Contacts of the helix formed by residues 276 - 298 (chain A) in PDB entry 4N7X
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 ALA 276 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A ALA* 3.5 37.4 - - + +
267A GLY 4.5 0.2 - - - -
268A LYS* 3.5 28.9 - - + +
272A SER 4.0 0.4 + - - -
273A PRO 3.2 11.9 + - - +
274A LEU 3.1 0.8 - - - -
275A ALA* 1.3 77.9 - - - +
277A LEU* 1.3 63.0 + - - +
278A PRO 3.6 0.4 - - - -
279A GLY 3.5 3.5 + - - -
280A ALA* 3.1 20.4 + - - +
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 4.4 4.0 - - + -
208A SER* 4.6 3.4 - - - +
211A HIS* 3.5 28.9 - - + +
212A ILE* 3.7 36.6 - - + +
215A VAL* 3.5 38.1 - - + -
219A VAL* 5.1 1.6 - - + -
273A PRO 4.1 1.4 + - - +
274A LEU* 3.0 24.6 + - + +
276A ALA* 1.3 75.2 - - - +
278A PRO* 1.4 69.6 - - + +
280A ALA* 2.9 20.9 + - + +
281A LEU* 2.9 24.6 + - + +
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Residues in contact with PRO 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 3.8 22.7 - - + +
95A GLY* 3.8 28.5 - - - +
96A MET* 3.8 22.7 - - + +
99A VAL* 4.2 4.9 - - + -
219A VAL* 4.3 15.3 - - + -
223A VAL* 4.0 6.3 - - + +
274A LEU 3.4 12.3 - - - +
275A ALA 3.8 9.6 - - - +
277A LEU* 1.4 90.7 - - + +
279A GLY* 1.3 51.7 + - - +
281A LEU* 3.2 2.4 + - + +
282A PHE* 2.8 36.3 + - - +
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Residues in contact with GLY 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLY 4.7 0.8 + - - -
99A VAL* 3.7 20.9 - - - +
260A SER* 3.1 29.7 - - - +
264A ALA* 4.2 7.6 - - - +
275A ALA 5.0 1.0 + - - -
276A ALA 3.5 7.6 + - - -
277A LEU 3.2 0.6 - - - -
278A PRO* 1.3 78.5 - - - +
280A ALA* 1.3 56.7 + - - +
282A PHE* 4.3 0.2 - - - -
283A SER* 2.9 25.6 + - - -
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Residues in contact with ALA 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A VAL* 3.9 18.8 - - + +
208A SER* 3.7 29.2 - - - +
212A ILE* 5.6 1.3 - - + -
264A ALA* 4.5 2.6 - - + +
276A ALA 3.1 14.2 + - - +
277A LEU* 2.9 16.2 + - + +
279A GLY* 1.3 77.6 - - - +
281A LEU* 1.3 65.2 + - + +
283A SER* 3.2 16.3 - - - -
284A VAL* 3.5 11.4 + - - +
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Residues in contact with LEU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ILE* 4.1 38.1 - - + -
215A VAL* 5.0 3.1 - - + -
219A VAL* 3.7 34.3 - - + +
220A ILE* 4.3 26.2 - - + +
223A VAL* 4.3 11.7 - - + -
277A LEU* 2.9 27.5 + - + +
278A PRO 3.7 4.7 - - - +
280A ALA* 1.3 73.5 - - - +
282A PHE* 1.3 62.1 + - - +
284A VAL* 2.9 11.5 + - + +
285A TRP* 2.9 27.4 + - - +
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Residues in contact with PHE 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A MET* 6.4 0.9 - - + -
99A VAL* 3.9 22.7 - - + -
223A VAL* 3.5 42.7 - - + +
226A HIS* 3.6 28.9 - + + -
227A ASN* 3.7 15.0 - - + -
256A GLY 3.4 21.8 - - - -
258A GLN* 4.1 11.2 - - - -
260A SER* 4.0 8.5 - - - -
278A PRO 2.8 21.5 + - - +
279A GLY* 3.8 5.6 - - - +
281A LEU* 1.3 72.7 - - - +
283A SER* 1.3 63.1 + - - +
285A TRP* 4.4 0.4 - - - +
286A HIS* 3.0 70.7 + + + -
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Residues in contact with SER 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ILE* 5.7 1.7 - - - +
201A ILE* 4.2 12.0 - - - +
204A VAL* 3.9 25.0 - - - +
260A SER* 3.3 19.0 + - - -
261A GLY* 5.5 0.7 - - - -
279A GLY 2.9 14.5 + - - -
280A ALA* 3.2 18.1 + - - -
282A PHE* 1.3 77.6 - - - +
284A VAL* 1.3 56.4 + - - +
286A HIS* 3.8 3.8 - - - -
287A ASN* 2.9 28.8 + - - +
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Residues in contact with VAL 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA* 5.2 1.3 - - + +
14A LEU* 5.6 2.0 - - + -
17A SER* 3.6 21.8 - - - +
201A ILE* 4.3 15.9 - - + +
204A VAL* 5.5 0.7 - - + -
205A VAL* 3.6 29.6 - - + -
212A ILE* 6.4 0.2 - - + -
280A ALA 3.7 13.0 - - - +
281A LEU* 2.9 10.6 + - + +
283A SER* 1.3 80.7 - - - +
285A TRP* 1.3 65.8 + - - +
287A ASN* 3.3 7.3 + - - +
288A LEU* 3.2 37.3 + - + +
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Residues in contact with TRP 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ILE* 6.0 2.9 - - + -
223A VAL* 4.0 14.6 - - + -
224A ILE* 3.5 60.0 - - + +
227A ASN* 3.0 39.1 + - + -
281A LEU 2.9 15.2 + - - +
282A PHE* 4.3 0.4 - + - +
284A VAL* 1.3 78.2 - - - +
286A HIS* 1.3 57.3 + - - +
288A LEU* 2.9 32.5 + - + +
289A SER* 2.9 40.1 + - - -
292A LEU* 6.6 0.4 - - + -
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Residues in contact with HIS 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ALA* 4.9 4.8 - - + +
227A ASN* 3.7 21.0 + - - +
257A MET* 3.5 44.4 + - + +
258A GLN 3.6 13.4 + - - -
260A SER* 3.9 9.3 + - - -
282A PHE* 3.0 54.5 + + + +
283A SER* 3.5 8.7 + - - -
285A TRP* 1.3 77.7 - - - +
287A ASN* 1.3 97.3 + - - +
289A SER* 3.8 7.5 + - - -
290A GLY* 2.9 25.3 + - - -
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Residues in contact with ASN 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 3.6 18.6 - - + -
13A ALA* 5.7 0.7 - - + -
107A ALA* 3.5 20.8 - - - +
111A MET* 3.4 20.8 - - - +
197A ILE* 3.6 17.0 - - - +
201A ILE* 4.0 14.1 - - + +
257A MET* 3.7 2.1 - - - +
283A SER 2.9 23.0 + - - -
284A VAL 3.3 7.4 + - - +
285A TRP 3.1 0.6 - - - -
286A HIS* 1.3 99.1 + - - +
288A LEU* 1.3 59.7 + - - +
291A SER* 2.8 32.1 + - - -
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Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PRO* 3.7 22.6 - - + +
13A ALA* 3.7 30.3 - - + -
14A LEU* 4.1 30.7 - - + +
284A VAL* 3.2 29.6 + - + +
285A TRP* 2.9 36.0 + - + +
287A ASN* 1.3 75.9 - - - +
289A SER* 1.3 62.6 + - - +
291A SER* 2.9 19.3 + - - -
292A LEU* 3.2 20.4 + - + +
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Residues in contact with SER 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ASN* 2.7 36.9 + - - -
231A LEU* 4.2 9.7 - - - +
285A TRP* 2.9 33.5 + - - -
286A HIS* 3.8 1.2 - - - -
288A LEU* 1.3 73.5 - - - +
290A GLY* 1.3 60.0 + - - +
292A LEU* 3.8 9.3 - - - +
293A LEU* 3.0 31.2 + - - +
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Residues in contact with GLY 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A MET* 4.2 8.1 - - - +
231A LEU* 5.9 4.0 - - - -
253A ILE* 4.9 4.9 - - - +
257A MET* 4.4 13.0 - - - -
286A HIS 2.9 23.4 + - - -
288A LEU 3.2 0.2 - - - -
289A SER* 1.3 76.5 + - - +
291A SER* 1.3 54.5 + - - +
293A LEU* 3.3 6.7 + - - +
294A ALA* 2.8 36.6 + - - +
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Residues in contact with SER 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ARG* 5.7 1.0 - - - +
9A PHE* 3.4 25.7 - - - -
10A PRO* 3.4 24.6 - - - +
111A MET* 3.8 17.4 - - - -
114A LEU* 5.8 0.2 - - - -
194A MET* 4.5 3.4 - - - -
287A ASN 2.8 22.7 + - - -
288A LEU 2.9 11.3 + - - -
290A GLY* 1.3 74.0 - - - +
292A LEU* 1.3 53.6 + - - +
294A ALA* 3.7 3.0 - - - +
295A GLY* 2.6 32.1 + - - -
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ARG 5.7 0.7 - - - +
10A PRO* 3.7 28.5 - - + -
285A TRP* 6.6 0.4 - - + -
288A LEU* 3.2 22.3 + - + +
289A SER* 3.8 7.9 - - - +
290A GLY 3.2 0.4 - - - -
291A SER* 1.3 78.6 + - - +
293A LEU* 1.3 60.6 + - - +
295A GLY* 3.3 1.1 + - - -
296A TYR* 2.9 29.1 + - - +
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Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A LEU* 4.0 36.8 - - + -
252A ALA* 4.9 1.1 - - + -
253A ILE* 4.2 9.6 - - + -
289A SER 3.0 18.5 + - - +
290A GLY* 3.7 3.6 - - - +
292A LEU* 1.3 76.2 - - - +
294A ALA* 1.3 58.3 + - - +
296A TYR* 3.3 13.6 + - + +
297A TRP* 2.9 75.9 + - + +
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Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A MET* 3.3 32.1 - - + +
114A LEU* 3.9 16.2 - - + +
115A ALA* 3.8 16.8 - - + -
253A ILE* 4.7 1.3 - - + +
290A GLY 2.8 22.1 + - - +
291A SER* 3.7 7.4 - - - +
293A LEU* 1.3 72.0 - - - +
295A GLY* 1.3 59.9 + - - +
297A TRP 3.4 0.9 + - - -
298A SER* 2.9 30.8 + - - -
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Residues in contact with GLY 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ARG* 3.3 32.8 + - - -
114A LEU* 6.0 0.4 - - - -
291A SER 2.6 22.5 + - - -
292A LEU* 3.7 2.0 - - - -
294A ALA* 1.3 71.8 - - - +
296A TYR* 1.3 62.5 + - - +
298A SER* 2.7 22.8 + - - -
299A GLY 4.0 0.9 + - - -
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Residues in contact with TYR 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A LEU 2.9 16.4 + - - +
293A LEU* 3.3 14.6 + - + +
295A GLY* 1.3 77.6 - - - +
297A TRP* 1.3 90.0 + + - +
299A GLY* 3.3 8.7 + - - -
300A LYS* 3.3 50.0 - - + +
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Residues in contact with TRP 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ALA* 3.8 24.2 - - + +
116A LYS* 4.5 1.7 - - - +
235A TYR* 3.7 38.5 + + + -
245A GLU* 4.3 3.0 + - - -
249A ARG* 2.9 88.3 + - + +
252A ALA* 3.9 10.3 - - + -
253A ILE* 4.2 2.9 - - + -
293A LEU* 2.9 51.8 + - + +
294A ALA 3.4 0.2 + - - -
296A TYR* 1.3 96.4 - + - +
298A SER* 1.3 57.2 + - - +
299A GLY 3.0 10.1 + - - -
300A LYS* 3.1 13.7 + - + +
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Residues in contact with SER 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ARG* 3.3 17.5 + - - +
114A LEU* 3.2 28.0 + - - -
116A LYS* 3.7 25.0 + - - +
294A ALA 2.9 11.5 + - - -
295A GLY* 2.7 21.9 + - - -
297A TRP* 1.3 76.1 - - - +
299A GLY* 1.3 54.5 + - - +
300A LYS 3.6 0.2 - - - -
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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