Contacts of the strand formed by residues 86 - 96 (chain D) in PDB entry 5IXG


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 GLN 86 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56D  THR*     3.4    28.2    -      -       +      +
     57D  THR      3.1    12.3    -      -       -      +
     58D  ASP*     2.5    30.9    +      -       -      +
     59D  ILE*     4.1     5.5    -      -       -      +
     84D  PHE*     4.2    11.4    -      -       -      +
     85D  PRO*     1.3    92.0    -      -       +      +
     87D  ALA*     1.3    59.7    +      -       -      +
     88D  ASN*     4.1    11.4    -      -       -      +
    108D  THR*     4.4     4.9    -      -       -      +
    109D  LEU*     5.2     0.2    -      -       -      -
    110D  HIS      5.1     5.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 87 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56D  THR*     3.4     3.3    -      -       -      +
     57D  THR*     2.9    34.2    +      -       -      +
     59D  ILE*     4.1     8.6    -      -       +      +
     86D  GLN*     1.3    74.0    -      -       -      +
     88D  ASN*     1.3    62.5    +      -       -      +
    107D  LEU*     4.6     1.1    -      -       +      -
    108D  THR      3.2    14.6    -      -       -      +
    109D  LEU*     4.2     7.0    -      -       +      -
    201D  OTP      3.9    43.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 88 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54D  ASP*     5.7     0.9    -      -       -      +
     55D  VAL      3.4     5.6    -      -       -      +
     56D  THR*     3.0    40.8    +      -       -      +
     86D  GLN*     4.1     9.7    -      -       -      +
     87D  ALA*     1.3    76.0    +      -       -      +
     89D  TYR*     1.3    60.0    +      -       -      +
     90D  LYS*     4.9    16.4    -      -       +      +
    106D  ASN      3.7     1.1    -      -       -      +
    107D  LEU*     3.5     6.5    -      -       -      +
    108D  THR*     2.8    53.3    +      -       -      +
    201D  OTP      4.5     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 89 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53D  VAL*     4.4     8.7    -      -       +      -
     54D  ASP*     3.5     1.9    -      -       -      -
     55D  VAL*     2.8    57.3    +      -       +      +
     88D  ASN*     1.3    73.4    -      -       -      +
     90D  LYS*     1.3    69.0    +      -       -      +
     91D  GLY      4.3     0.4    -      -       -      -
    103D  VAL*     3.1    38.8    +      -       +      +
    105D  GLY*     3.3    12.3    +      -       -      -
    106D  ASN      3.5    24.2    -      -       -      -
    107D  LEU*     4.0     6.7    -      -       +      -
    116D  LEU*     2.9    49.3    +      -       +      -
    118D  LEU*     3.6    24.9    -      -       +      +
    201D  OTP      3.7    18.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 90 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53D  VAL      3.3     6.5    -      -       -      +
     54D  ASP*     3.5    35.6    +      -       +      +
     88D  ASN*     4.4    15.2    -      -       +      +
     89D  TYR*     1.3    83.7    -      -       -      +
     91D  GLY*     1.3    60.8    +      -       -      +
    105D  GLY*     3.1     1.6    -      -       -      -
    106D  ASN*     2.9    36.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 91 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52D  THR*     3.2     7.3    -      -       -      -
     53D  VAL*     2.8    31.7    +      -       -      +
     89D  TYR*     4.3     2.8    -      -       -      -
     90D  LYS*     1.3    75.8    -      -       -      +
     92D  THR*     1.3    63.6    +      -       -      -
    103D  VAL*     3.8    12.3    -      -       -      -
    104D  VAL      3.3    12.3    -      -       -      -
    105D  GLY*     3.7     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 92 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50D  THR*     6.0     1.6    -      -       -      -
     51D  GLY      3.4    12.8    +      -       -      +
     52D  THR*     4.7     6.7    -      -       +      +
     91D  GLY*     1.3    75.5    +      -       -      -
     93D  ILE*     1.4    72.2    +      -       -      +
     94D  LYS*     3.7    19.2    +      -       -      +
    103D  VAL*     3.3     4.5    -      -       -      -
    104D  VAL*     2.8    38.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 93 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42D  VAL*     3.7    29.4    -      -       +      -
     43D  THR      3.9     5.2    -      -       -      +
     44D  LEU*     4.1    11.4    -      -       +      -
     49D  LYS      4.4     1.9    -      -       -      +
     50D  THR*     4.3     3.5    -      -       -      -
     51D  GLY*     2.9    27.7    +      -       -      +
     52D  THR      3.9    11.7    -      -       -      +
     53D  VAL*     4.0    17.7    -      -       +      -
     92D  THR*     1.4    81.7    -      -       -      +
     94D  LYS*     1.3    64.0    +      -       -      +
     95D  PHE*     3.8    18.9    -      -       +      -
    100D  PRO*     3.7    30.5    -      -       +      -
    102D  SER      3.4     7.9    -      -       -      +
    103D  VAL*     4.4     7.9    -      -       +      +
    120D  ILE*     4.8     2.9    -      -       +      -
    201D  OTP      4.9     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 94 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49D  LYS      5.5     0.7    -      -       -      -
     92D  THR*     3.9    25.6    -      -       +      +
     93D  ILE*     1.3    76.6    -      -       -      +
     95D  PHE*     1.3    58.0    +      -       -      +
    100D  PRO*     3.5     4.5    -      -       -      +
    101D  VAL*     2.8    32.4    +      -       +      -
    102D  SER*     2.9    21.8    +      -       -      +
    104D  VAL*     3.7    44.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 95 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44D  LEU*     3.8    22.4    -      -       +      -
     46D  ARG*     3.8    29.2    -      -       +      -
     49D  LYS*     3.5    53.3    +      -       +      -
     50D  THR      3.6     8.3    -      -       -      -
     93D  ILE*     3.8    20.0    -      -       +      -
     94D  LYS*     1.3    81.4    -      -       -      +
     96D  ASP*     1.3    61.4    +      -       -      +
     97D  GLY      4.2     7.6    -      -       -      +
     98D  ASP      3.3    28.3    -      -       -      -
     99D  LYS      3.2    11.4    -      -       -      -
    100D  PRO*     3.7    13.9    -      -       +      -
    101D  VAL*     3.9     2.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 96 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145A  SER*     5.4     2.2    -      -       -      -
    159A  PHE      4.5     0.5    -      -       -      +
    160A  LYS*     3.4    23.7    -      -       +      +
    161A  MET*     2.7    34.4    +      -       -      +
    162A  LYS*     2.9    35.0    +      -       -      +
     95D  PHE*     1.3    73.7    -      -       -      +
     97D  GLY*     1.3    64.6    +      -       -      +
     98D  ASP      3.7     1.4    +      -       -      -
     99D  LYS*     2.9    18.0    +      -       -      +
    101D  VAL*     3.6    28.0    -      -       +      +
----------------------------------------------------------
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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