Contacts of the strand formed by residues 207 - 218 (chain C) in PDB entry 3HB8
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 GLU 207 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ARG* 2.9 43.2 + - - -
202C TYR 3.6 1.4 - - - +
203C VAL* 3.4 6.3 - - - +
204C VAL* 2.9 38.7 + - + +
205C ASN* 2.9 6.7 + - - +
206C SER* 1.3 78.3 - - - +
208C LEU* 1.3 60.7 + - - +
209C SER* 3.9 3.1 + - - +
243C LEU* 4.5 3.1 - - - +
244C LYS* 3.1 40.2 + - + +
245C PRO 4.4 2.5 - - - +
246C GLY* 3.3 10.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 208 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C ILE* 3.7 15.0 - - + -
201C PHE* 4.3 9.0 - - + -
202C TYR 3.6 14.8 - - - +
203C VAL* 3.6 19.3 - - + -
206C SER 4.3 0.2 + - - -
207C GLU* 1.3 72.9 - - - +
209C SER* 1.3 71.1 + - - +
234C THR* 3.6 22.3 - - + +
237C ILE* 3.3 35.0 - - + -
238C ALA* 3.6 26.9 - - + +
241C THR* 4.2 3.8 - - - +
243C LEU* 4.0 14.8 - - + +
244C LYS 3.0 8.3 + - - +
245C PRO 3.6 0.2 - - - -
246C GLY 2.8 21.4 + - - -
247C ASP 4.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 209 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ARG* 5.2 0.7 + - - -
201C PHE* 3.5 10.1 - - - -
202C TYR* 2.7 52.6 + - - -
204C VAL* 5.7 2.1 - - - +
207C GLU* 3.9 3.3 + - - +
208C LEU* 1.3 76.4 - - - +
210C CYS* 1.3 65.8 + - - +
234C THR* 4.6 0.4 - - - -
246C GLY* 3.9 4.0 - - - -
247C ASP* 3.0 38.0 + - - -
249C ILE* 4.9 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 210 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C CYS* 4.4 9.2 - - - -
200C GLN 3.3 8.7 - - - -
201C PHE* 3.2 30.5 - - + -
209C SER* 1.3 80.3 - - - +
211C GLN* 1.3 64.7 + - - +
212C LEU 4.2 0.2 - - - -
230C TYR* 4.7 9.6 - - - -
233C LEU* 5.4 0.2 - - - -
234C THR* 3.2 24.5 - - - +
247C ASP 3.1 6.0 + - - +
248C PHE* 3.2 18.8 - - + -
249C ILE* 2.7 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 211 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C GLN* 3.3 15.2 - - - +
199C CYS* 3.0 6.3 - - - +
200C GLN* 2.7 54.8 + - + +
210C CYS* 1.3 77.1 - - - +
212C LEU* 1.3 65.1 + - - +
213C TYR* 5.7 1.8 - - + -
249C ILE* 3.3 27.4 - - + +
251C THR* 2.6 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C HIS* 3.7 28.5 - - + +
198C LEU 3.5 17.9 - - - +
199C CYS* 4.0 3.8 - - + -
210C CYS 4.2 0.2 - - - -
211C GLN* 1.3 75.3 - - - +
213C TYR* 1.3 67.2 + - - +
214C GLN* 4.0 13.9 - - - +
226C ASN* 4.8 4.3 - - + +
230C TYR* 3.4 41.5 - - + -
248C PHE* 3.8 22.6 - - + -
249C ILE 2.9 6.5 + - - -
250C HIS* 3.9 20.9 - - + +
251C THR* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 213 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C PHE* 4.8 10.0 - - - -
196C HIS 3.8 1.4 - - - -
197C ALA* 3.1 41.9 + - + -
198C LEU* 2.9 30.6 + - + +
211C GLN* 4.3 2.2 + - + +
212C LEU* 1.3 71.4 - - - +
214C GLN* 1.3 59.6 + - - +
215C ARG* 4.0 23.7 - - + +
251C THR* 3.6 28.0 - - + -
252C LEU 4.9 1.1 - - - -
253C GLY* 4.0 22.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 214 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C CYS* 3.2 14.6 - - + +
196C HIS* 3.6 14.7 + - - +
212C LEU* 3.9 4.1 + - + +
213C TYR* 1.3 73.6 - - - +
215C ARG* 1.3 65.8 + - - +
216C SER 3.0 25.3 + - - +
217C GLY* 3.2 16.6 - - - -
223C VAL* 4.4 2.2 - - - +
226C ASN* 3.0 40.8 - - - +
250C HIS* 3.0 25.1 + - + +
251C THR 2.9 15.0 + - - +
252C LEU* 3.4 10.5 - - + +
253C GLY 3.0 19.4 + - - -
365C UMP 4.5 4.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 215 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C PHE* 5.3 0.7 - - - -
182C TRP* 3.8 22.9 - - - -
193C PRO* 3.2 33.4 + - - +
194C PRO 2.8 20.3 + - - +
195C CYS* 3.0 26.2 + - - +
197C ALA* 4.8 5.3 - - + +
213C TYR* 3.9 24.9 + - + +
214C GLN* 1.3 70.8 - - - +
216C SER* 1.3 79.7 + - - +
253C GLY* 3.5 2.1 - - - +
254C ASP* 2.7 28.4 + - - +
365C UMP 2.9 41.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C CYS* 3.9 16.1 - - - -
214C GLN* 3.0 20.1 + - - +
215C ARG* 1.3 109.4 - - - +
217C GLY* 1.3 57.7 - - - +
252C LEU* 4.0 0.4 - - - -
254C ASP* 3.7 12.6 + - - +
256C HIS* 3.4 20.3 - - - -
365C UMP 3.3 17.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 217 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C GLN* 3.2 16.2 - - - -
216C SER* 1.3 76.0 + - - +
218C ASP* 1.3 61.4 + - - -
219C MET* 3.2 5.0 + - - +
223C VAL* 4.1 5.1 - - - +
252C LEU* 3.5 15.0 - - - +
254C ASP 3.2 9.7 + - - -
255C ALA* 3.7 2.4 - - - -
256C HIS* 2.9 33.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 218 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C GLN* 4.5 1.2 - - - +
216C SER 4.3 0.6 - - - -
217C GLY* 1.3 68.1 - - - -
219C MET* 1.3 63.3 + - - +
220C GLY* 2.8 17.7 + - - -
221C LEU* 4.0 14.1 + - - +
222C GLY* 2.9 25.0 + - - -
223C VAL* 2.9 10.8 + - - +
256C HIS* 3.8 11.2 - - - +
258C TYR* 4.4 21.8 + - - -
261C HIS* 4.4 9.4 + - - -
365C UMP 3.7 39.9 + - + +
----------------------------------------------------------
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