Contacts of the strand formed by residues 185 - 192 (chain B) in PDB entry 6YB9
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.
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 CYS 185 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B GLU 4.9 0.7 - - - +
180B TRP* 3.4 40.5 + - + +
181B LEU* 3.9 11.3 + - - +
183B GLN* 3.2 14.5 - - - -
184B ASN* 1.3 78.2 - - - +
186B THR* 1.3 62.2 - - - +
187B LEU 3.7 2.1 + - - -
216B LEU* 3.7 22.4 - - + -
217B TRP 3.7 5.8 - - - +
218B PRO* 4.3 8.7 - - - -
251B TRP* 3.4 38.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ARG* 5.9 2.2 - - + -
103B ILE* 3.8 28.9 - - + -
177B GLU* 6.0 0.4 - - - +
181B LEU* 5.6 5.1 - - - +
184B ASN 4.3 0.4 - - - -
185B CYS* 1.3 69.3 - - - +
187B LEU* 1.3 69.2 + - - +
188B VAL* 3.4 8.6 + - + +
216B LEU* 3.6 4.7 - - - -
217B TRP* 2.9 40.6 + - + -
220B GLY* 3.3 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ARG* 4.1 5.7 - - - +
173B PHE* 3.6 36.4 - - + +
176B LEU* 3.6 21.3 - - + -
177B GLU* 3.4 47.8 + - - +
180B TRP* 4.3 15.5 - - + +
185B CYS 3.7 4.8 + - - -
186B THR* 1.3 74.3 - - - +
188B VAL* 1.3 62.6 + - - +
189B ASP 4.1 2.5 - - - +
190B MET* 5.1 2.9 - - + -
214B TRP* 3.7 43.5 - - + -
215B ARG 3.7 8.1 - - - +
216B LEU* 4.4 6.1 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
102B ARG* 2.9 31.1 + - - -
103B ILE* 3.3 32.5 + - + +
105B THR* 3.7 29.4 - - + -
173B PHE* 4.1 1.3 - - - -
186B THR* 3.8 13.0 - - + +
187B LEU* 1.3 72.3 - - - +
189B ASP* 1.3 64.0 + - - +
215B ARG* 3.0 16.9 + - + +
217B TRP* 3.3 49.8 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
100B CYS 3.0 17.7 - - - +
101B ARG* 3.7 21.9 + - + -
103B ILE 4.6 1.3 - - - +
105B THR* 3.7 12.6 - - - +
173B PHE* 3.8 4.5 - - - -
187B LEU* 3.7 3.9 - - - +
188B VAL* 1.3 82.3 - - + +
190B MET* 1.3 65.6 + - - +
214B TRP* 3.4 3.5 - - - +
215B ARG* 2.8 51.6 + - - +
703B OK8 2.6 33.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TRP 3.9 0.8 - - - +
99B VAL* 3.2 8.0 - - - +
100B CYS* 3.0 32.6 + - + +
169B THR* 3.7 12.1 - - + +
172B ILE* 3.7 11.0 - - + -
173B PHE* 3.5 56.1 - - + +
176B LEU* 4.2 21.3 - - - -
187B LEU* 5.1 2.7 - - + -
189B ASP* 1.3 78.7 + - - +
191B LYS* 1.3 60.5 + - - +
192B ILE* 3.8 27.4 - - + -
209B ILE* 5.2 2.7 - - + -
213B SER* 3.1 15.0 - - - +
214B TRP* 3.9 9.6 - - + -
703B OK8 3.5 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B GLU* 3.8 34.9 + - + -
98B TRP 3.3 7.0 - - - +
99B VAL* 4.2 4.0 - - + -
190B MET* 1.3 71.6 - - - +
192B ILE* 1.3 78.4 + - - +
193B GLU* 3.0 26.5 + - - +
207B ASP* 4.2 10.3 + - - -
208B VAL 5.0 3.3 + - - +
213B SER* 2.7 36.6 + - - +
703B OK8 3.2 58.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TRP* 3.0 47.1 + - + +
169B THR* 3.8 18.6 - - + +
172B ILE* 3.9 20.0 - - + -
190B MET* 3.8 23.8 - - + -
191B LYS* 1.3 81.9 - - - +
193B GLU* 1.3 68.2 + - - +
194B PHE* 3.6 30.1 - - + -
205B LEU* 3.8 11.2 - - + -
208B VAL 5.2 4.9 - - - -
209B ILE* 3.9 27.4 - - + -
----------------------------------------------------------
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