Contacts of the helix formed by residues 254 - 276 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D ASP* 5.1 0.7 - - - +
231D LEU* 4.9 20.9 - - + +
234D ARG* 3.7 22.0 + - - +
247D PHE* 3.1 47.6 + + + +
248D SER* 5.3 0.4 - - - -
252D ASN* 2.9 23.6 + - - -
253D TRP* 1.3 73.8 - - - +
255D TRP* 1.3 100.1 + + + +
257D PRO* 3.2 11.5 - - - +
258D VAL* 4.0 19.8 + - + +
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Residues in contact with TRP 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D LEU* 5.3 6.7 - - + -
172D PHE* 4.6 10.4 - + - -
252D ASN* 3.8 19.0 - - - +
254D TRP* 1.3 116.3 - + + +
256D VAL* 1.3 59.6 + - + +
258D VAL* 3.0 20.3 + - + +
259D VAL* 3.0 65.0 + - + +
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Residues in contact with VAL 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D LEU* 4.6 10.8 - - + +
171D GLY 3.9 4.0 - - - +
172D PHE* 3.5 36.8 - - + +
175D GLU* 4.4 5.4 - - + +
253D TRP* 3.4 46.8 - - + +
255D TRP* 1.3 81.4 - - + +
257D PRO* 1.3 68.8 - - + +
259D VAL* 4.1 7.2 - - - -
260D ALA* 2.8 49.4 + - + +
261D PRO* 3.2 1.2 - - - +
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Residues in contact with PRO 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160D THR* 4.3 6.7 - - - +
175D GLU* 5.3 2.9 - - + -
224D ALA* 4.3 9.8 - - + +
226D ASN 4.4 0.7 - - - +
227D PRO* 3.5 14.2 - - - +
230D ASP* 3.1 44.4 - - + +
231D LEU* 6.4 0.7 - - + -
234D ARG* 4.8 0.7 - - - +
253D TRP* 3.0 29.8 - - + +
254D TRP* 3.2 12.6 - - - +
256D VAL* 1.3 96.5 - - + +
258D VAL* 1.3 55.6 + - + +
261D PRO* 3.1 25.2 - - + +
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Residues in contact with VAL 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D PRO* 3.7 31.9 - - + +
231D LEU* 4.3 25.8 - - + -
254D TRP* 4.2 16.2 - - + +
255D TRP* 3.0 45.3 + - + +
257D PRO* 1.3 79.5 - - + +
259D VAL* 1.3 62.8 + - + +
261D PRO* 4.1 0.9 - - - -
262D LEU* 4.1 11.6 + - - +
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Residues in contact with VAL 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D PHE* 3.4 30.8 - - + -
255D TRP* 3.0 53.5 + - + +
256D VAL* 4.1 0.7 - - - -
258D VAL* 1.3 80.6 - - + +
260D ALA* 1.3 67.5 + - - +
261D PRO 3.4 0.7 - - - -
262D LEU* 3.7 13.0 + - + +
263D LEU* 3.2 25.5 + - + +
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Residues in contact with ALA 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D PHE* 3.9 26.0 - - + +
175D GLU* 3.4 22.7 - - + -
176D ALA* 3.7 8.0 - - - -
256D VAL* 2.8 33.6 + - + +
259D VAL* 1.3 78.3 - - - +
261D PRO* 1.3 63.1 - - + +
263D LEU* 3.5 2.3 + - - +
264D GLY* 3.0 24.6 + - - -
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Residues in contact with PRO 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D ALA* 3.8 3.4 - - + -
175D GLU* 4.1 4.3 - - + +
179D THR* 3.3 20.3 - - + +
224D ALA 3.3 22.4 - - - +
225D ILE 3.2 21.3 - - - +
227D PRO* 3.8 13.5 - - + -
256D VAL 3.2 7.9 - - - +
257D PRO* 3.1 28.0 - - + +
258D VAL 4.1 0.4 - - - -
259D VAL 3.7 1.8 - - - +
260D ALA* 1.3 92.5 - - + +
262D LEU* 1.3 53.3 + - - +
264D GLY 3.0 0.2 + - - -
265D ALA* 2.8 33.4 + - - +
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Residues in contact with LEU 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D ALA* 4.9 8.5 - - + +
96D ALA* 3.9 13.3 - - + +
99D PHE* 3.9 48.3 - - + -
112D PHE* 5.2 4.7 - - + -
227D PRO* 4.8 3.6 - - + +
258D VAL 4.1 13.3 + - - +
259D VAL* 3.7 15.6 + - + +
260D ALA 3.4 0.6 - - - -
261D PRO* 1.3 79.9 - - - +
263D LEU* 1.3 62.4 + - + +
264D GLY 3.5 0.3 + - - -
265D ALA* 3.8 1.0 + - - +
266D TYR* 3.6 21.1 + - - +
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Residues in contact with LEU 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D PHE* 4.3 21.8 - - + -
176D ALA* 4.0 20.2 - - + -
259D VAL* 3.2 21.1 + - + +
260D ALA 3.9 2.9 - - - +
262D LEU* 1.3 79.3 - - + +
264D GLY* 1.3 58.1 + - - +
266D TYR* 4.4 5.7 - - - +
267D LEU* 3.7 18.8 + - + +
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Residues in contact with GLY 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D ALA* 3.4 25.4 - - - -
179D THR* 4.1 1.8 - - - -
180D GLY* 2.9 28.1 - - - -
260D ALA 3.0 13.1 + - - -
261D PRO 3.0 2.7 + - - -
263D LEU* 1.3 78.3 - - - +
265D ALA* 1.3 59.0 + - - +
266D TYR 3.3 1.6 - - - -
267D LEU* 3.5 3.7 + - - +
268D GLY 2.9 13.5 + - - -
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Residues in contact with ALA 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D ALA* 3.6 28.3 - - + +
97D VAL* 5.4 0.7 - - + -
100D ALA* 3.7 6.7 - - + +
179D THR* 3.7 11.6 - - + +
183D GLN* 3.3 35.3 - - + +
261D PRO 2.8 19.8 + - - +
262D LEU 4.4 2.2 - - - +
264D GLY* 1.3 73.0 - - - +
266D TYR* 1.3 59.0 + - - +
269D GLY 2.9 21.7 + - - -
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Residues in contact with TYR 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D PHE* 5.4 13.5 - + + -
100D ALA* 4.5 10.2 - - + +
103D ALA* 4.0 28.7 - - + -
104D LEU* 6.3 2.5 - - + -
262D LEU 3.6 15.6 + - - +
263D LEU* 4.7 4.7 - - - +
264D GLY 3.3 0.6 - - - -
265D ALA* 1.3 75.5 - - - +
267D LEU* 1.3 66.6 + - - +
269D GLY* 3.3 1.0 + - - -
270D ILE* 3.1 57.6 + - + +
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Residues in contact with LEU 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D ALA* 5.5 3.4 - - + +
177D TRP* 5.5 14.1 - - + -
180D GLY* 5.7 2.9 - - - -
263D LEU* 3.7 19.4 + - + +
264D GLY* 3.5 7.1 + - - +
266D TYR* 1.3 80.3 - - - +
268D GLY* 1.3 58.5 + - - +
270D ILE* 3.1 37.4 - - + +
271D ILE* 3.1 39.6 - - + +
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Residues in contact with GLY 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D GLY* 3.3 30.9 - - - -
183D GLN* 4.2 5.6 - - - -
184D LEU* 4.0 7.8 - - - +
264D GLY 2.9 11.5 + - - -
265D ALA 3.8 1.8 - - - -
266D TYR 3.2 0.2 - - - -
267D LEU* 1.3 77.4 - - - +
269D GLY* 1.3 60.2 + - - +
271D ILE* 3.0 24.3 - - - +
272D TYR* 3.5 9.9 + - - +
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Residues in contact with GLY 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ALA* 5.4 1.8 - - - -
104D LEU* 3.1 26.4 - - - +
183D GLN* 3.8 0.4 - - - +
187D PHE* 3.5 28.3 - - - -
265D ALA 2.9 15.6 + - - -
266D TYR* 3.3 1.8 + - - -
268D GLY* 1.3 74.6 - - - +
270D ILE* 1.3 64.5 + - - +
272D TYR* 3.4 8.8 + - - +
273D LEU 3.5 5.2 + - - -
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Residues in contact with ILE 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D LEU* 4.3 15.7 - - + -
266D TYR* 3.1 48.0 + - + +
267D LEU* 3.1 38.8 - - + +
269D GLY* 1.3 74.4 - - - +
271D ILE* 1.3 69.0 + - + +
272D TYR 3.2 0.3 + - - -
273D LEU* 3.4 2.6 + - - +
274D VAL* 3.0 30.4 + - + +
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Residues in contact with ILE 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D GLY 4.3 6.1 - - - +
181D MET* 6.0 0.2 - - - -
184D LEU* 3.3 25.6 - - + +
267D LEU* 3.1 32.3 - - + +
268D GLY* 3.0 31.9 - - - +
270D ILE* 1.3 82.4 - - + +
272D TYR* 1.3 57.5 + - - +
274D VAL* 3.6 8.1 - - + -
275D PHE* 3.0 54.2 + - + +
276D ILE* 3.9 1.2 + - - +
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Residues in contact with TYR 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D LEU* 3.7 23.1 - - + -
187D PHE* 3.9 23.3 - - + -
188D ALA* 3.4 31.6 - - + +
191D ASP* 2.6 41.3 + - - +
194D ASN* 4.0 8.7 + - - -
268D GLY 3.5 7.8 + - - +
269D GLY 3.4 9.8 + - - +
270D ILE 3.1 1.0 - - - -
271D ILE* 1.3 82.0 - - - +
273D LEU* 1.3 59.0 + - + +
274D VAL 2.9 0.8 + - - -
276D ILE* 2.9 48.9 + - + +
277D GLY* 2.6 35.0 + - - -
280D ILE* 5.3 0.9 - - + +
401D GOL 3.9 21.1 - - - -
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Residues in contact with LEU 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D LEU* 3.9 36.3 - - + +
269D GLY 3.5 3.1 + - - +
270D ILE 3.4 3.6 + - - +
272D TYR* 1.3 81.8 - - + +
274D VAL* 1.3 56.0 + - - +
277D GLY* 3.7 14.5 - - - +
278D SER* 2.8 27.0 + - - -
401D GOL 4.6 18.4 - - - +
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Residues in contact with VAL 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D ILE* 3.0 24.6 + - + +
271D ILE* 3.6 7.6 - - + -
272D TYR 3.0 1.0 - - - -
273D LEU* 1.3 79.0 - - - +
275D PHE* 1.3 90.5 + - + +
276D ILE 3.6 0.4 - - - -
278D SER* 3.7 20.2 - - - +
279D THR* 5.0 1.2 - - - +
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Residues in contact with PHE 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D LEU* 6.3 0.4 - - + -
271D ILE* 3.0 35.8 + - + +
274D VAL* 1.3 107.9 - - + +
276D ILE* 1.3 61.1 + - + +
279D THR* 3.2 15.9 - - - +
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Residues in contact with ILE 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D LEU* 5.2 6.5 - - + -
188D ALA* 5.2 2.0 - - + -
194D ASN* 4.2 18.4 - - - +
271D ILE 4.1 2.0 - - - +
272D TYR* 2.9 62.6 - - + +
275D PHE* 1.3 80.2 - - + +
277D GLY* 1.3 59.1 + - - +
278D SER 3.3 1.1 - - - -
279D THR* 2.1 38.1 + - - +
280D ILE* 3.2 12.9 + - + +
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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