Contacts of the strand formed by residues 917 - 927 (chain B) in PDB entry 5IY8


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 LYS 917 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    817B  GLN*     4.0     0.7    -      -       -      -
    818B  GLU*     3.1    54.9    +      -       +      +
    829B  PHE*     3.8    39.7    +      -       +      +
    851B  ASP      5.9     0.2    +      -       -      -
    909B  VAL*     4.1    23.3    -      -       +      -
    910B  THR      3.6     9.6    -      -       -      +
    911B  LEU*     4.4     2.9    -      -       -      -
    915B  GLY      4.0     0.6    +      -       -      -
    916B  TYR*     1.3    73.3    -      -       -      +
    918B  PHE*     1.3    63.2    +      -       -      +
     31L  ARG*     4.9    10.9    -      -       -      +
     34L  ILE*     4.7    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 918 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115B  LEU      4.3     4.3    -      -       -      -
    116B  ARG      5.2     0.2    -      -       -      -
    117B  ASN*     3.0    32.5    -      -       -      -
    815B  LYS*     3.7    37.9    -      -       +      -
    816B  GLU      3.8    13.7    -      -       -      -
    817B  GLN*     4.2    13.2    -      -       +      -
    829B  PHE*     5.1     1.1    -      -       -      -
    908B  MET*     4.6     0.2    -      -       +      -
    909B  VAL*     3.6     3.6    -      -       -      +
    910B  THR*     2.7    53.3    +      -       +      +
    912B  ASN*     3.5    42.6    -      -       +      +
    917B  LYS*     1.3    76.1    -      -       -      +
    919B  CYS*     1.3    65.6    +      -       -      +
    920B  LYS*     3.6    26.2    -      -       +      -
     56Y    G      5.1     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 919 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    815B  LYS*     3.4     5.1    -      -       -      +
    816B  GLU*     3.2    40.4    +      -       -      +
    829B  PHE*     3.9    14.1    -      -       +      -
    853B  LEU*     3.9    20.0    -      -       +      -
    867B  ILE*     3.8    23.8    -      -       -      -
    908B  MET*     3.1    16.2    -      -       -      +
    909B  VAL*     4.6     4.0    -      -       +      -
    918B  PHE*     1.3    79.5    -      -       -      +
    920B  LYS*     1.3    66.9    +      -       -      +
    921B  ILE*     4.3     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 920 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114B  ARG      3.5    20.8    +      -       -      -
    115B  LEU*     3.3    20.9    +      -       -      +
    117B  ASN*     3.6    13.3    +      -       -      +
    189B  GLY      5.6     1.2    +      -       -      -
    744B  MET*     3.6    50.2    +      -       +      +
    746B  THR*     6.1     2.4    -      -       -      +
    813B  SER*     5.0     5.4    -      -       -      -
    814B  TYR      3.4     7.2    -      -       -      +
    815B  LYS*     4.2    12.9    -      -       +      +
    907B  VAL*     3.9     0.5    -      -       -      -
    908B  MET*     3.0    41.5    +      -       +      +
    918B  PHE*     3.6    19.1    -      -       +      -
    919B  CYS*     1.3    78.8    -      -       -      +
    921B  ILE*     1.3    63.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 921 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    812B  ARG      3.8     0.9    -      -       -      +
    813B  SER*     3.4     1.7    -      -       -      -
    814B  TYR*     2.7    44.5    +      -       +      +
    853B  LEU*     4.2    10.5    -      -       +      -
    854B  ILE*     4.1    15.3    -      -       +      +
    866B  ILE*     3.7    39.5    -      -       +      +
    867B  ILE*     3.9    22.4    -      -       +      -
    904B  VAL*     4.6     6.3    -      -       +      -
    906B  GLN      3.5     8.1    -      -       -      +
    907B  VAL*     3.7    25.6    -      -       +      +
    919B  CYS*     4.3     3.6    -      -       -      -
    920B  LYS*     1.3    78.4    -      -       -      +
    922B  ARG*     1.3    60.5    +      -       -      +
    923B  VAL*     4.4    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 922 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    740B  PHE*     3.9     5.4    +      -       -      -
    741B  HIS*     3.5    22.2    +      -       -      +
    743B  ARG      2.7    33.3    +      -       -      -
    744B  MET*     4.1    10.0    -      -       -      +
    745B  ASP      5.4     1.1    -      -       -      -
    811B  TYR*     3.8    38.8    +      -       +      -
    812B  ARG      3.5     5.4    -      -       -      +
    813B  SER*     3.2    23.3    -      -       -      +
    904B  VAL*     3.4     4.4    -      -       -      +
    905B  ASP*     2.2    62.4    +      -       -      -
    906B  GLN*     2.7    50.8    +      -       +      +
    920B  LYS      4.2     0.4    +      -       -      -
    921B  ILE*     1.3    71.7    -      -       -      +
    923B  VAL*     1.3    61.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 923 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    810B  PHE      3.1    12.5    -      -       -      +
    811B  TYR*     3.2    14.7    -      -       -      -
    812B  ARG*     2.8    16.7    +      -       +      +
    814B  TYR*     3.8    32.5    -      -       +      -
    860B  VAL*     4.1    18.8    -      -       +      -
    866B  ILE*     5.3     0.7    -      -       +      -
    896B  LEU*     5.0     7.2    -      -       +      -
    899B  SER*     5.4     7.0    -      -       -      -
    901B  THR      5.3     1.8    -      -       -      +
    902B  GLY*     4.5     4.9    -      -       -      -
    903B  ILE      3.3    23.3    -      -       -      +
    904B  VAL*     4.1     6.7    -      -       +      +
    921B  ILE*     4.4    11.9    -      -       +      -
    922B  ARG*     1.3    78.7    -      -       -      +
    924B  ARG*     1.3    60.1    +      -       -      +
    925B  SER*     5.3     1.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 924 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    809B  VAL*     3.4    31.2    -      -       +      -
    810B  PHE      3.3     3.1    -      -       -      -
    811B  TYR*     3.6    17.0    -      -       +      -
    857B  GLY*     5.9     0.2    -      -       -      -
    902B  GLY*     3.5     1.7    -      -       -      -
    903B  ILE*     2.5    68.4    +      -       +      +
    904B  VAL      4.3     1.2    +      -       -      -
    905B  ASP*     3.0    33.7    +      -       +      +
    923B  VAL*     1.3    73.1    -      -       -      +
    925B  SER*     1.3    60.4    +      -       -      +
     60C  HIS*     3.7    28.9    +      -       -      +
     61C  ASP*     3.3    23.2    +      -       -      +
     62C  GLU*     2.8    45.8    +      -       -      +
     48L  ARG*     5.3     2.8    -      -       -      +
     55L  PHE*     5.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 925 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    808B  SER      3.9     0.2    -      -       -      +
    809B  VAL*     3.3     4.2    -      -       -      +
    810B  PHE*     2.7    58.1    +      -       -      +
    899B  SER*     5.8     2.9    -      -       -      -
    901B  THR*     4.0    21.6    +      -       -      +
    902B  GLY*     4.4     3.7    -      -       -      -
    923B  VAL*     5.9     1.3    -      -       -      -
    924B  ARG*     1.3    76.9    -      -       -      +
    926B  VAL*     1.3    68.6    +      -       -      +
    927B  ARG*     3.7    16.6    +      -       -      -
     62C  GLU*     5.0     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 926 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    752B  TYR*     3.1    28.5    -      -       +      +
    807B  ARG*     5.6     8.3    -      -       +      +
    808B  SER      3.5     5.8    -      -       -      +
    809B  VAL*     4.7     3.1    -      -       +      -
    925B  SER*     1.3    80.6    +      -       -      +
    927B  ARG*     1.3    64.5    +      -       -      +
    928B  ILE*     3.6    12.8    +      -       +      +
     60C  HIS*     4.5     1.8    -      -       +      -
     62C  GLU*     3.1    39.8    +      -       +      +
      1K  MET*     5.9     3.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 927 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    749B  HIS*     4.7     1.0    +      -       +      -
    807B  ARG*     4.1     1.4    -      -       -      -
    808B  SER*     3.1    32.3    +      -       -      +
    810B  PHE*     2.8    53.1    -      -       +      -
    899B  SER*     4.9     3.2    +      -       -      +
    925B  SER*     3.7    15.3    +      -       -      -
    926B  VAL*     1.3    72.5    -      -       -      +
    928B  ILE*     1.3    60.5    +      -       -      +
    929B  PRO*     3.8     0.3    -      -       -      +
   1050B  ARG*     2.9    29.7    +      -       -      +
   1054B  MET*     3.8    32.8    -      -       +      +
   1056B  ASP*     5.9     7.4    -      -       -      +
   1057B  ASP*     3.3    34.0    +      -       -      +
----------------------------------------------------------
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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