Contacts of the helix formed by residues 219 - 238 (chain C) in PDB entry 1YXU
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 HIS 219 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C ASP 3.7 18.2 + - - -
196C THR* 3.8 8.2 + - - +
197C VAL* 3.7 32.3 - - + +
198C TYR* 4.4 1.8 - - - -
211C GLU* 5.1 0.6 + - - -
217C ARG* 5.4 3.0 + - - -
218C TYR* 1.3 83.0 - - - +
220C GLY* 1.3 66.4 + - - +
221C ARG 3.6 1.8 - - - +
222C SER* 3.2 17.0 + - - +
223C ALA* 3.0 22.9 + - - +
275C PRO* 6.3 3.6 - - + -
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Residues in contact with GLY 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C LEU* 3.5 37.2 - - - +
193C LEU* 4.8 4.7 - - - -
194C LYS 4.9 3.6 + - - -
198C TYR* 3.5 15.8 - - - -
218C TYR* 4.7 0.4 - - - -
219C HIS* 1.3 71.9 - - - +
221C ARG* 1.3 57.3 - - - +
223C ALA* 3.5 4.6 - - - +
224C ALA* 2.9 27.7 + - - +
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Residues in contact with ARG 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C HIS* 4.4 20.8 - - + +
193C LEU* 3.4 36.3 - - + +
194C LYS 3.4 17.8 + - - -
195C ASP* 2.9 31.0 + - - +
219C HIS* 3.6 1.0 - - - +
220C GLY* 1.3 70.1 - - - +
222C SER* 1.3 61.3 + - - +
224C ALA* 3.1 8.8 + - - +
225C VAL* 2.9 35.0 + - + +
281C PHE* 4.9 8.2 - - + -
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Residues in contact with SER 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C GLU* 4.1 4.7 + - - -
219C HIS* 3.2 22.4 + - - +
221C ARG* 1.3 77.2 - - - +
223C ALA* 1.3 63.4 + - - +
225C VAL* 3.3 6.0 + - - +
226C TRP 3.1 14.0 + - - -
275C PRO* 3.6 41.4 - - - +
278C ARG* 3.0 23.4 + - - +
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Residues in contact with ALA 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C LEU* 6.1 0.7 - - + -
207C TYR 5.0 0.2 - - - +
209C PRO* 4.1 23.1 - - + +
211C GLU* 4.5 0.4 - - - -
218C TYR* 3.5 26.7 - - + -
219C HIS 3.0 19.2 + - - +
220C GLY* 3.5 4.5 - - - +
222C SER* 1.3 76.4 + - - +
224C ALA* 1.3 62.4 + - - +
226C TRP* 3.5 4.9 + - - +
227C SER* 3.2 22.0 + - - -
278C ARG* 4.2 7.2 - - - +
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Residues in contact with ALA 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C VAL* 4.8 0.4 - - + -
159C HIS* 3.9 24.9 - - + +
164C LEU* 4.5 3.6 - - + -
168C ILE* 4.2 15.0 - - + +
220C GLY 2.9 13.9 + - - +
221C ARG 3.4 8.5 - - - +
223C ALA* 1.3 78.0 - - - +
225C VAL* 1.3 56.9 + - - +
227C SER* 2.6 26.1 + - - -
228C LEU* 3.0 18.7 + - - +
281C PHE* 4.6 5.8 - - + -
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Residues in contact with VAL 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C ARG* 2.9 21.0 + - + +
222C SER* 3.3 6.3 + - - +
224C ALA* 1.3 72.4 - - - +
226C TRP* 1.3 67.0 + - - +
228C LEU* 2.9 17.1 + - - +
229C GLY 3.0 9.9 + - - -
270C CYS* 3.7 17.1 - - + +
278C ARG* 3.9 7.9 - - + -
279C PRO* 3.4 51.4 - - + +
280C THR* 4.9 2.2 - - - -
281C PHE* 4.0 23.3 - - + -
284C ILE* 4.0 10.1 - - + -
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Residues in contact with TRP 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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206C VAL 5.1 0.4 + - - -
207C TYR 3.3 20.5 + - - -
208C SER 3.3 11.9 + - - -
209C PRO* 3.7 12.3 - - + -
210C PRO* 3.3 40.6 - - + -
222C SER 3.1 6.3 + - - -
223C ALA 3.5 8.5 - - - +
225C VAL* 1.3 76.2 - - - +
227C SER* 1.3 62.8 + - - +
229C GLY 2.9 11.8 + - - -
230C ILE* 3.1 24.2 + - + +
242C PHE* 3.7 29.4 - + - -
248C ILE* 3.7 22.0 - - + +
251C GLY* 4.8 1.3 - - - -
270C CYS 3.8 10.5 + - - -
271C LEU* 3.2 56.2 - - + +
272C ALA 3.7 3.8 - - - -
273C LEU* 4.4 3.4 - - + -
278C ARG* 3.7 27.6 - - - +
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Residues in contact with SER 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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166C ARG 6.4 0.4 - - - -
168C ILE* 3.6 38.2 + - - +
207C TYR* 3.6 29.0 - - - -
223C ALA 3.2 7.6 + - - -
224C ALA* 2.6 23.2 + - - -
226C TRP* 1.3 79.4 - - - +
228C LEU* 1.3 56.6 + - - +
230C ILE* 3.2 7.5 + - - +
231C LEU* 3.0 27.5 + - - +
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Residues in contact with LEU 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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148C PHE* 3.3 31.8 - - + -
151C VAL* 4.0 18.4 - - + -
152C LEU* 3.6 30.3 - - + -
155C VAL* 4.4 7.2 - - + -
168C ILE* 3.9 29.4 - - + -
224C ALA 3.0 18.4 + - - +
225C VAL* 2.9 14.9 + - + +
227C SER* 1.3 77.9 + - - +
229C GLY* 1.3 56.0 + - - +
231C LEU* 3.4 4.5 + - + +
232C LEU* 2.9 23.7 + - - +
270C CYS* 4.9 0.7 - - - -
281C PHE* 3.8 19.3 - - + -
284C ILE* 4.6 6.1 - - + -
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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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225C VAL 3.0 6.5 + - - -
226C TRP 2.9 8.8 + - - -
228C LEU* 1.3 75.2 - - - +
230C ILE* 1.3 63.8 + - - +
232C LEU* 3.9 4.7 - - - +
233C TYR* 3.1 24.8 + - - +
267C ILE* 4.1 9.7 - - - +
270C CYS* 3.6 23.9 - - - +
271C LEU* 3.9 12.7 - - - +
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Residues in contact with ILE 230 (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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206C VAL 4.0 15.3 - - - +
207C TYR* 3.5 35.7 - - + -
226C TRP* 3.1 31.6 + - + +
227C SER* 3.5 7.0 - - - +
229C GLY* 1.3 75.7 - - - +
231C LEU* 1.3 57.3 + - - +
233C TYR* 3.4 3.5 + - - +
234C ASP* 2.9 26.7 + - - +
240C ILE* 4.1 7.0 - - + -
241C PRO* 3.8 23.2 - - + +
242C PHE* 3.6 31.0 - - + -
271C LEU* 3.7 14.1 - - + +
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Residues in contact with LEU 231 (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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129C LEU* 4.1 20.9 - - + -
148C PHE* 4.4 12.3 - - + -
151C VAL* 4.0 22.9 - - + -
168C ILE* 4.1 11.2 - - + -
169C LYS* 4.2 2.7 - - - -
170C ASP* 3.9 28.9 - - + +
173C ILE* 3.8 20.6 - - + -
207C TYR* 4.0 8.5 - - + +
227C SER 3.0 13.3 + - - +
228C LEU* 3.5 10.3 - - + +
230C ILE* 1.3 76.2 - - - +
232C LEU* 1.3 64.3 + - - +
234C ASP* 3.3 9.6 + - - +
235C MET* 3.0 30.9 + - + +
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Residues in contact with LEU 232 (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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144C ALA 4.6 0.7 - - - +
148C PHE* 3.8 20.2 - - + -
228C LEU 2.9 17.0 + - - +
229C GLY* 3.9 5.6 - - - +
230C ILE 3.3 0.2 - - - -
231C LEU* 1.3 74.0 - - - +
233C TYR* 1.3 65.3 + - - +
235C MET* 3.1 31.4 + - + +
236C VAL* 3.1 23.2 + - + +
263C CYS* 4.5 4.0 - - - -
266C LEU* 3.8 33.0 - - + -
267C ILE* 3.8 23.8 - - + +
270C CYS* 5.8 0.9 - - - -
289C TRP* 3.8 30.3 - - + -
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Residues in contact with TYR 233 (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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295B LEU* 5.1 0.3 - - - +
229C GLY 3.1 18.2 + - - +
230C ILE 3.6 3.6 - - - +
232C LEU* 1.3 76.4 - - - +
234C ASP* 1.3 55.9 + - - +
236C VAL* 3.4 1.1 + - - -
237C CYS* 2.9 55.6 + - + +
239C ASP 3.2 15.5 - - - -
240C ILE 3.9 0.9 - - - -
241C PRO* 3.5 37.5 - - + +
253C VAL* 3.8 25.8 - - + -
254C PHE* 2.5 30.1 + - - -
255C PHE* 3.8 19.7 - + - -
256C ARG* 3.4 28.7 + - - +
267C ILE* 4.0 17.1 - - + +
271C LEU* 5.3 0.4 - - + -
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Residues in contact with ASP 234 (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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133C ILE* 3.8 10.7 - - - +
170C ASP* 2.5 35.8 - - - +
207C TYR* 3.9 2.1 + - - +
230C ILE 2.9 17.4 + - - +
231C LEU* 3.4 12.3 - - - +
233C TYR* 1.3 77.2 - - - +
235C MET* 1.3 56.6 + - - +
238C GLY* 2.8 30.7 + - - -
239C ASP* 3.1 30.1 + - - +
240C ILE* 3.4 14.8 + - + +
700C IMD 3.3 17.7 - - - -
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Residues in contact with MET 235 (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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129C LEU* 4.1 24.5 - - + -
133C ILE* 4.3 10.3 - - + +
137C GLY 4.8 0.3 - - - +
138C ALA* 3.8 2.1 - - - -
139C LEU* 2.9 46.2 + - + +
144C ALA* 4.0 14.4 - - + +
147C PHE* 3.9 27.1 - - - -
148C PHE* 3.6 41.5 - - + -
151C VAL* 6.1 0.7 - - - -
231C LEU* 3.0 29.7 + - + +
232C LEU* 3.1 13.2 + - + +
234C ASP* 1.3 77.7 - - - +
236C VAL* 1.3 61.1 + - - +
237C CYS 3.6 0.3 + - - -
238C GLY* 4.8 0.2 - - - -
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Residues in contact with VAL 236 (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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138C ALA* 3.6 12.9 - - - +
139C LEU 4.0 10.4 - - - +
141C GLU* 4.4 11.9 - - + -
144C ALA* 3.6 27.6 - - + -
232C LEU* 3.1 17.9 + - + +
233C TYR 3.8 4.5 - - - +
235C MET* 1.3 75.8 - - - +
237C CYS* 1.3 62.1 + - - +
257C GLN* 3.8 11.3 - - - +
258C ARG 4.9 1.4 - - - +
259C VAL* 3.6 29.2 - - + +
263C CYS* 4.1 15.7 - - - -
267C ILE* 4.0 19.3 - - + -
289C TRP* 4.9 0.2 - - + -
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Residues in contact with CYS 237 (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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138C ALA* 3.9 7.0 - - - +
233C TYR* 2.9 59.6 + - + +
236C VAL* 1.3 81.4 - - - +
238C GLY* 1.3 58.6 + - - +
239C ASP* 3.2 4.9 + - - +
255C PHE* 3.6 20.6 - - - -
256C ARG* 3.9 26.7 - - + -
257C GLN* 3.6 20.2 - - - +
259C VAL* 4.0 6.3 - - - -
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Residues in contact with GLY 238 (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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133C ILE* 3.5 18.2 - - - +
137C GLY* 4.5 1.6 - - - -
138C ALA* 4.0 15.8 - - - +
234C ASP* 2.8 17.0 + - - -
236C VAL 3.7 0.8 - - - -
237C CYS* 1.3 76.9 - - - +
239C ASP* 1.3 65.0 + - - +
700C IMD 3.0 23.9 + - - -
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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