Contacts of the strand formed by residues 97 - 108 (chain B) in PDB entry 2Y1Z


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 VAL 97 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1153A  MPD      4.2    23.3    -      -       +      -
     93B  VAL*     3.6     1.7    -      -       -      -
     94B  LEU*     2.7    48.6    +      -       +      +
     95B  GLY      3.4     0.6    -      -       -      -
     96B  ASP*     1.3    95.4    -      -       -      +
     98B  ILE*     1.3    75.2    +      -       -      +
    121B  LYS*     4.2    22.7    -      -       +      -
    122B  TYR      3.4    10.8    -      -       -      +
    123B  ARG*     4.6     6.1    -      -       +      -
    124B  ILE*     4.0     2.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 98 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75B  PHE*     4.5    15.7    -      -       +      -
     77B  VAL*     5.1     2.0    -      -       +      -
     91B  VAL*     4.5     4.9    -      -       +      -
     92B  LYS      3.6     6.3    -      -       -      +
     93B  VAL*     4.7    10.5    -      -       +      +
     97B  VAL*     1.3    76.5    -      -       -      +
     99B  GLU*     1.3    71.2    +      -       -      +
    100B  VAL*     4.0     8.7    -      -       +      -
    121B  LYS*     3.0     6.1    -      -       -      -
    122B  TYR*     2.8    64.7    +      -       +      +
    124B  ILE*     3.7    29.6    -      -       +      -
    133B  ILE*     4.4    10.3    -      -       +      -
    145B  VAL*     3.8    32.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 99 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90B  LYS      3.9     0.6    -      -       -      +
     91B  VAL*     3.7     0.2    -      -       -      -
     92B  LYS*     2.8    52.2    +      -       +      +
     94B  LEU*     3.9    25.4    -      -       +      +
     97B  VAL*     4.0     0.6    +      -       +      -
     98B  ILE*     1.3    76.4    -      -       -      +
    100B  VAL*     1.3    68.8    +      -       -      +
    101B  HIS*     6.0     2.5    -      -       -      -
    119B  HIS*     3.2    27.7    +      -       +      -
    120B  GLY      3.4     2.0    -      -       -      -
    121B  LYS*     3.6    29.2    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 100 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  ILE*     5.4     0.7    -      -       +      -
     79B  LEU*     4.1    12.8    -      -       +      -
     90B  LYS      3.4     4.3    -      -       -      +
     91B  VAL*     4.2    19.1    -      -       +      -
     98B  ILE*     4.0     9.0    -      -       +      -
     99B  GLU*     1.3    81.8    -      -       -      +
    101B  HIS*     1.3    64.6    +      -       -      +
    118B  PHE*     4.1    14.6    -      -       +      -
    119B  HIS*     3.4     7.3    +      -       -      -
    120B  GLY*     2.8    45.9    +      -       -      +
    122B  TYR*     3.1    38.8    -      -       +      +
    143B  LEU*     4.6     3.4    -      -       +      -
    145B  VAL*     4.4     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 101 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88B  GLU      3.8     1.3    +      -       -      +
     89B  LEU*     3.5     1.9    -      -       -      -
     90B  LYS*     2.8    52.2    +      -       +      +
     99B  GLU*     5.9     3.1    -      -       +      -
    100B  VAL*     1.3    77.4    -      -       -      +
    102B  GLY*     1.3    64.1    +      -       -      +
    103B  LYS*     3.8    29.4    +      -       +      -
    117B  GLU*     3.2    24.0    +      -       -      +
    118B  PHE*     3.2    31.3    -      -       -      -
    119B  HIS*     4.2    17.7    -      +       +      +
----------------------------------------------------------
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Residues in contact with GLY 102 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84B  PHE*     3.4     9.4    -      -       -      -
     88B  GLU      3.4    10.1    -      -       -      -
     89B  LEU*     4.0     3.1    -      -       -      -
    101B  HIS*     1.3    77.6    +      -       -      +
    103B  LYS*     1.3    61.2    +      -       -      +
    117B  GLU*     3.3     5.9    -      -       -      +
    118B  PHE*     3.1    52.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 103 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84B  PHE*     3.4     2.3    -      -       -      -
     88B  GLU*     3.3    29.8    +      -       -      +
    101B  HIS*     3.8    19.2    -      -       +      +
    102B  GLY*     1.3    75.0    -      -       -      +
    104B  HIS*     1.3    62.6    +      -       -      +
    105B  GLU*     3.4    33.7    +      -       +      -
    115B  SER*     5.2     3.8    -      -       -      +
    116B  ARG      3.3     9.0    -      -       -      +
    117B  GLU*     4.5    21.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 104 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83B  HIS*     3.9    19.8    +      -       +      +
     84B  PHE*     3.7    16.2    -      -       +      -
     88B  GLU*     3.1    37.9    -      -       -      +
    103B  LYS*     1.3    75.0    -      -       -      +
    105B  GLU*     1.3    66.5    +      -       -      +
    106B  GLU*     3.5    41.6    +      -       +      +
    114B  ILE*     3.9     6.5    +      -       +      +
    115B  SER*     3.4     2.8    -      -       -      -
    116B  ARG*     2.7    59.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 105 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88B  GLU*     4.7     3.0    +      -       -      +
    103B  LYS*     3.4    33.4    +      -       +      -
    104B  HIS*     1.3    83.4    -      -       -      +
    106B  GLU*     1.3    67.2    +      -       -      +
    107B  ARG*     4.2     1.5    +      -       +      -
    113B  PHE*     4.6    17.7    -      -       +      -
    114B  ILE      3.4     3.6    -      -       -      +
    115B  SER*     3.8    22.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 106 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104B  HIS*     3.5    33.2    +      -       +      +
    105B  GLU*     1.3    73.9    -      -       -      +
    107B  ARG*     1.3    61.2    +      -       -      +
    112B  GLY      3.9     1.4    -      -       -      +
    113B  PHE*     3.4     7.3    -      -       -      -
    114B  ILE*     2.9    52.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 107 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105B  GLU*     4.2     1.9    +      -       +      -
    106B  GLU*     1.3    73.9    -      -       -      +
    108B  GLN*     1.3    62.8    +      -       -      +
    109B  ASP*     4.1    32.0    +      -       -      +
    112B  GLY      3.7     4.0    -      -       -      +
    113B  PHE*     4.3    20.6    -      -       +      -
   1152B  MRD      4.3    25.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 108 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  MET*     6.0     1.6    -      -       -      +
    106B  GLU      4.2     0.2    -      -       -      -
    107B  ARG*     1.3    75.0    -      -       -      +
    109B  ASP*     1.3    60.7    +      -       -      +
    111B  HIS*     2.7    45.9    +      -       +      +
    112B  GLY*     2.8    30.7    +      -       -      +
   1152B  MRD      4.3     1.3    -      -       -      +
----------------------------------------------------------
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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