      +
    512D  ARG*     2.8    41.0    +      -       -      -
    548D  VAL*     4.2    12.6    -      -       +      +
    549D  LEU*     1.3    78.1    -      -       -      +
    551D  ILE*     1.3    63.1    +      -       -      +
    552D  GLU*     6.0     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 551 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461D  ILE*     3.7    26.7    -      -       +      +
    464D  ARG*     3.4     2.7    -      -       -      +
    465D  LEU*     2.8    52.0    +      -       +      +
    491D  LEU*     4.8     3.8    -      -       +      -
    493D  LEU*     4.4    12.3    -      -       +      -
    501D  LEU*     3.8    18.6    -      -       +      -
    502D  ALA      3.5     2.7    -      -       -      -
    503D  ILE*     4.1    21.5    -      -       +      -
    549D  LEU*     4.1    12.1    -      -       +      -
    550D  GLU*     1.3    79.3    -      -       -      +
    552D  GLU*     1.3    64.4    +      -       -      +
    563D  LEU*     3.9    40.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 552 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461D  ILE*     5.5     0.7    -      -       -      -
    463D  LYS      3.6     8.1    -      -       -      +
    464D  ARG*     4.2    21.9    +      -       +      -
    501D  LEU*     3.5     9.3    -      -       -      -
    502D  ALA*     3.0    56.1    +      -       +      +
    504D  HIS*     4.3    13.6    -      -       -      +
    512D  ARG*     5.4     3.7    +      -       -      -
    550D  GLU*     5.7     2.0    -      -       +      -
    551D  ILE*     1.3    77.1    -      -       -      +
    553D  ASN*     1.3    62.7    +      -       -      +
    554D  THR*     3.4    13.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 553 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461D  ILE*     5.6     0.4    -      -       -      +
    462D  GLY      4.1     4.1    +      -       -      +
    463D  LYS*     2.7    61.4    +      -       +      +
    495D  TYR*     3.2    18.8    +      -       -      +
    500D  ASP*     3.7     8.0    -      -       -      +
    501D  LEU*     4.9     0.9    -      -       -      -
    552D  GLU*     1.3    71.7    -      -       -      +
    554D  THR*     1.3    55.5    +      -       -      +
    555D  SER*     2.8    26.1    +      -       -      -
    557D  ALA      2.9    28.5    +      -       -      -
    558D  ASN*     4.7     0.2    -      -       -      +
    559D  ASN*     2.9    33.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 554 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    463D  LYS*     4.6     1.8    -      -       -      +
    500D  ASP*     2.7    31.1    +      -       -      +
    502D  ALA*     3.5    32.5    -      -       +      +
    518D  ALA*     3.6    21.6    -      -       +      +
    552D  GLU*     4.0    14.1    -      -       +      +
    553D  ASN*     1.3    71.8    -      -       -      +
    555D  SER*     1.3    58.5    +      -       -      +
    556D  GLU*     5.8     0.3    -      -       -      +
----------------------------------------------------------
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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