Contacts of the helix formed by residues 209 - 229 (chain C) in PDB entry 5Y1Z
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 209 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133C ILE* 4.2 5.6 - - - -
136C ALA* 4.0 17.5 - - + +
137C GLU* 3.6 28.3 - - + -
146C MET* 4.2 10.1 - - + -
154C LEU* 3.6 13.8 - - - +
158C LEU* 5.2 0.3 - - - +
207C TYR* 3.3 7.7 + - - +
208C GLY* 1.3 79.5 - - - +
210C THR* 1.3 66.6 + - - +
211C GLU* 3.3 20.2 + - - +
212C ALA* 3.3 35.7 + - - +
213C PHE* 3.4 4.7 + - - +
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Residues in contact with THR 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C MET* 4.8 3.6 - - - -
154C LEU* 4.0 14.8 - - + -
158C LEU* 5.2 0.4 - - - -
209C CYS* 1.3 74.9 - - - +
211C GLU* 1.3 70.7 + - - +
213C PHE* 3.1 7.3 + - - +
214C LEU* 3.0 20.8 + - - +
249C MET* 3.7 34.2 - - - +
252C ILE* 3.9 28.0 - - + -
253C GLU* 2.8 37.5 + - + +
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Residues in contact with GLU 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LYS* 4.8 19.5 - - + -
133C ILE* 4.2 13.7 - - + +
136C ALA* 3.3 29.8 - - + +
143C SER* 5.9 2.1 - - - -
146C MET* 5.7 0.2 - - - +
209C CYS* 3.5 13.7 - - - +
210C THR* 1.3 81.9 + - - +
212C ALA* 1.3 66.8 + - - +
214C LEU* 3.3 7.1 + - + +
215C ALA* 2.9 26.5 + - - +
253C GLU* 4.2 9.2 - - - +
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Residues in contact with ALA 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C ILE* 3.5 21.8 - - + +
137C GLU* 4.0 11.2 - - - +
206C MET 5.4 0.2 - - - +
207C TYR* 3.9 17.3 - - + -
208C GLY 4.3 2.5 - - - +
209C CYS* 3.3 28.4 - - - +
211C GLU* 1.3 78.0 - - - +
213C PHE* 1.3 63.1 + - - +
215C ALA* 3.6 2.1 - - - +
216C ASP* 3.0 24.4 + - - +
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Residues in contact with PHE 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C LEU* 3.8 35.2 - - + -
161C ALA* 4.7 3.1 - - + -
162C ILE* 3.7 33.2 - - + -
165C MET* 4.1 8.1 - - + -
198C LEU* 3.5 27.1 - - + -
202C ALA* 4.6 1.3 - - + -
207C TYR* 3.6 34.3 - + + -
209C CYS 3.4 2.7 + - - +
210C THR 3.1 11.4 + - - +
212C ALA* 1.3 79.8 - - - +
214C LEU* 1.3 57.5 + - - +
216C ASP* 3.3 4.5 + - - +
217C ALA* 2.9 26.5 + - - +
245C CYS* 3.7 20.2 - - - -
249C MET* 3.6 28.0 - - + -
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Residues in contact with LEU 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C THR 3.0 14.9 + - - +
211C GLU* 3.3 6.5 + - + +
213C PHE* 1.3 77.7 - - - +
215C ALA* 1.3 57.8 + - - +
217C ALA* 3.2 3.1 + - + +
218C LYS* 3.0 57.9 + - + +
242C ILE* 4.1 5.6 - - + +
245C CYS* 3.9 17.3 - - + -
246C GLU* 3.7 48.5 - - + +
249C MET* 4.1 13.2 - - + -
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Residues in contact with ALA 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C TRP* 3.7 3.8 - - - -
108C ARG* 3.0 30.8 + - - +
129C GLU* 3.9 20.9 - - + +
133C ILE* 4.4 13.7 - - + -
211C GLU 2.9 19.1 + - - +
212C ALA 3.6 4.0 - - - +
214C LEU* 1.3 75.4 - - - +
216C ASP* 1.3 66.1 + - - +
218C LYS* 3.4 21.5 + - - +
219C TRP* 3.9 0.5 + - - -
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Residues in contact with ASP 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ARG* 4.1 1.1 - - - +
191C HIS* 4.2 4.0 - - - -
193C MET* 3.6 22.9 - - - +
198C LEU* 4.1 3.8 - - + -
201C ASN* 3.9 10.6 + - - -
207C TYR* 2.5 38.0 + - + +
212C ALA 3.0 17.1 + - - +
213C PHE 3.7 4.5 - - - +
215C ALA* 1.3 76.1 - - - +
217C ALA* 1.3 64.3 + - - +
219C TRP* 3.2 43.8 + - - +
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Residues in contact with ALA 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C MET* 4.1 7.2 - - + -
198C LEU* 4.0 26.4 - - + +
213C PHE* 2.9 14.5 + - + +
214C LEU 3.2 9.1 + - - +
216C ASP* 1.3 76.3 - - - +
218C LYS* 1.3 55.9 + - - +
220C ILE* 2.9 34.2 + - - +
242C ILE* 3.5 12.3 - - + +
245C CYS* 3.9 22.7 - - + -
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Residues in contact with LYS 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C TRP* 3.6 30.1 - - + +
129C GLU* 4.4 13.1 + - - +
214C LEU* 3.0 52.0 + - + +
215C ALA* 3.7 2.9 - - - +
216C ASP 3.2 0.4 - - - -
217C ALA* 1.3 72.0 - - - +
219C TRP* 1.3 64.4 + - - +
220C ILE 3.1 0.2 - - - -
221C LEU* 3.1 6.8 + - + +
222C HIS* 2.9 23.0 + - - +
242C ILE* 3.9 23.3 - - + -
246C GLU* 3.9 15.6 + - - -
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Residues in contact with TRP 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ASP* 3.6 17.7 - - + -
92C TRP* 3.6 16.8 - + - -
107C PRO* 4.3 24.5 - - + +
108C ARG* 3.7 41.9 - - + +
191C HIS* 3.3 53.3 + + + -
193C MET* 3.6 16.6 - - + -
215C ALA 4.0 3.1 - - - -
216C ASP* 3.2 42.4 + - - +
217C ALA 3.1 0.4 - - - -
218C LYS* 1.3 77.5 - - - +
220C ILE* 1.3 63.1 + - - +
222C HIS* 3.6 26.2 - + - -
223C ASN* 2.8 38.2 + - - +
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Residues in contact with ILE 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C MET* 5.6 0.2 - - + -
173C PHE* 3.6 36.1 - - + +
193C MET* 3.5 29.8 - - + +
194C ASP* 3.7 26.0 - - - -
195C LEU* 3.8 24.5 - - + +
198C LEU* 4.1 9.6 - - + -
217C ALA* 2.9 17.3 + - - +
219C TRP* 1.3 76.2 - - - +
221C LEU* 1.3 57.1 + - - +
223C ASN* 4.0 2.9 - - - +
224C CYS* 3.0 27.0 + - - +
238C ALA* 4.7 5.8 - - + -
241C VAL* 4.8 9.4 - - + -
242C ILE* 4.4 3.1 - - + -
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Residues in contact with LEU 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C HIS* 5.6 2.2 - - + +
217C ALA 4.2 0.2 + - - -
218C LYS* 3.1 9.2 + - + +
220C ILE* 1.3 77.5 - - - +
222C HIS* 1.3 67.7 + - - +
224C CYS* 3.0 2.3 + - + +
225C ILE* 2.9 47.1 + - + +
235C THR* 4.2 4.9 - - + -
238C ALA* 3.8 27.1 - - + +
239C LYS* 4.1 36.6 - - + -
242C ILE* 4.1 27.3 - - + +
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Residues in contact with HIS 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ASP* 2.7 21.4 + - - -
90C TYR* 3.7 8.3 - - + -
91C CYS 3.1 26.7 - - - -
92C TRP* 4.1 21.7 + + + -
95C HIS* 2.7 37.5 + - + +
218C LYS 2.9 15.7 + - - +
219C TRP* 3.6 22.4 - + - +
221C LEU* 1.3 76.8 - - - +
223C ASN* 1.3 76.3 + - - +
225C ILE* 3.2 3.5 + - - +
226C ILE* 3.0 53.0 + - + +
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Residues in contact with ASN 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C TYR* 4.0 12.7 + - - +
189C ILE* 3.4 39.8 - - + +
190C PHE 5.4 0.3 + - - -
191C HIS 2.9 25.5 + - - -
192C PRO* 3.8 6.9 - - - +
193C MET* 3.9 6.6 + - - +
219C TRP* 2.8 33.4 + - - +
220C ILE* 4.0 3.9 - - - +
222C HIS* 1.3 87.8 - - - +
224C CYS* 1.3 65.4 + - - +
226C ILE* 3.2 1.7 + - - +
227C TYR* 2.9 27.7 + - - +
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Residues in contact with CYS 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C PHE* 4.0 14.4 - - + -
185C TYR* 5.3 0.6 + - - -
220C ILE 3.0 16.2 + - - +
221C LEU 3.4 9.2 - - - +
223C ASN* 1.3 76.3 - - - +
225C ILE* 1.3 56.5 + - - +
227C TYR* 5.3 0.4 - - - -
228C ASN* 2.8 46.3 + - - +
229C GLY 3.6 0.3 + - - -
234C LEU* 3.6 17.7 - - - -
235C THR* 3.3 37.6 + - - +
238C ALA* 4.2 8.7 - - + -
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Residues in contact with ILE 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C CYS 5.3 0.4 - - - +
95C HIS* 3.5 48.2 - - + +
221C LEU* 2.9 42.1 + - + +
222C HIS 3.2 6.5 + - - +
224C CYS* 1.3 75.3 - - - +
226C ILE* 1.3 59.7 + - - +
229C GLY* 2.8 27.9 + - - +
230C GLY* 4.0 17.9 - - - +
235C THR* 3.7 21.8 - - + -
239C LYS* 5.5 6.7 - - - +
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Residues in contact with ILE 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ASP* 4.8 1.6 - - - +
90C TYR* 3.6 52.8 - - + +
95C HIS* 4.0 13.9 - - + +
188C TYR* 4.0 13.8 - - + +
189C ILE* 3.8 17.5 - - + -
222C HIS* 3.0 59.4 + - + +
223C ASN* 3.2 9.2 + - - +
225C ILE* 1.3 80.0 - - - +
227C TYR* 1.3 62.1 + - - +
229C GLY* 4.3 1.2 + - - -
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Residues in contact with TYR 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C HIS* 3.0 41.9 + + + +
184C ASP* 2.9 38.2 + - - -
185C TYR* 3.8 39.0 - + + -
188C TYR* 4.0 22.7 - + + -
189C ILE* 4.4 6.3 - - + -
223C ASN 2.9 15.8 + - - +
224C CYS* 4.6 0.4 - - - +
226C ILE* 1.3 79.9 - - + +
228C ASN* 1.3 79.0 + - - +
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Residues in contact with ASN 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C HIS* 5.6 3.4 - - - -
224C CYS* 2.8 25.2 + - - +
227C TYR* 1.3 100.6 + - - +
229C GLY* 1.3 62.9 + - - +
232C HIS* 3.3 44.1 + - + +
234C LEU* 3.6 24.8 - - - +
235C THR* 4.4 2.0 - - - +
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Residues in contact with GLY 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C CYS 3.6 0.2 + - - -
225C ILE* 2.8 19.8 + - - -
226C ILE 4.3 1.0 + - - -
227C TYR 3.7 1.0 - - - -
228C ASN* 1.3 80.2 - - - +
230C GLY* 1.3 64.6 + - - -
231C ASN 3.2 3.6 - - - -
232C HIS* 3.1 8.8 + - - +
235C THR* 2.8 22.5 + - - -
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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
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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) + - + + + + + -
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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