Contacts of the strand formed by residues 79 - 86 (chain A) in PDB entry 5Y1Z


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 79 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  SER*     3.7     2.8    -      -       -      -
     70A  VAL*     2.9    37.4    +      -       -      +
     77A  LEU      4.2     7.2    -      -       -      +
     78A  PRO*     1.3    78.2    -      -       -      +
     80A  TYR*     1.3    63.4    +      -       -      +
     81A  VAL*     5.3     0.4    -      -       -      -
    113A  ASP*     3.1    21.6    +      -       -      +
    133A  LEU*     3.7    56.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 80 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  VAL*     4.2     3.5    +      -       +      -
     21A  ILE*     3.4    48.7    +      -       +      +
     67A  PHE*     3.5    33.0    -      +       +      -
     68A  CYS      3.6     1.3    -      -       -      -
     69A  SER*     3.4    36.2    +      -       -      -
     78A  PRO*     3.7    30.5    -      -       +      +
     79A  LYS*     1.3    75.0    -      -       -      +
     81A  VAL*     1.3    63.3    +      -       -      +
    111A  GLY*     3.4    26.5    -      -       -      +
    112A  VAL*     3.7     1.0    -      -       -      -
    113A  ASP*     2.6    41.5    +      -       -      +
    114A  VAL*     3.0     8.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 81 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  LEU*     5.0     2.7    -      -       +      -
     66A  GLY      3.2     2.8    -      -       -      +
     67A  PHE*     3.5     6.2    -      -       -      -
     68A  CYS*     3.0    42.0    +      -       +      +
     70A  VAL*     4.3    11.2    -      -       +      -
     80A  TYR*     1.3    78.0    -      -       -      +
     82A  LEU*     1.3    67.8    +      -       -      +
     83A  ILE*     4.2    13.7    -      -       +      -
    112A  VAL*     4.9     0.4    -      -       -      -
    114A  VAL*     3.4    14.6    -      -       +      +
    116A  VAL*     3.9    26.9    -      -       +      -
    129A  ILE*     3.6    31.2    -      -       +      -
    133A  LEU*     4.3    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 82 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  TYR*     6.1     0.2    -      -       +      -
     65A  TYR*     4.1    22.9    -      -       +      -
     66A  GLY      3.1    18.6    -      -       -      +
     67A  PHE*     4.5    14.1    -      -       +      +
     80A  TYR      4.2     0.2    -      -       -      -
     81A  VAL*     1.3    74.1    -      -       -      +
     83A  ILE*     1.3    66.1    +      -       -      +
     84A  ASN      3.6     1.1    +      -       -      +
    102A  VAL*     4.5    10.1    -      -       +      +
    105A  VAL*     4.1    23.3    -      -       +      -
    106A  ALA*     4.1    25.4    -      -       +      +
    109A  PHE*     5.2     3.4    -      -       +      -
    112A  VAL*     3.8    20.8    -      -       +      +
    114A  VAL      2.9     8.8    +      -       -      +
    115A  ILE*     3.3    17.0    -      -       +      +
    116A  VAL      2.9    25.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 83 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  LEU*     3.7    21.3    -      -       +      -
     54A  LEU*     3.5    30.5    -      -       +      -
     58A  PHE*     3.7    26.2    -      -       +      -
     64A  MET      3.5     0.2    -      -       -      +
     65A  TYR*     3.3    10.0    -      -       -      +
     66A  GLY      2.8    34.5    +      -       -      +
     68A  CYS*     5.4     0.9    -      -       +      -
     81A  VAL*     4.2    12.8    -      -       +      -
     82A  LEU*     1.3    73.2    -      -       -      +
     84A  ASN*     1.3    59.6    +      -       -      +
     85A  TRP*     3.3     6.2    +      -       +      +
    116A  VAL*     3.3    12.3    -      -       +      +
    118A  ALA*     3.8    27.1    -      -       +      -
    124A  ILE*     4.1    16.6    -      -       +      -
    129A  ILE*     5.2     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 84 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  VAL*     5.0     1.0    -      -       -      +
     64A  MET      4.1     1.1    -      -       -      -
     65A  TYR*     3.4    16.9    +      -       +      -
     82A  LEU*     3.6     2.9    +      -       +      -
     83A  ILE*     1.3    68.5    -      -       -      +
     85A  TRP*     1.3    59.6    +      -       -      +
     86A  VAL*     3.7    17.2    +      -       -      +
     99A  ALA*     5.8     2.2    -      -       -      +
    102A  VAL*     3.4    35.0    -      -       +      +
    115A  ILE*     4.2    12.6    -      -       +      -
    116A  VAL      2.8     9.3    +      -       -      +
    117A  ASN*     2.8    32.5    +      -       -      +
    118A  ALA      2.9    24.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 85 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  PHE*     3.5    62.6    -      +       +      -
     59A  GLU      2.8    22.7    +      -       -      +
     60A  ASN*     3.9    21.8    -      -       -      -
     62A  LYS      3.3    17.5    +      -       -      -
     63A  VAL*     3.3     6.9    -      -       -      +
     64A  MET*     2.9    52.5    +      -       +      +
     83A  ILE*     3.3     2.4    +      -       +      -
     84A  ASN*     1.3    73.0    +      -       -      +
     86A  VAL*     1.3    62.5    +      -       -      +
     87A  GLY*     3.5     9.3    -      -       -      +
    118A  ALA*     3.3    26.9    -      -       +      -
    119A  SER      3.5    18.2    -      -       -      -
    120A  SER*     3.4    36.3    -      -       -      -
    121A  VAL*     3.9     7.6    -      -       +      -
    124A  ILE*     4.3     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 86 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  LYS      4.1     1.6    -      -       -      -
     63A  VAL*     4.2    12.8    -      -       +      +
     84A  ASN*     4.3    21.8    -      -       -      +
     85A  TRP*     1.3    81.4    -      -       -      +
     87A  GLY*     1.3    77.4    +      -       -      +
     90A  VAL*     3.9    18.6    -      -       +      +
     95A  LYS*     3.8    45.5    -      -       +      +
     98A  CYS*     5.9     1.3    -      -       +      -
    118A  ALA      2.9     8.2    +      -       -      +
    119A  SER*     2.9    33.6    +      -       -      +
----------------------------------------------------------
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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