Contacts of the strand formed by residues 112 - 123 (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 GLY 112 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  MET*     4.7     3.8    -      -       -      -
    121A  LYS      3.3     7.9    -      -       -      -
    122A  TYR*     4.3    11.7    -      -       -      -
    106B  GLU      3.9     0.8    -      -       -      +
    107B  ARG*     3.7     0.9    -      -       -      +
    108B  GLN*     2.8    46.9    +      -       -      +
    111B  HIS*     1.3    75.6    -      -       -      +
    113B  PHE*     1.3    61.0    +      -       -      +
   1152B  MRD      3.5     4.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 113 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119A  HIS*     4.3    14.6    -      +       +      -
    120A  GLY*     3.0     5.2    -      -       -      -
    121A  LYS*     2.7    57.9    +      -       +      +
    122A  TYR*     4.4     6.4    -      -       -      -
    105B  GLU*     4.6    21.3    -      -       +      -
    106B  GLU      3.4     9.4    -      -       -      -
    107B  ARG*     4.3    20.4    -      -       +      -
    112B  GLY*     1.3    74.6    -      -       -      +
    114B  ILE*     1.3    66.0    +      -       -      +
    115B  SER*     3.7    31.2    -      -       -      -
   1152B  MRD      4.1    18.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 114 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  LEU*     3.8    28.3    -      -       +      -
    118A  PHE*     3.9    16.4    -      -       +      -
    119A  HIS      3.4    15.0    -      -       -      +
    120A  GLY*     4.4     2.2    -      -       -      -
    122A  TYR*     3.9    13.5    -      -       +      +
    104B  HIS*     3.9     5.6    +      -       +      +
    105B  GLU*     3.4     3.5    -      -       -      +
    106B  GLU*     2.9    67.1    +      -       +      +
    113B  PHE*     1.3    76.6    -      -       -      +
    115B  SER*     1.3    61.6    +      -       -      +
    116B  ARG*     4.1    23.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 115 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  PHE*     3.0     7.8    -      -       -      +
    119A  HIS*     2.7    54.5    +      -       -      -
    103B  LYS*     5.2     4.5    -      -       -      +
    104B  HIS      3.4     4.5    -      -       -      -
    105B  GLU*     3.8    18.9    +      -       -      +
    113B  PHE*     3.7    27.8    -      -       -      -
    114B  ILE*     1.3    75.1    -      -       -      +
    116B  ARG*     1.3    65.8    +      -       -      +
    117B  GLU*     5.5     4.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 116 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  LEU*     5.9     3.2    -      -       -      +
     80A  ASP      3.6    22.2    +      -       -      -
     84A  PHE*     5.4     5.6    -      -       -      -
    116A  ARG*     4.0    21.8    -      -       -      +
    117A  GLU      3.6     3.6    -      -       -      +
    118A  PHE*     3.9    21.7    -      -       +      +
     81B  VAL      6.2     0.2    -      -       -      -
     82B  LYS      6.1     0.2    -      -       -      +
     83B  HIS*     3.3    48.1    -      -       -      +
     84B  PHE*     3.6    24.2    -      -       +      -
    103B  LYS*     3.3     4.7    -      -       -      +
    104B  HIS*     2.7    57.5    +      -       +      +
    114B  ILE*     4.1    17.6    -      -       +      +
    115B  SER*     1.3    79.4    +      -       -      +
    117B  GLU*     1.3    62.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 117 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  SER      4.1     0.4    -      -       -      +
    116A  ARG*     3.5     1.0    -      -       -      +
    117A  GLU*     2.8    60.1    +      -       +      +
    119A  HIS*     5.5     4.0    +      -       +      +
     84B  PHE*     4.2     3.2    -      -       -      -
    101B  HIS*     3.2    23.9    +      -       +      +
    102B  GLY      3.3    12.8    -      -       -      +
    103B  LYS*     4.5    21.3    -      -       +      +
    115B  SER*     5.5     4.5    +      -       -      +
    116B  ARG*     1.3    76.9    -      -       -      +
    118B  PHE*     1.3    68.5    +      -       -      +
    119B  HIS*     5.8     1.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 118 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  ILE*     4.2    16.4    -      -       +      -
    115A  SER      3.2    11.2    -      -       -      +
    116A  ARG*     3.7    24.2    -      -       +      +
     79B  LEU*     4.5     7.9    -      -       +      -
     80B  ASP      6.0     0.2    -      -       -      -
     81B  VAL*     3.6    29.6    -      -       +      -
     84B  PHE*     3.5    22.9    -      +       +      -
     89B  LEU*     3.6    19.1    -      -       +      -
    100B  VAL*     4.1    23.3    -      -       +      -
    101B  HIS*     3.2    26.1    -      -       -      -
    102B  GLY*     3.1    45.9    +      -       -      -
    117B  GLU*     1.3    77.2    -      -       -      +
    119B  HIS*     1.3    64.4    +      -       -      +
    143B  LEU*     4.7     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 119 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  PHE*     3.8    26.2    -      +       -      -
    114A  ILE*     3.3     4.7    -      -       -      -
    115A  SER*     2.9    43.2    +      -       -      +
     99B  GLU*     3.2    38.9    +      -       +      -
    100B  VAL*     3.4    14.3    +      -       -      -
    101B  HIS*     4.2    16.6    -      +       +      +
    117B  GLU*     5.8     2.0    -      -       +      +
    118B  PHE*     1.3    77.7    -      -       -      +
    120B  GLY*     1.3    60.8    +      -       -      +
    121B  LYS*     4.2     8.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 120 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  PHE*     3.2    18.2    -      -       -      -
    114A  ILE*     4.2     4.5    -      -       -      -
     99B  GLU*     3.4     1.2    -      -       -      +
    100B  VAL*     2.8    51.1    +      -       -      +
    119B  HIS*     1.3    77.4    -      -       -      +
    121B  LYS*     1.3    68.4    +      -       -      +
    122B  TYR*     4.5     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 121 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  GLY*     3.1     4.0    -      -       -      -
    113A  PHE*     3.0    55.9    +      -       +      -
   1153A  MPD      4.2    14.5    -      -       +      +
     94B  LEU*     4.9     8.6    -      -       -      +
     97B  VAL*     4.2    15.7    -      -       +      +
     98B  ILE      3.0     9.0    -      -       -      +
     99B  GLU*     3.6    36.8    +      -       +      -
    119B  HIS*     4.2    10.5    -      -       +      -
    120B  GLY*     1.3    79.7    -      -       -      +
    122B  TYR*     1.3    66.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 122 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111A  HIS      3.2    12.3    -      -       -      +
    112A  GLY*     4.4     7.4    -      -       -      -
    113A  PHE      4.1     4.5    -      -       -      -
   1153A  MPD      4.2     6.1    -      -       -      -
     66B  MET*     2.9    42.1    -      -       +      +
     68B  MET*     4.3    16.2    -      -       +      -
     75B  PHE*     5.5     0.4    -      -       +      -
     77B  VAL*     3.8    30.1    -      -       +      -
     79B  LEU*     3.1    28.2    -      -       +      +
     97B  VAL*     3.4     2.8    -      -       -      -
     98B  ILE*     2.8    65.1    +      -       +      +
    100B  VAL*     3.1    24.5    -      -       +      +
    120B  GLY      4.5     0.2    -      -       -      -
    121B  LYS*     1.3    85.4    -      -       -      +
    123B  ARG*     1.3    64.2    +      -       -      +
    145B  VAL*     5.5     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 123 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110A  GLU*     3.6    31.7    +      -       -      +
    111A  HIS*     3.0    46.5    +      -       +      +
   1153A  MPD      4.1     7.1    -      -       +      +
     68B  MET*     4.7     1.9    -      -       -      +
     75B  PHE*     4.2    11.1    -      -       -      -
     96B  ASP*     3.7    22.7    -      -       -      +
     97B  VAL*     4.5     8.5    -      -       +      +
    122B  TYR*     1.3    76.1    -      -       -      +
    124B  ILE*     1.3    70.4    +      -       -      +
    125B  PRO*     3.5    10.7    -      -       -      +
----------------------------------------------------------
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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