Contacts of the strand formed by residues 59 - 66 (chain 0) 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 ARG 59 (chain 0).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     570  MET*     3.9    13.7    -      -       -      +
     580  MET*     1.4    80.5    -      -       -      +
     600  HIS*     1.3    58.1    +      -       -      +
     610  LEU*     5.2     3.4    -      -       -      +
     950  TYR*     3.5    28.0    -      -       -      +
     990  ASN*     3.5    28.1    -      -       +      +
    1010  ILE      3.6     4.6    +      -       -      +
    1020  SER*     3.2     5.1    -      -       -      -
    1030  GLN*     2.7    36.7    +      -       -      -
    1640  SER*     3.4    14.6    -      -       -      +
    1660  GLU*     2.9    37.1    +      -       -      +
    2350  HIS*     3.2    20.2    +      -       -      +
    2360  VAL      3.1    17.8    +      -       -      -
    2370  SER      3.1    26.2    +      -       -      -
    2380  PRO*     3.7     0.8    -      -       -      +
    2390  PRO*     3.8    15.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 60 (chain 0). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     580  MET*     4.0    14.4    -      -       +      +
     590  ARG*     1.3    77.2    -      -       -      +
     610  LEU*     1.3    58.8    +      -       -      +
     620  TYR      4.4     0.2    -      -       -      -
    1030  GLN*     3.2    44.3    +      -       +      +
    1200  LEU*     3.8     5.3    -      -       +      +
    1560  LEU*     4.4    18.2    -      -       +      +
    1590  MET*     3.1    49.7    -      -       +      +
    1600  PRO*     4.7     1.8    -      -       -      +
    1630  THR*     3.6    25.6    +      -       -      +
    1640  SER*     3.4    14.1    +      -       -      +
    1660  GLU*     3.0    28.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 61 (chain 0). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     590  ARG*     5.2     3.1    -      -       -      +
     600  HIS*     1.3    72.2    -      -       -      +
     620  TYR*     1.3    63.4    +      -       -      +
     630  VAL*     4.3     7.9    -      -       +      -
     910  PHE*     3.8    24.7    -      -       +      -
     950  TYR*     3.5    39.0    -      -       +      +
    1030  GLN      3.0     7.9    +      -       -      +
    1040  ILE*     3.1    34.2    -      -       +      +
    1050  GLY      3.1     3.3    +      -       -      -
    1200  LEU*     5.1     1.0    -      -       -      +
    1660  GLU*     3.4    30.3    -      -       +      +
    1670  VAL      4.4     0.4    -      -       -      -
    1680  LEU*     3.8    27.1    -      -       +      +
    2350  HIS*     5.8     1.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 62 (chain 0). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     610  LEU*     1.3    70.3    -      -       -      +
     630  VAL*     1.3    64.4    +      -       -      +
     640  VAL*     3.4     3.5    +      -       +      +
    1050  GLY*     3.4    24.0    -      -       -      -
    1060  ILE      4.5     1.1    -      -       -      -
    1070  ILE*     3.7    38.1    -      -       +      -
    1160  LYS*     6.1     2.1    -      -       +      +
    1180  THR      5.1     2.4    +      -       -      -
    1190  GLU*     5.1     1.7    -      -       -      -
    1200  LEU*     3.7    34.4    +      -       +      +
    1510  ILE*     5.1     4.1    -      -       +      +
    1520  ALA*     4.1    22.9    -      -       +      -
    1550  THR*     2.9    43.0    +      -       -      +
    1560  LEU*     3.4    20.4    -      -       +      -
    1660  GLU      2.7    15.3    +      -       -      +
    1670  VAL*     3.4    10.6    -      -       +      +
    1680  LEU      3.0    23.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 63 (chain 0). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     610  LEU*     4.3    11.0    -      -       +      -
     620  TYR*     1.3    71.6    -      -       -      +
     640  VAL*     1.3    63.3    +      -       -      +
     650  VAL*     5.5     1.6    -      -       +      -
     880  LEU*     4.1    31.2    -      -       +      -
     910  PHE*     4.3    20.9    -      -       +      -
     920  VAL*     6.1     2.5    -      -       +      -
    1040  ILE*     3.7    23.6    -      -       +      -
    1050  GLY      3.0     7.8    +      -       -      +
    1060  ILE*     3.4    20.3    -      -       +      +
    1070  ILE*     3.0    27.1    +      -       -      +
    1310  LEU*     5.9     3.1    -      -       +      -
    1680  LEU*     3.6     9.6    -      -       +      +
    1700  ILE*     4.2    11.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 64 (chain 0). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     620  TYR*     3.8     6.3    -      -       +      +
     630  VAL*     1.3    75.6    -      -       -      +
     650  VAL*     1.3    66.6    +      -       -      +
    1070  ILE*     3.3    22.7    -      -       +      +
    1090  THR*     4.7     9.4    -      -       +      +
    1450  LEU*     5.0     5.6    -      -       +      -
    1480  SER*     4.5    23.1    -      -       -      +
    1490  LEU*     5.6     1.6    -      -       +      -
    1520  ALA*     5.6     1.1    -      -       +      -
    1670  VAL*     3.8    26.7    -      -       +      -
    1680  LEU      2.8    10.0    +      -       -      +
    1690  ILE*     3.4    27.3    -      -       +      -
    1700  ILE*     3.1    27.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 65 (chain 0). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     630  VAL*     5.5     1.3    -      -       +      -
     640  VAL*     1.3    78.1    -      -       -      +
     660  ASP*     1.3    74.5    +      -       -      +
     670  GLY*     3.3     1.3    +      -       -      +
     710  MET*     4.1    15.0    -      -       +      -
     810  LEU*     5.3     5.2    -      -       +      -
     840  THR*     4.7     2.7    -      -       -      +
     850  LEU*     4.5    24.2    -      -       +      -
     880  LEU*     4.6    18.6    -      -       +      -
    1060  ILE*     5.0     6.5    -      -       +      -
    1070  ILE      3.1    18.0    +      -       -      +
    1080  VAL*     3.5    17.9    -      -       +      +
    1090  THR*     3.0    27.8    +      -       -      -
    1170  LEU*     4.5    12.1    -      -       +      -
    1310  LEU*     5.7     1.3    -      -       +      -
    1690  ILE*     6.1     0.2    -      -       -      -
    1700  ILE*     3.9     5.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 66 (chain 0). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     650  VAL*     1.3    77.5    -      -       -      +
     670  GLY*     1.3    56.3    +      -       -      +
     680  SER*     2.6    28.5    +      -       -      -
     700  THR*     4.0     1.8    +      -       -      -
     710  MET*     3.1    32.9    -      -       +      +
     810  LEU*     4.9     0.3    -      -       -      +
    1090  THR*     3.8    12.4    +      -       -      +
    1430  PRO*     4.2     2.8    -      -       -      +
    1450  LEU*     6.6     0.4    -      -       +      -
    1700  ILE      3.0    22.1    +      -       -      +
    1710  PHE*     4.1     4.5    -      -       +      -
    1720  SER*     3.1    30.3    +      -       -      +
    1730  SER*     2.6    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