Contacts of the strand formed by residues 66 - 77 (chain A) in PDB entry 1Y7V


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 LEU 66 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  HIS*     3.9    22.4    -      -       +      -
     64A  GLY      4.0     4.9    -      -       -      +
     65A  LEU*     1.3    75.2    -      -       -      +
     67A  LEU*     1.3    64.2    +      -       -      +
     68A  THR*     3.7    14.4    +      -       -      +
    437A  VAL      3.4     3.3    -      -       -      +
    438A  ALA*     3.4     1.4    -      -       -      -
    439A  SER*     2.9    48.0    +      -       -      +
    471A  THR*     3.2    36.8    -      -       +      +
    473A  LYS*     3.7    30.3    -      -       +      +
    479A  PHE*     4.7     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 67 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  LEU*     4.0    16.2    -      -       +      -
     66A  LEU*     1.3    74.0    -      -       -      +
     68A  THR*     1.3    56.1    +      -       -      +
    436A  LEU*     4.0    22.0    -      -       +      +
    437A  VAL      3.4     3.1    -      -       -      +
    438A  ALA*     3.8    30.3    -      -       +      +
    442A  ASN*     4.8     1.8    -      -       -      +
    444A  LEU*     5.1     2.5    -      -       +      -
    446A  ALA*     4.1    25.6    -      -       +      -
    458A  VAL*     5.3     1.1    -      -       +      -
    460A  VAL*     4.4    11.0    -      -       +      -
    470A  LEU*     3.5    29.2    -      -       +      -
    471A  THR      2.7    11.8    +      -       -      +
    472A  ILE*     3.0    16.4    -      -       +      +
    473A  LYS      2.6    30.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 68 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  LEU*     3.7    16.1    +      -       -      +
     67A  LEU*     1.3    73.9    -      -       -      +
     69A  LEU*     1.3    75.2    +      -       -      +
     70A  GLN*     3.5    13.3    +      -       -      +
    436A  LEU*     3.4     4.7    -      -       -      +
    437A  VAL*     3.0    40.4    +      -       -      -
    473A  LYS*     3.2    39.9    -      -       +      +
    475A  PRO*     4.4     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 69 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67A  LEU      4.0     0.4    +      -       -      -
     68A  THR*     1.3    86.3    -      -       -      +
     70A  GLN*     1.3    61.9    +      -       -      +
     71A  PRO*     3.4    24.0    -      -       +      +
    434A  VAL*     3.7    12.8    -      -       +      -
    435A  GLY      3.8     0.2    -      -       -      -
    436A  LEU*     3.6    11.0    -      -       +      +
    448A  ALA*     3.5    30.3    -      -       +      -
    449A  LEU      4.9     2.7    -      -       -      +
    450A  MET*     5.3     3.6    -      -       +      -
    456A  ALA*     4.5     7.9    -      -       +      -
    458A  VAL*     4.4    11.2    -      -       +      -
    472A  ILE*     5.1     0.9    -      -       +      +
    473A  LYS      2.7    15.9    +      -       -      +
    474A  ASP*     3.8    18.2    -      -       +      +
    475A  PRO*     3.5     7.1    -      -       -      +
    494A  TRP*     4.4    12.3    -      -       +      -
    496A  ARG*     3.6    30.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 70 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  THR*     3.6    16.5    -      -       -      +
     69A  LEU*     1.3    81.0    +      -       -      +
     71A  PRO*     1.3    71.1    -      -       -      +
     72A  GLU*     2.9     6.6    +      -       -      +
     73A  GLN*     2.9    31.0    +      -       +      +
    434A  VAL*     4.4     0.4    -      -       -      -
    435A  GLY*     3.0    32.8    +      -       -      +
    436A  LEU      4.6     0.7    -      -       -      +
    437A  VAL*     4.0    22.4    -      -       +      +
    475A  PRO*     5.3     4.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 71 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  LEU*     3.4    20.8    -      -       +      +
     70A  GLN*     1.3    90.7    -      -       -      +
     72A  GLU*     1.3    70.9    +      -       +      +
     73A  GLN      3.5     0.2    +      -       -      -
     74A  LYS*     2.8    33.5    +      -       -      +
    434A  VAL*     3.9    17.0    -      -       +      +
    450A  MET*     4.3     8.7    -      -       -      -
    475A  PRO*     4.4    12.1    -      -       +      -
    496A  ARG*     3.4    36.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 72 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  GLN*     2.9     4.0    +      -       -      +
     71A  PRO*     1.3    92.4    -      -       +      +
     73A  GLN*     1.3    60.3    +      -       -      +
     74A  LYS*     3.3    27.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 73 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  GLN*     2.9    23.2    +      -       +      +
     72A  GLU*     1.3    75.1    -      -       -      +
     74A  LYS*     1.3    62.3    +      -       -      +
     75A  PHE*     3.7    20.3    -      -       +      -
    434A  VAL*     3.1     8.8    -      -       -      +
    435A  GLY*     3.0    35.7    +      -       -      +
    436A  LEU      5.3     0.2    +      -       -      -
    437A  VAL*     5.7     5.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 74 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  PRO      2.8    29.7    +      -       -      +
     72A  GLU*     3.3    26.6    +      -       -      +
     73A  GLN*     1.3    73.6    -      -       -      +
     75A  PHE*     1.3    70.2    +      -       -      +
    432A  GLN*     3.2    33.8    +      -       +      +
    433A  ARG      3.8     2.0    -      -       -      -
    434A  VAL*     4.3     6.6    -      -       +      +
    450A  MET*     4.0    25.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 75 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  GLN*     3.7    30.7    -      -       +      -
     74A  LYS*     1.3    78.0    -      -       -      +
     76A  GLN*     1.3    76.6    +      -       -      +
     77A  LYS*     3.8     0.3    +      -       -      +
    374A  HIS*     4.9    16.4    -      +       -      +
    432A  GLN*     2.7    25.0    +      -       -      +
    433A  ARG*     2.8    64.7    +      -       +      +
    434A  VAL      3.8     2.5    -      -       -      -
    435A  GLY*     3.7    22.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 76 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  PHE*     1.3    86.2    -      -       -      +
     77A  LYS*     1.3    62.7    +      -       -      +
     78A  VAL*     3.9     3.7    +      -       +      +
    328A  HIS*     6.5     0.9    -      -       +      -
    371A  LEU*     3.0    32.2    +      -       -      +
    374A  HIS*     3.3    35.3    +      -       +      +
    375A  VAL      2.9    25.3    +      -       -      +
    376A  VAL*     3.7    20.0    -      -       +      -
    432A  GLN*     3.5     0.5    -      -       -      -
    433A  ARG*     3.0    38.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 77 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  PHE      3.8     0.4    +      -       -      +
     76A  GLN*     1.3    74.4    -      -       -      +
     78A  VAL*     1.3    63.7    +      -       -      +
     79A  LYS*     3.6     0.3    +      -       -      -
    376A  VAL*     3.2    22.2    -      -       -      +
    430A  GLY*     4.2    19.2    +      -       -      +
    431A  SER      3.2     5.8    -      -       -      +
    432A  GLN*     4.0    34.3    -      -       +      +
----------------------------------------------------------
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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