Contacts of the strand formed by residues 187 - 195 (chain B) in PDB entry 5YDJ


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 187 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179B  THR*     4.7     4.9    -      -       +      -
    180B  VAL      3.7     8.5    -      -       -      +
    181B  ASP*     4.6     8.7    -      -       -      +
    185B  GLY      3.9     2.2    +      -       -      +
    186B  LYS*     1.3    75.6    -      -       -      +
    188B  VAL*     1.3    65.7    +      -       -      +
    264B  ARG*     3.6    64.4    +      -       +      +
    265B  PRO*     6.0     0.2    -      -       -      +
    298B  SER*     4.9     1.7    -      -       -      -
    809B  SO4      2.7    32.9    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 188 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178B  ILE      3.9     0.2    -      -       -      +
    179B  THR*     3.4     4.9    -      -       -      +
    180B  VAL*     3.0    53.2    +      -       +      +
    182B  ALA*     4.5     4.9    -      -       +      +
    187B  LYS*     1.3    79.9    -      -       -      +
    189B  ASP*     1.3    66.2    +      -       -      +
    190B  VAL*     3.9     9.9    -      -       +      -
    261B  VAL*     4.3     5.4    -      -       +      -
    262B  ALA      3.5    14.4    -      -       -      +
    263B  PRO*     4.2     5.8    -      -       +      -
    264B  ARG*     4.4     3.8    -      -       -      -
    294B  ARG*     3.9    27.8    -      -       +      +
    298B  SER*     3.7    28.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 189 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166B  LEU*     4.6     9.3    -      -       +      +
    178B  ILE      3.7     5.6    -      -       -      +
    179B  THR*     3.3    21.3    +      -       -      -
    188B  VAL*     1.3    72.2    -      -       -      +
    190B  VAL*     1.3    60.8    +      -       -      +
    191B  TRP*     3.5    23.6    -      -       +      -
    261B  VAL*     3.5     1.7    -      -       -      +
    262B  ALA*     2.8    40.8    +      -       +      +
    263B  PRO      5.2     0.5    -      -       -      +
    264B  ARG*     3.4    31.7    +      -       -      +
    266B  ARG*     3.0    31.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 190 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177B  GLY*     3.2     4.3    -      -       -      -
    178B  ILE*     2.9    59.8    +      -       +      +
    180B  VAL*     3.6    27.8    -      -       +      -
    188B  VAL*     3.9     4.7    -      -       +      -
    189B  ASP*     1.3    79.3    -      -       -      +
    191B  TRP*     1.3    65.1    +      -       -      +
    192B  LEU*     3.7    30.5    -      -       +      +
    221B  THR      4.3     0.2    -      -       -      +
    260B  VAL      3.5     5.8    -      -       -      +
    261B  VAL*     3.8    23.1    -      -       +      -
    294B  ARG*     4.7     7.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 191 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166B  LEU*     2.9    28.4    +      -       +      -
    168B  VAL*     4.2     9.6    -      -       +      +
    175B  ILE*     4.0     6.7    +      -       +      -
    176B  ARG      4.1     0.4    -      -       -      -
    177B  GLY*     3.4    23.6    -      -       -      +
    189B  ASP*     3.5    28.9    -      -       +      -
    190B  VAL*     1.3    75.8    -      -       -      +
    192B  LEU*     1.3    61.1    +      -       -      +
    194B  ILE*     3.8    17.2    -      -       +      +
    221B  THR*     3.5    24.5    -      -       +      -
    259B  ASN*     3.5     3.5    -      -       -      -
    260B  VAL*     2.6    51.5    +      -       +      +
    262B  ALA*     3.7    17.9    -      -       +      -
    266B  ARG*     3.4    38.6    -      -       -      -
    347B  PHE*     3.6    38.8    -      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 192 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190B  VAL*     3.7    32.7    -      -       +      -
    191B  TRP*     1.3    79.1    -      -       -      +
    193B  GLY*     1.3    57.5    +      -       -      +
    221B  THR*     2.8    39.0    +      -       -      -
    222B  THR*     3.2    19.4    +      -       -      +
    223B  THR      3.1    21.2    +      -       -      +
    224B  PRO*     3.9    24.7    -      -       +      -
    259B  ASN*     3.9    15.5    -      -       +      +
    260B  VAL      4.3     3.1    -      -       -      +
    261B  VAL*     4.5     9.0    -      -       +      -
    293B  HIS*     6.0     1.1    -      -       +      -
    294B  ARG*     6.0     3.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 193 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192B  LEU*     1.3    73.1    -      -       -      +
    194B  ILE*     1.3    63.7    +      -       -      +
    195B  PRO*     3.3     9.7    -      -       -      +
    219B  LEU*     4.8     2.6    -      -       -      +
    221B  THR*     3.3     7.9    +      -       -      -
    223B  THR      3.7     7.5    +      -       -      -
    225B  PRO*     3.9    11.1    -      -       -      +
    257B  TYR*     3.4    26.7    -      -       -      -
    258B  ILE      3.6     0.8    +      -       -      -
    259B  ASN*     3.4    12.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 194 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170B  THR*     5.3     0.7    -      -       +      -
    175B  ILE*     3.8    28.5    -      -       +      -
    191B  TRP*     3.8    23.6    -      -       +      +
    193B  GLY*     1.3    73.7    -      -       -      +
    195B  PRO*     1.4    78.1    -      -       +      +
    196B  TYR      3.5     0.5    +      -       -      -
    215B  TRP*     5.0     4.7    -      -       +      -
    221B  THR*     3.2    17.5    -      -       -      +
    257B  TYR*     3.3     1.4    -      -       -      -
    258B  ILE*     2.7    45.7    +      -       +      +
    260B  VAL*     3.8    15.9    -      -       +      -
    339B  TRP*     3.6    41.3    -      -       +      +
    347B  PHE*     4.2     1.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 195 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193B  GLY      3.3    10.5    -      -       -      +
    194B  ILE*     1.4    94.5    -      -       +      +
    196B  TYR*     1.3    59.8    +      -       -      +
    197B  ALA      3.7    10.8    -      -       -      +
    212B  ALA*     4.3    11.2    -      -       +      +
    215B  TRP*     3.9    23.2    -      -       +      -
    219B  LEU*     3.5    28.5    -      -       +      -
    256B  LEU      3.9     3.6    -      -       -      +
    257B  TYR*     3.4    26.2    -      -       +      +
    339B  TRP*     4.5     4.7    +      -       -      -
----------------------------------------------------------
 Back to top of page


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