Contacts of the helix formed by residues 254 - 276 (chain C) in PDB entry 6N1G
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 TRP 254 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C ASP* 5.0 0.7 - - - +
231C LEU* 4.9 19.5 - - + +
234C ARG* 3.6 24.1 - - - +
247C PHE* 2.8 51.1 + + + +
248C SER* 5.0 0.7 - - - -
252C ASN* 3.4 9.4 - - - +
253C TRP* 1.3 77.0 - - - +
255C TRP* 1.3 101.7 + + + +
257C PRO* 3.2 11.4 - - - +
258C VAL* 3.9 21.0 + - + +
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Residues in contact with TRP 255 (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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168C LEU* 5.2 12.1 - - + -
172C PHE* 4.5 11.2 - + - -
252C ASN* 4.0 12.1 + - + +
253C TRP 3.3 0.6 - - - -
254C TRP* 1.3 115.0 - + + +
256C VAL* 1.3 59.0 + - - +
258C VAL* 3.0 35.7 + - + +
259C VAL* 3.0 53.0 + - + +
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Residues in contact with VAL 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C LEU* 4.5 10.3 - - + +
171C GLY* 3.8 7.9 - - - +
172C PHE* 3.7 33.4 - - + +
175C GLU* 4.5 6.6 - - + +
252C ASN 5.0 0.4 + - - -
253C TRP* 3.4 47.3 - - + +
255C TRP* 1.3 79.9 - - - +
257C PRO* 1.3 70.4 - - + +
259C VAL* 4.2 6.5 - - - -
260C ALA* 2.9 47.7 + - + +
261C PRO* 3.2 1.4 - - - +
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Residues in contact with PRO 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C THR* 4.3 7.6 - - - +
175C GLU* 5.4 2.2 - - + -
224C ALA* 4.3 9.4 - - + +
226C ASN 4.4 0.5 - - - -
227C PRO* 3.5 14.2 - - - +
230C ASP* 3.2 46.9 - - + +
231C LEU* 5.5 1.3 - - + +
253C TRP* 2.9 27.6 - - + +
254C TRP 3.2 11.2 - - - +
256C VAL* 1.3 95.5 - - + +
258C VAL* 1.3 56.4 + - - +
261C PRO* 3.0 26.2 - - + +
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Residues in contact with VAL 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C PRO* 3.7 29.9 - - + +
231C LEU* 4.1 27.4 - - + -
254C TRP* 4.0 16.6 - - + +
255C TRP* 3.0 47.3 + - + +
257C PRO* 1.3 81.4 - - + +
259C VAL* 1.3 61.7 + - + +
260C ALA 3.7 0.2 - - - -
261C PRO* 4.1 0.2 - - - -
262C LEU* 4.1 11.6 - - - +
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Residues in contact with VAL 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C PHE* 3.3 29.1 - - + -
255C TRP* 3.0 57.1 + - + +
256C VAL* 4.2 0.2 - - - -
258C VAL* 1.3 78.5 - - + +
260C ALA* 1.3 67.5 + - - +
261C PRO 3.5 0.9 - - - -
262C LEU* 3.7 10.3 + - + +
263C LEU* 3.2 25.6 + - + +
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Residues in contact with ALA 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C PHE* 4.1 25.1 - - + -
175C GLU* 3.6 17.0 - - + -
176C ALA* 3.8 8.6 - - - +
256C VAL* 2.9 37.0 + - + +
259C VAL* 1.3 78.7 - - - +
261C PRO* 1.3 62.8 - - + +
263C LEU* 3.4 2.9 + - - +
264C GLY* 2.9 24.6 + - - -
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Residues in contact with PRO 261 (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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96C ALA* 3.8 2.9 - - + -
175C GLU* 4.2 7.2 - - + +
179C THR* 3.3 18.6 - - + +
224C ALA 3.3 22.0 - - - +
225C ILE 3.1 22.4 - - - +
227C PRO* 3.8 12.8 - - + -
256C VAL 3.2 8.5 - - - +
257C PRO* 3.0 28.5 - - + +
258C VAL 4.1 0.2 - - - -
259C VAL 3.7 1.8 - - - +
260C ALA* 1.3 91.5 - - + +
262C LEU* 1.3 56.8 + - - +
264C GLY 3.0 0.3 + - - -
265C ALA* 2.8 29.8 + - - +
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Residues in contact with LEU 262 (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 ALA* 4.8 9.2 - - + +
96C ALA* 3.8 12.9 - - + +
99C PHE* 3.8 48.4 - - + -
112C PHE* 5.2 5.4 - - + -
227C PRO* 4.7 4.7 - - + +
258C VAL 4.1 14.7 + - - +
259C VAL* 3.7 13.2 + - + +
260C ALA 3.3 0.6 - - - -
261C PRO* 1.3 79.9 - - - +
263C LEU* 1.3 62.9 + - + +
264C GLY 3.5 0.3 + - - -
265C ALA* 4.4 1.0 - - - +
266C TYR* 3.5 20.8 + - - +
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Residues in contact with LEU 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C PHE* 4.7 19.5 - - + -
176C ALA* 4.3 16.1 - - + +
259C VAL* 3.2 21.5 + - + +
260C ALA* 4.0 4.7 - - - +
261C PRO 3.3 0.2 - - - -
262C LEU* 1.3 78.1 - - + +
264C GLY* 1.3 57.9 - - - +
266C TYR* 4.3 6.2 - - - +
267C LEU* 3.8 24.6 + - + +
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Residues in contact with GLY 264 (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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176C ALA* 3.4 25.5 - - - +
179C THR* 4.4 1.1 - - - -
180C GLY* 3.0 18.1 - - - -
260C ALA 2.9 14.1 + - - -
261C PRO 3.0 3.5 + - - -
263C LEU* 1.3 76.5 - - - +
265C ALA* 1.3 59.4 + - - +
266C TYR 3.3 1.8 - - - -
267C LEU* 3.4 4.5 + - - +
268C GLY 2.9 22.2 + - - -
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Residues in contact with ALA 265 (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 ASN* 5.7 0.4 - - - +
96C ALA* 3.6 28.5 - - + +
97C VAL 4.5 0.4 - - - +
100C ALA* 3.7 6.7 - - - +
179C THR* 3.7 12.7 - - + +
183C GLN* 3.2 34.4 - - + +
261C PRO 2.8 15.4 + - - +
262C LEU 4.4 1.8 - - - +
264C GLY* 1.3 75.0 - - - +
266C TYR* 1.3 59.0 + - - +
269C GLY 2.9 21.5 + - - -
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Residues in contact with TYR 266 (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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99C PHE* 5.5 13.5 - + + -
100C ALA* 4.5 10.2 - - + +
103C ALA* 4.0 29.2 - - + -
104C LEU* 6.3 1.1 - - + -
262C LEU 3.5 15.5 + - - +
263C LEU* 4.6 5.4 - - - +
264C GLY 3.3 0.6 - - - -
265C ALA* 1.3 75.6 - - - +
267C LEU* 1.3 64.8 + - - +
269C GLY* 3.2 1.3 + - - -
270C ILE* 3.0 59.5 + - + +
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Residues in contact with LEU 267 (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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176C ALA* 5.7 3.1 - - + +
177C TRP* 5.5 14.1 - - + -
180C GLY* 5.9 2.2 - - - -
263C LEU* 3.8 20.3 + - + +
264C GLY* 3.4 9.5 + - - +
266C TYR* 1.3 79.9 - - - +
268C GLY* 1.3 59.3 + - - +
270C ILE* 3.2 17.2 - - + +
271C ILE* 3.1 41.6 + - + +
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Residues in contact with GLY 268 (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 GLY* 3.3 30.7 - - - -
183C GLN* 4.1 6.5 - - - -
184C LEU* 4.0 9.2 - - - +
264C GLY 2.9 11.5 + - - -
265C ALA 3.8 1.6 - - - -
267C LEU* 1.3 79.2 - - - +
269C GLY* 1.3 59.6 + - - +
271C ILE* 3.1 21.8 - - - +
272C TYR* 3.4 9.4 + - - +
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Residues in contact with GLY 269 (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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100C ALA* 5.4 2.0 - - - -
104C LEU* 3.1 25.0 - - - +
183C GLN* 3.7 0.6 - - - +
187C PHE* 3.6 26.9 - - - -
265C ALA 2.9 15.7 + - - -
266C TYR* 3.2 2.2 + - - -
268C GLY* 1.3 75.9 - - - +
270C ILE* 1.3 64.5 + - - +
272C TYR* 3.3 9.5 + - - +
273C LEU 3.5 6.1 + - - -
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Residues in contact with ILE 270 (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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104C LEU* 4.6 15.0 - - + -
266C TYR* 3.0 51.0 + - + +
267C LEU* 3.2 25.6 - - + +
269C GLY* 1.3 73.5 - - - +
271C ILE* 1.3 71.8 + - + +
273C LEU 3.6 0.7 + - - -
274C VAL* 2.9 38.1 + - + +
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Residues in contact with ILE 271 (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 GLY 4.9 0.4 - - - +
184C LEU* 3.2 26.0 - - + +
267C LEU* 3.1 29.3 + - + +
268C GLY* 3.1 26.0 - - - +
270C ILE* 1.3 84.0 - - + +
272C TYR* 1.3 56.0 + - - +
274C VAL* 4.7 2.0 - - + -
275C PHE* 3.1 73.2 + - + +
276C ILE* 4.8 0.5 - - - +
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Residues in contact with TYR 272 (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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104C LEU* 5.6 0.2 - - + -
184C LEU* 3.8 18.2 - - + -
187C PHE* 3.9 25.8 - - + -
188C ALA* 3.5 27.5 - - + +
191C ASP* 2.4 40.3 + - - +
194C ASN* 4.2 7.6 + - - -
268C GLY 3.9 8.1 - - - +
269C GLY 3.3 9.8 + - - +
270C ILE 3.1 0.6 - - - -
271C ILE* 1.3 78.3 - - - +
273C LEU* 1.3 58.3 + - + +
274C VAL 2.9 4.6 + - - -
276C ILE* 2.7 71.0 + - + +
277C GLY* 2.8 17.8 + - - -
280C ILE* 5.0 1.3 - - + -
401C GOL 3.9 16.2 - - - -
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Residues in contact with LEU 273 (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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104C LEU* 3.5 38.8 - - + +
269C GLY 3.5 3.9 + - - +
270C ILE* 3.6 2.2 + - - +
272C TYR* 1.3 81.4 - - + +
274C VAL* 1.3 60.4 + - + +
277C GLY* 3.8 17.0 - - - +
278C SER* 3.0 25.3 + - - -
401C GOL 4.7 22.7 - - - +
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Residues in contact with VAL 274 (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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270C ILE* 2.9 30.3 + - + +
271C ILE* 4.7 0.2 - - - -
272C TYR 3.0 0.8 - - - -
273C LEU* 1.3 85.5 - - + +
275C PHE* 1.3 86.2 + - + +
276C ILE 3.6 0.2 - - - -
278C SER* 3.6 20.2 - - - -
279C THR* 5.0 0.9 + - - -
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Residues in contact with PHE 275 (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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184C LEU* 6.4 0.2 - - + -
271C ILE* 3.1 49.9 + - + +
274C VAL* 1.3 100.9 - - + +
276C ILE* 1.3 65.8 + - + +
279C THR* 3.4 16.9 + - - +
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Residues in contact with ILE 276 (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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184C LEU* 4.7 17.3 - - + -
188C ALA* 5.5 2.0 - - + -
194C ASN* 5.1 10.3 - - - +
271C ILE 4.8 0.2 - - - +
272C TYR* 2.7 54.7 + - + +
274C VAL 3.6 0.2 - - - -
275C PHE* 1.3 83.5 - - + +
277C GLY* 1.3 56.1 + - - +
279C THR* 2.7 35.7 + - + -
280C ILE* 2.9 19.5 + - + +
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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