Contacts of the helix formed by residues 205 - 221 (chain C) in PDB entry 4UX9
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 ASN 205 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C GLU* 4.4 0.5 - - - +
203C LYS* 4.3 12.2 + - - +
204C GLU* 1.3 73.0 - - - +
206C VAL* 1.4 60.0 + - - +
207C ASP 3.1 1.8 - - - -
208C LEU* 3.0 33.7 + - + +
209C TRP 3.5 0.2 + - - -
306C ALA* 2.6 42.8 + - - +
309C ARG* 3.1 37.7 + - - +
310C ILE 3.7 17.4 + - - +
311C SER* 4.8 4.8 - - - +
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Residues in contact with VAL 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C ILE* 3.5 22.4 - - + -
150C ARG* 5.0 7.2 - - + -
193C ALA* 3.6 18.8 - - + +
195C GLU* 3.4 26.9 + - + +
196C VAL* 3.8 22.0 - - + -
202C TYR* 4.1 14.4 - - + -
203C LYS 3.3 19.1 + - - +
204C GLU 3.1 2.0 + - - -
205C ASN* 1.4 78.5 + - - +
207C ASP* 1.4 65.6 + - - +
209C TRP* 3.3 18.0 + - - +
210C SER* 3.6 8.7 + - - -
309C ARG* 3.7 1.3 - - - +
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Residues in contact with ASP 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C ILE* 4.3 6.5 - - + +
143C HIS* 2.8 29.2 + - + +
148C ILE* 3.4 9.9 - - - +
149C HIS* 3.0 22.4 + - - +
150C ARG* 2.9 28.9 + - - -
152C LEU* 3.7 20.1 - - + +
204C GLU 3.6 7.2 - - - +
206C VAL* 1.4 78.0 - - - +
208C LEU* 1.3 58.0 + - - +
209C TRP 3.3 0.2 - - - -
210C SER* 3.3 11.2 + - - -
211C VAL* 3.2 28.3 + - - +
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Residues in contact with LEU 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C LEU* 4.1 8.5 - - + -
139C ILE* 5.2 2.5 - - + -
143C HIS* 4.5 9.2 - - + -
205C ASN* 3.0 30.9 + - + +
207C ASP* 1.3 75.8 - - + +
209C TRP* 1.3 59.2 + - - +
211C VAL* 3.4 7.2 + - + +
212C GLY 3.0 22.3 + - - -
301C MET* 3.7 36.0 - - + +
309C ARG* 4.3 7.6 - - + -
310C ILE* 4.1 16.2 - - + +
311C SER 3.9 18.4 - - - +
312C VAL* 3.4 33.0 - - + +
315C ALA* 3.9 9.9 - - + -
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Residues in contact with TRP 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C TYR 5.0 0.4 + - - -
191C TYR 3.4 21.0 + - - -
192C ARG 3.3 13.7 + - - -
193C ALA* 3.4 17.9 - - + -
194C PRO* 3.6 29.2 - - + -
205C ASN 3.5 3.2 + - - -
206C VAL 3.3 13.0 + - - +
208C LEU* 1.3 75.4 - - - +
210C SER* 1.3 62.2 + - - +
212C GLY* 3.1 3.5 + - - -
213C CYS* 3.0 39.1 + - - -
225C PHE* 3.6 23.4 - + - -
237C VAL* 4.0 14.1 - - + -
241C LEU* 3.5 22.9 - - + -
301C MET 3.8 16.4 - - - -
302C LEU* 3.8 9.6 - - + +
303C VAL 3.6 40.8 - - - -
304C ILE* 4.0 1.8 - - + -
309C ARG* 3.9 10.4 - - - +
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Residues in contact with SER 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C ARG 5.0 5.9 + - - -
152C LEU* 3.6 37.1 + - - +
187C VAL* 5.8 1.2 - - - +
191C TYR* 3.7 20.4 + - - +
193C ALA* 5.9 0.2 - - - +
206C VAL 3.6 10.6 + - - -
207C ASP* 3.3 13.9 + - - -
209C TRP* 1.3 79.1 - - - +
211C VAL* 1.4 55.8 - - - +
213C CYS* 3.2 8.2 + - - +
214C ILE* 3.0 33.7 + - - +
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Residues in contact with VAL 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LEU* 4.2 20.9 - - + -
135C MET* 4.3 14.8 - - + -
136C LEU* 4.6 11.4 - - + -
139C ILE* 3.5 30.1 - - + -
152C LEU* 4.3 4.0 - - + -
207C ASP 3.2 15.3 + - - +
208C LEU* 3.8 9.9 - - + +
209C TRP 3.2 0.2 - - - -
210C SER* 1.4 71.0 - - - +
212C GLY* 1.3 56.0 + - - +
214C ILE* 3.2 8.7 + - + +
215C MET* 2.8 33.4 + - - +
301C MET* 3.6 24.9 - - + -
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Residues in contact with GLY 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C LEU 3.0 15.1 + - - -
209C TRP 3.1 4.7 + - - -
211C VAL* 1.3 74.6 - - - +
213C CYS* 1.4 54.7 + - - +
216C GLY* 2.9 24.8 + - - -
298C LEU* 3.3 14.1 - - - +
301C MET* 3.8 20.1 - - - -
302C LEU* 3.6 21.0 - - - +
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Residues in contact with CYS 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C TYR 4.0 9.9 - - - +
191C TYR* 3.7 21.9 - - + -
209C TRP* 3.0 44.1 + - - -
210C SER 3.2 9.2 + - - +
212C GLY* 1.4 73.6 - - - +
214C ILE* 1.3 60.3 + - - +
216C GLY* 3.6 0.5 + - - -
217C GLU* 3.0 29.6 + - - +
224C LEU* 3.9 14.5 - - + +
225C PHE* 3.8 26.2 - - - -
302C LEU* 4.1 1.3 - - - -
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Residues in contact with ILE 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C LEU* 3.4 33.4 - - + -
119C ILE* 5.0 1.1 - - + +
135C MET* 4.4 11.9 - - + -
152C LEU* 3.9 9.0 - - + +
153C LYS* 3.8 23.3 - - - +
154C PRO* 4.1 22.7 - - + -
157C ILE* 3.8 14.8 - - + -
191C TYR* 4.4 5.2 - - + -
210C SER 3.0 28.6 + - - +
211C VAL* 3.8 8.3 - - + +
213C CYS* 1.3 72.3 - - - +
215C MET* 1.3 62.5 + - - +
217C GLU* 3.3 9.1 + - - +
218C MET* 2.9 34.8 + - + +
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Residues in contact with MET 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C MET* 3.8 23.1 - - + -
132C LEU* 3.8 34.2 - - + +
211C VAL* 2.8 17.5 + - + +
212C GLY* 3.8 4.5 - - - +
214C ILE* 1.3 77.3 - - - +
216C GLY* 1.3 61.0 + - - +
218C MET* 3.0 22.7 + - - +
219C VAL* 3.1 14.8 + - + +
280C PHE* 5.1 0.4 - - + -
294C ALA* 3.3 39.0 - - + +
297C LEU* 3.9 22.9 - - + -
298C LEU* 3.7 24.0 - - + -
301C MET* 4.7 5.6 - - - +
320C TYR* 4.3 1.3 - - + -
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Residues in contact with GLY 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C GLY 2.9 18.0 + - - -
213C CYS 4.0 1.6 - - - -
215C MET* 1.3 74.4 - - - +
217C GLU* 1.3 56.1 + - - +
219C VAL* 3.3 4.3 + - - +
220C CYS* 2.9 35.7 + - - -
224C LEU* 4.1 11.0 - - - -
275C PHE* 3.9 22.0 - - - -
298C LEU* 3.7 5.8 - - - +
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Residues in contact with GLU 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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119C ILE* 3.6 36.6 - - + +
154C PRO* 4.0 3.9 - - - +
191C TYR* 2.7 40.2 + - - -
213C CYS 3.0 15.2 + - - +
214C ILE* 3.5 7.4 - - - +
216C GLY* 1.3 76.8 - - - +
218C MET* 1.4 52.6 + - - +
221C HIS* 2.7 32.7 + - - -
222C LYS 3.3 29.4 + - - +
223C ILE* 3.7 22.6 + - - +
224C LEU* 4.9 2.2 + - - +
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Residues in contact with MET 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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115C LEU* 4.4 9.2 - - + -
118C VAL* 4.2 8.0 - - + +
119C ILE* 4.1 23.9 - - + +
121C MET 4.9 1.0 - - - +
123C LEU* 3.8 28.9 - - + -
128C MET* 3.8 27.6 - - + +
131C LEU* 3.8 25.8 - - + -
132C LEU* 4.5 6.5 - - + -
135C MET* 4.5 7.6 - - - -
214C ILE* 2.9 32.6 + - + +
215C MET* 3.0 15.0 + - - +
217C GLU* 1.4 75.5 - - - +
219C VAL* 1.3 57.3 + - - +
221C HIS* 3.2 28.2 + - - -
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Residues in contact with VAL 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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128C MET* 3.8 25.1 - - + -
215C MET 3.1 15.0 + - - +
216C GLY 3.7 6.7 - - - +
218C MET* 1.3 76.0 - - - +
220C CYS* 1.3 58.4 + - - +
221C HIS* 3.6 11.0 + - - -
275C PHE* 4.2 15.0 - - + -
279C LEU* 3.4 47.5 - - + +
280C PHE* 3.7 40.4 - - + +
298C LEU* 4.6 6.1 - - + -
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Residues in contact with CYS 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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222B LYS* 5.2 7.0 - - - -
279B LEU* 3.8 11.4 - - - +
216C GLY 2.9 20.4 + - - +
219C VAL* 1.3 74.5 - - - +
221C HIS* 1.3 74.0 + - - +
222C LYS* 3.1 27.7 + - + +
224C LEU* 4.6 8.1 - - + -
274C LEU 4.7 3.6 - - - -
275C PHE* 3.7 28.9 - - - -
279C LEU* 4.0 21.4 - - + +
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Residues in contact with HIS 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B PRO* 4.1 11.0 - - + +
278B VAL* 3.5 30.0 - - + +
279B LEU* 3.8 20.4 - - + -
119C ILE* 2.6 40.0 + - - +
120C GLN* 4.3 6.9 + - - -
121C MET 3.4 20.2 - - - -
122C GLU* 3.8 19.1 + - + +
123C LEU 5.6 0.7 - - - -
217C GLU 2.7 20.6 + - - -
218C MET 3.2 19.2 + - - -
219C VAL 3.6 11.8 + - - -
220C CYS* 1.3 83.4 - - - +
222C LYS* 1.3 63.6 + - - +
279C LEU* 4.9 5.9 + - + -
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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
------------------------------------------------------------
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