Contacts of the helix formed by residues 198 - 211 (chain C) in PDB entry 1Y9D
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 ASP 198 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C GLU 3.7 3.4 + - - -
197C PRO* 1.3 68.9 - - - +
199C VAL* 1.3 65.6 + - - +
200C GLN* 3.6 9.3 + - - +
201C ALA* 3.1 36.4 + - + +
202C VAL* 3.0 22.1 + - - +
204C ARG* 4.8 2.1 + - - -
322C VAL* 5.2 3.9 - - + +
323C LEU 5.4 1.6 + - - -
324C ALA* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 199 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C PRO 4.1 9.2 - - - +
198C ASP* 1.3 74.3 + - - +
200C GLN* 1.3 66.5 + - + +
202C VAL* 3.4 7.4 + - - +
203C THR* 2.9 36.5 + - - +
336C GLN* 6.0 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 200 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C ASP* 3.3 9.3 + - - +
199C VAL* 1.3 86.5 - - + +
201C ALA* 1.3 57.1 + - - +
203C THR* 3.5 18.5 + - - +
204C ARG* 3.0 47.0 + - - +
207C GLN* 5.7 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 201 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C ASP* 3.1 28.8 + - + +
200C GLN* 1.3 74.9 - - - +
202C VAL* 1.3 59.5 + - - +
204C ARG* 3.3 23.5 + - - +
205C LEU* 2.8 30.7 + - - +
320C ILE* 4.2 3.8 - - + +
321C ALA 5.2 2.9 - - - +
322C VAL* 3.6 24.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 202 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C PRO* 3.3 33.7 - - + -
198C ASP 3.0 13.2 + - - +
199C VAL* 3.8 7.6 - - - +
201C ALA* 1.3 75.0 - - - +
203C THR* 1.3 50.9 + - - +
205C LEU* 3.4 7.0 + - - +
206C THR* 2.5 47.7 + - - +
322C VAL* 4.5 7.2 - - + -
329C THR* 4.1 14.1 - - + -
332C ALA* 4.1 12.6 - - + -
333C ILE* 4.1 16.2 - - + -
336C GLN* 3.7 23.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 203 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C VAL* 2.9 23.6 + - - +
200C GLN* 3.7 22.7 + - - +
202C VAL* 1.3 73.1 - - - +
204C ARG* 1.3 66.2 + - - +
206C THR* 3.2 3.7 + - - -
207C GLN* 2.9 43.7 + - + +
336C GLN* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 204 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C ASP* 4.8 2.2 + - - -
200C GLN* 3.0 34.4 + - - +
201C ALA* 3.6 30.6 - - - +
203C THR* 1.3 75.4 - - - +
205C LEU* 1.3 65.0 + - - +
207C GLN* 3.3 16.6 + - - +
208C THR* 3.0 27.7 + - - -
319C ASP 5.3 1.8 + - - -
320C ILE* 4.1 33.4 - - + +
321C ALA 5.6 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C ALA 2.8 17.7 + - - +
202C VAL* 3.5 6.1 - - - +
204C ARG* 1.3 76.1 - - - +
206C THR* 1.3 67.1 + - - +
208C THR 3.3 1.6 + - - -
209C LEU* 3.0 22.4 + - + +
281C LEU* 3.8 30.1 - - + -
303C LEU* 3.6 24.5 - - + +
304C GLN 4.2 6.3 - - - +
305C ILE* 4.1 11.0 - - + -
320C ILE* 4.1 19.6 - - + +
322C VAL* 4.1 17.9 - - + -
329C THR* 5.6 1.1 - - + -
333C ILE* 3.5 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 206 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C VAL* 2.5 33.2 + - - +
203C THR* 3.6 6.7 - - - -
205C LEU* 1.3 77.6 - - - +
207C GLN* 1.3 56.7 + - - +
209C LEU* 3.2 5.8 + - + +
210C LEU* 2.9 37.8 + - + +
237C LEU* 5.5 1.1 - - + -
333C ILE* 3.7 28.5 - - + +
336C GLN* 4.3 11.9 - - + +
337C VAL* 3.5 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 207 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C GLN* 5.7 0.2 + - - -
203C THR* 2.9 28.3 + - + +
204C ARG* 3.5 28.9 - - - +
206C THR* 1.3 75.1 - - - +
208C THR* 1.3 64.7 + - - +
210C LEU* 3.3 8.3 + - - +
211C ALA* 3.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 208 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C ARG 3.0 15.4 + - - -
205C LEU 3.8 3.6 - - - -
207C GLN* 1.3 79.2 - - - +
209C LEU* 1.3 62.3 - - - +
211C ALA* 3.5 7.2 + - + +
212C ALA 3.4 14.6 + - - -
279C VAL* 3.9 9.2 - - + +
301C TYR* 3.7 46.7 - - + -
303C LEU* 3.9 17.5 - - + -
320C ILE* 3.3 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C LEU* 3.0 22.9 + - + +
206C THR* 3.2 6.3 + - + +
208C THR* 1.3 78.2 - - - +
210C LEU* 1.3 60.1 + - - +
212C ALA* 3.3 19.4 - - - +
215C PRO* 4.2 17.8 - - + +
216C LEU 5.0 2.9 - - - +
217C ILE* 4.8 7.4 - - + -
233C LEU* 4.8 10.5 - - + -
237C LEU* 4.0 14.8 - - + -
239C ILE* 3.7 28.5 - - + -
279C VAL* 4.3 14.6 - - + -
281C LEU* 4.5 27.8 - - + -
303C LEU* 3.9 12.3 - - + +
333C ILE* 5.2 5.4 - - + -
340C ARG* 4.6 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 210 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C THR* 2.9 24.9 + - + +
207C GLN* 3.3 7.6 + - - +
209C LEU* 1.3 77.4 - - - +
211C ALA* 1.3 57.6 - - - +
212C ALA 3.5 3.1 + - - +
237C LEU* 3.8 24.7 - - + -
336C GLN 5.7 1.1 - - - +
337C VAL* 4.0 22.4 - - + -
340C ARG* 2.8 58.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 211 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C GLN 3.1 17.8 + - - +
208C THR* 3.8 7.6 - - + +
209C LEU 3.3 0.2 - - - -
210C LEU* 1.3 74.8 - - - +
212C ALA* 1.3 63.9 + - - +
213C GLU* 3.6 1.7 + - - +
278C ASP* 4.8 0.7 - - - +
----------------------------------------------------------
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