Contacts of the helix formed by residues 202 - 216 (chain C) in PDB entry 1USK
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 TYR 202 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ILE* 3.8 36.8 - - + -
18C TRP* 4.5 3.1 - - - -
78C CYS* 3.9 10.3 - - - +
79C SER 4.6 0.5 + - - -
80C SER* 5.6 1.7 + - - -
146C ASP* 3.8 14.3 + - - -
148C GLN* 3.7 24.6 - - + +
150C TYR* 3.5 38.9 - + + +
199C TYR* 3.8 7.9 + - - -
201C GLY* 1.3 74.3 - - - -
203C TYR* 1.3 65.8 + - - +
204C PRO* 3.3 13.9 - - + -
205C GLU* 3.5 10.7 + - - +
206C MET* 3.4 14.6 + - - +
227C GLY* 3.7 13.9 - - - +
228C VAL* 3.8 3.8 - - - -
1347C LEU* 2.7 40.4 + - + -
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Residues in contact with TYR 203 (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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14C PRO 3.5 10.1 + - - -
15C ILE* 3.3 26.1 - - + -
16C ALA 3.9 0.2 + - - -
17C GLN* 3.5 19.5 + - + +
18C TRP* 3.4 26.9 - + - -
202C TYR* 1.3 71.2 - - - +
204C PRO* 1.3 86.9 - - + +
206C MET* 3.7 1.3 - - - +
207C GLY* 2.9 30.1 + - - -
227C GLY 3.2 17.3 + - - +
228C VAL* 3.8 28.7 - - - +
230C ASN* 3.7 23.1 - - + -
232C SER* 3.5 28.7 + - - -
233C LEU* 4.0 10.0 - - + +
236C ILE* 4.1 9.8 - - + +
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Residues in contact with PRO 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C PRO* 3.6 31.4 - - + +
15C ILE* 4.0 5.2 - - + -
202C TYR* 3.3 16.4 - - + +
203C TYR* 1.3 109.8 - - + +
205C GLU* 1.3 74.6 + - - +
207C GLY* 3.7 0.5 + - - -
208C GLN* 3.5 26.3 + - - +
236C ILE* 4.1 14.1 - - + +
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Residues in contact with GLU 205 (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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14C PRO* 5.8 2.4 - - - +
146C ASP* 4.6 5.9 - - - +
175C ILE* 4.1 16.2 - - + -
176C THR 4.6 0.7 - - - +
177C ALA* 3.9 10.6 - - - +
178C GLY* 3.0 32.1 + - - +
179C GLU 4.7 3.9 - - - +
182C PHE* 4.0 20.3 - - + -
199C TYR* 3.1 29.4 + - + +
202C TYR* 3.5 13.4 + - - +
203C TYR 3.2 0.4 - - - -
204C PRO* 1.3 91.4 - - - +
206C MET* 1.3 65.2 + - - +
207C GLY 3.2 0.2 - - - -
208C GLN* 3.5 1.0 + - - -
209C MET* 3.1 26.2 + - - +
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Residues in contact with MET 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C TYR* 3.9 31.9 - - + -
202C TYR 3.4 3.9 + - - +
203C TYR 3.3 7.3 + - - +
205C GLU* 1.3 78.9 - - - +
207C GLY* 1.3 56.3 + - - +
209C MET* 3.5 8.2 + - - +
210C LEU* 3.0 69.4 + - + +
222C PHE* 3.6 30.5 - - + -
223C MET 4.5 7.4 - - - +
228C VAL* 3.8 27.8 - - + -
233C LEU* 3.9 7.9 - - + -
244C MET* 3.8 24.5 - - - +
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Residues in contact with GLY 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C TYR 2.9 16.4 + - - -
206C MET* 1.3 75.2 - - - +
208C GLN* 1.3 64.1 + - - +
211C ARG* 3.2 18.4 + - - +
233C LEU* 4.1 8.1 - - - -
236C ILE* 3.6 21.5 - - - +
237C ALA* 3.4 24.8 - - - +
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Residues in contact with GLN 208 (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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179C GLU 4.5 7.4 - - - +
180C LYS* 4.2 26.3 - - + +
182C PHE* 3.5 26.2 - - + -
204C PRO 3.5 16.9 + - - +
205C GLU 4.0 0.4 - - - +
206C MET 3.5 0.2 - - - -
207C GLY* 1.3 72.2 - - - +
209C MET* 1.3 66.6 - - - +
211C ARG* 3.3 11.2 + - - +
212C GLN* 3.1 45.1 + - - +
236C ILE* 3.7 20.8 + - - +
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Residues in contact with MET 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C ILE* 4.5 3.1 - - + -
182C PHE* 4.1 39.9 - - + -
185C LEU* 4.2 19.7 - - + -
186C ILE* 4.2 6.3 - - + +
189C LEU* 5.8 2.5 - - + -
197C VAL* 5.0 4.9 - - - -
199C TYR* 3.5 45.1 - - + -
205C GLU 3.1 19.3 + - - +
206C MET* 3.7 8.3 - - + +
208C GLN* 1.3 79.6 - - - +
210C LEU* 1.3 61.4 + - - +
212C GLN* 3.6 1.6 + - - +
213C ALA* 3.1 25.3 + - - +
222C PHE* 4.0 29.8 - - + -
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Residues in contact with LEU 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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206C MET* 3.0 43.0 + - + +
207C GLY 3.8 4.0 - - - +
209C MET* 1.3 74.9 - - - +
211C ARG* 1.3 64.5 + - - +
213C ALA* 3.3 5.4 + - - +
214C ARG* 3.2 25.3 + - - +
222C PHE* 3.6 34.3 - - + -
233C LEU* 4.3 4.5 - - + -
237C ALA* 3.8 18.8 - - + -
240C ALA* 3.3 31.9 - - - +
241C ALA* 4.3 4.7 - - - -
244C MET* 3.9 26.2 - - + -
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Residues in contact with ARG 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B MET* 3.4 32.0 + - - +
12B SER* 4.6 6.3 - - - +
13B GLY 5.7 0.4 - - - +
16B ALA* 3.6 25.5 + - - +
17B GLN 4.4 0.4 - - - +
20B ASP* 3.0 38.8 + - - -
207C GLY 3.2 11.5 + - - +
208C GLN* 3.3 15.9 + - - +
210C LEU* 1.3 77.9 - - - +
212C GLN* 1.3 68.9 + - + +
214C ARG* 3.2 5.0 + - - +
215C SER* 3.1 22.5 + - - -
235C ASN 4.0 5.3 + - - -
236C ILE 2.9 28.2 + - - +
237C ALA 3.8 11.2 + - - +
238C GLY* 3.5 8.3 - - - +
239C ASP 5.7 0.2 - - - +
240C ALA* 3.8 10.5 - - - +
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Residues in contact with GLN 212 (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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180C LYS 2.6 29.9 + - - +
181C ASP* 4.0 5.4 - - - +
182C PHE* 3.1 34.6 + - - -
183C SER* 3.9 6.9 + - - -
186C ILE* 3.4 16.2 - - + +
208C GLN* 3.1 29.3 + - - +
209C MET* 4.8 0.4 - - - -
211C ARG* 1.3 85.4 - - + +
213C ALA* 1.3 60.8 + - - +
215C SER* 2.8 24.6 + - - +
216C VAL* 3.6 12.3 + - - +
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Residues in contact with ALA 213 (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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186C ILE* 3.6 12.0 - - + +
209C MET 3.1 19.3 + - - +
210C LEU 3.6 5.4 - - - +
211C ARG 3.2 0.2 - - - -
212C GLN* 1.3 77.2 - - - +
214C ARG* 1.3 63.4 + - - +
216C VAL* 3.4 9.2 - - - +
218C LEU* 3.0 52.4 + - + +
222C PHE* 4.1 19.3 - - + -
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Residues in contact with ARG 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 LEU* 3.5 4.6 + - - +
211C ARG 3.2 7.6 + - - +
213C ALA* 1.3 74.9 - - - +
215C SER* 1.3 65.7 + - - +
216C VAL 3.2 0.2 - - - -
217C GLY* 3.3 12.1 + - - +
218C LEU* 3.1 28.5 + - - +
219C LYS* 3.7 4.2 + - - -
220C THR 2.9 36.3 + - - +
221C GLN* 4.9 3.6 - - - +
222C PHE* 4.0 19.9 - - - +
240C ALA* 3.3 45.4 + - + +
242C GLU 4.8 8.9 + - - -
243C GLY 6.2 1.2 - - - -
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Residues in contact with SER 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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11B MET* 5.2 22.5 - - - +
211C ARG* 3.1 15.2 + - - -
212C GLN* 2.8 24.6 + - - +
214C ARG* 1.3 77.3 - - - +
216C VAL* 1.3 65.4 + - - +
217C GLY 3.4 0.9 + - - -
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Residues in contact with VAL 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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186C ILE* 3.4 29.6 - - + -
190C LYS* 2.6 45.4 + - - +
212C GLN 3.7 5.6 - - - +
213C ALA 3.4 13.9 - - - +
215C SER* 1.3 86.4 + - - +
217C GLY* 1.3 56.6 + - - +
218C LEU* 4.2 1.3 - - + +
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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
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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