Contacts of the helix formed by residues 281 - 302 (chain A) in PDB entry 3RT0
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 GLY 281 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A GLY 3.1 6.5 + - - -
280A GLU* 1.3 77.3 - - - +
282A ARG* 1.3 71.5 + - - -
283A GLN 3.4 2.9 - - - -
284A VAL* 3.3 14.4 + - - +
285A GLN* 3.1 19.5 + - - +
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Residues in contact with ARG 282 (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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218A LYS 3.6 9.6 + - - -
219A MET 2.8 38.1 - - - +
220A LEU 3.9 3.4 - - - +
221A MET 2.8 31.2 + - - -
222A GLY* 4.0 4.3 - - - -
223A ASP* 2.9 27.8 + - - +
279A GLY 5.3 1.2 + - - -
280A GLU 3.1 23.2 + - - -
281A GLY* 1.3 71.3 - - - -
283A GLN* 1.3 67.9 + - - +
285A GLN* 3.0 27.5 + - - +
286A TRP* 3.1 18.5 + - - -
417A PHE* 3.6 27.1 - - + -
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Residues in contact with GLN 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A GLY 3.4 0.4 - - - -
282A ARG* 1.3 79.3 - - - +
284A VAL* 1.3 65.3 + - + +
286A TRP* 3.4 2.9 + - - +
287A ASP* 2.8 49.0 + - - +
415A VAL* 2.8 32.6 + - + +
417A PHE* 4.2 29.9 - - + +
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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
----------------------------------------------------------
280A GLU* 4.0 23.1 - - + -
281A GLY* 3.3 19.6 + - - +
282A ARG 3.1 0.4 - - - -
283A GLN* 1.3 83.1 - - + +
285A GLN* 1.3 64.9 + - - +
287A ASP* 3.2 19.4 - - + +
288A LYS* 3.2 17.6 + - - +
284B VAL* 6.1 4.9 - - + -
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Residues in contact with GLN 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LYS* 3.9 5.9 + - - +
219A MET* 3.4 31.2 - - + +
269A ILE* 3.9 12.0 - - + +
273A LEU* 3.7 24.2 - - + +
277A ASN* 5.2 6.3 - - - +
280A GLU* 3.5 42.5 + - + +
281A GLY 3.1 8.3 + - - +
282A ARG* 3.0 34.1 + - - +
284A VAL* 1.3 77.2 - - - +
286A TRP* 1.3 62.5 + - + +
288A LYS* 3.3 7.0 + - - +
289A VAL* 3.2 25.3 + - - +
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Residues in contact with TRP 286 (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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215A LEU* 3.6 30.5 - - + -
219A MET* 2.9 52.9 + - + +
220A LEU* 4.3 14.4 - - + -
266A ILE* 4.2 19.1 - - + -
282A ARG* 3.1 25.3 + - - +
283A GLN* 4.0 3.1 - - - +
285A GLN* 1.3 73.0 - - - +
287A ASP* 1.3 64.8 - - - +
289A VAL* 3.4 10.6 + - + +
290A PHE* 2.9 48.8 + + - +
333A LEU* 3.5 22.4 - - + -
340A VAL* 4.2 12.6 - - + -
415A VAL* 4.0 20.6 - - + -
417A PHE* 3.6 26.0 - + + -
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Residues in contact with ASP 287 (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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283A GLN* 2.8 42.0 + - - +
284A VAL* 3.2 16.2 - - + +
286A TRP* 1.3 76.4 - - - +
288A LYS* 1.3 57.3 + - - +
290A PHE* 4.0 1.0 - - - +
291A THR* 2.8 41.6 + - - -
412A GLU* 5.6 1.9 - - - +
413A PRO 5.3 3.7 - - - +
414A GLU* 5.8 0.4 - - - -
415A VAL* 3.9 18.4 + - - +
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Residues in contact with LYS 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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269A ILE* 4.2 19.1 - - + -
272A GLU* 5.7 5.8 - - - +
280A GLU* 3.5 35.2 + - - -
284A VAL* 3.2 16.4 + - - +
285A GLN 3.3 7.6 + - - +
287A ASP* 1.3 76.2 - - - +
289A VAL* 1.3 70.6 + - + +
291A THR* 4.0 4.9 - - - -
292A SER* 2.9 33.9 + - - +
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Residues in contact with VAL 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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219A MET* 4.8 5.4 - - - -
262A LEU* 3.6 27.8 - - + -
265A GLU* 3.5 21.7 - - + +
266A ILE* 4.0 13.0 - - + -
269A ILE* 3.6 45.5 - - + -
285A GLN 3.2 6.8 + - - +
286A TRP* 3.7 18.2 - - + +
287A ASP 3.3 0.2 - - - -
288A LYS* 1.3 83.4 - - + +
290A PHE* 1.3 62.4 + - + +
293A CYS* 3.1 22.3 + - - +
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Residues in contact with PHE 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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258A LEU* 5.6 0.4 - - + -
262A LEU* 3.7 26.2 - - + -
286A TRP* 2.9 41.8 + + - +
289A VAL* 1.3 75.8 - - + +
291A THR* 1.3 62.0 + - - +
293A CYS* 4.2 3.1 - - - -
294A PHE* 2.9 47.1 + + - +
331A VAL* 3.5 25.6 - - + -
333A LEU* 3.7 23.3 - - + -
340A VAL* 3.8 25.8 - - + -
342A SER* 3.2 33.9 - - - +
413A PRO* 3.9 2.2 - - + -
415A VAL* 3.8 15.5 - - + -
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Residues in contact with THR 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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287A ASP* 2.8 32.0 + - - -
288A LYS* 4.0 5.4 - - - -
290A PHE* 1.3 77.9 - - - +
292A SER* 1.3 63.1 + - - +
295A LEU* 2.8 45.5 + - + +
412A GLU* 4.5 20.3 + - + +
413A PRO* 3.9 19.2 + - - +
415A VAL* 5.8 0.3 - - - +
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Residues in contact with SER 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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265A GLU* 3.5 29.4 + - - -
288A LYS* 2.9 22.8 + - - +
291A THR* 1.3 78.2 - - - +
293A CYS* 1.3 56.0 + - - +
295A LEU* 3.8 4.3 - - - +
296A THR* 2.7 39.3 + - - -
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Residues in contact with CYS 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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258A LEU* 3.8 32.5 - - - -
261A ALA* 4.3 5.0 - - - +
262A LEU* 3.8 38.8 - - + +
265A GLU* 4.1 8.2 - - + +
289A VAL 3.1 16.3 + - - +
290A PHE* 3.7 6.3 - - - +
291A THR 3.3 0.2 - - - -
292A SER* 1.3 81.4 - - - +
294A PHE* 1.3 69.7 + - - +
296A THR* 3.4 6.5 + - - -
297A VAL* 3.1 24.1 + - - +
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Residues in contact with PHE 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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258A LEU* 4.0 21.8 - - + -
290A PHE* 2.9 32.9 + + - +
291A THR 4.1 0.2 - - - +
293A CYS* 1.3 84.5 - - - +
295A LEU* 1.3 59.0 + - - +
297A VAL* 3.4 5.7 + - - +
298A ASP* 3.0 27.9 + - - +
329A ALA* 3.9 21.8 - - + -
331A VAL* 4.2 8.1 - - + -
342A SER* 3.4 28.7 - - - -
344A CYS* 3.5 30.1 - - + -
400A ILE* 3.8 16.3 - - + +
411A PRO 3.5 16.6 - - - +
413A PRO* 3.6 25.4 - - + -
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Residues in contact with LEU 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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291A THR* 2.8 41.5 + - + +
292A SER* 3.8 4.9 - - - +
294A PHE* 1.3 75.9 - - + +
296A THR* 1.3 61.5 + - - +
298A ASP* 3.2 5.5 + - - +
299A GLY* 2.8 28.1 + - - -
305A ILE* 4.1 3.4 - - - +
411A PRO* 3.4 37.5 - - + +
412A GLU* 4.3 11.4 - - + -
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Residues in contact with THR 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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257A ARG* 4.3 9.4 - - - +
261A ALA* 4.9 5.8 - - + -
264A GLU* 5.6 0.7 - - - +
265A GLU* 4.2 10.7 + - - +
292A SER* 2.7 26.1 + - - -
293A CYS* 3.7 7.4 - - - -
294A PHE 3.3 0.2 - - - -
295A LEU* 1.3 76.4 - - - +
297A VAL* 1.3 62.8 + - - +
299A GLY 3.3 0.2 + - - -
300A GLU* 3.0 44.7 + - + +
305A ILE* 3.8 20.3 - - + +
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Residues in contact with VAL 297 (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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253A TYR* 4.0 13.9 - - + -
254A CYS* 4.3 13.7 - - - -
257A ARG* 4.4 7.0 - - + -
258A LEU* 4.0 26.9 - - + -
261A ALA* 3.8 21.8 - - + -
293A CYS 3.1 13.9 + - - +
294A PHE* 3.7 8.3 - - - +
295A LEU 3.3 0.2 - - - -
296A THR* 1.3 77.7 - - - +
298A ASP* 1.3 58.7 + - - +
300A GLU* 3.4 9.9 + - - +
301A ILE* 3.0 45.5 + - + +
400A ILE* 4.2 8.7 - - + -
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Residues in contact with ASP 298 (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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294A PHE 3.0 17.3 + - - +
295A LEU* 3.6 6.7 - - - +
296A THR 3.2 0.4 - - - -
297A VAL* 1.3 75.7 - - - +
299A GLY* 1.3 64.7 + - - +
301A ILE* 3.4 5.2 + - - +
302A GLU* 3.1 25.1 + - - +
400A ILE* 3.8 10.3 - - + -
401A GLY* 2.8 31.9 + - - -
406A LYS* 3.0 36.0 + - - -
411A PRO* 3.7 23.7 - - + +
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Residues in contact with GLY 299 (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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295A LEU 2.8 14.7 + - - -
298A ASP* 1.3 73.1 + - - +
300A GLU* 1.3 62.8 + - - +
302A GLU* 3.3 7.8 + - - -
303A GLY 3.1 4.2 + - - -
304A LYS* 2.9 33.5 + - - -
305A ILE* 3.6 26.2 - - - -
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Residues in contact with GLU 300 (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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253A TYR* 2.6 36.6 + - - +
257A ARG* 2.9 41.5 + - - +
296A THR* 3.0 28.7 + - - +
297A VAL* 3.5 8.1 - - - +
299A GLY* 1.3 77.8 - - - +
301A ILE* 1.3 61.9 + - - +
303A GLY* 3.1 13.5 + - - -
305A ILE* 3.8 24.7 - - + +
306A GLY 4.4 5.4 - - - +
307A ARG* 3.7 35.4 + - + +
318A GLU 3.7 1.2 - - - +
320A VAL* 4.2 2.0 - - - -
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Residues in contact with ILE 301 (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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250A VAL* 3.7 36.1 - - + +
253A TYR* 3.5 23.8 - - + -
254A CYS* 4.8 0.2 - - - -
297A VAL* 3.0 27.6 + - + +
298A ASP* 3.5 9.0 - - - +
300A GLU* 1.3 76.0 - - - +
302A GLU* 1.3 58.9 + - + +
303A GLY 3.2 0.2 - - - -
319A ALA* 3.2 6.9 - - - +
320A VAL* 2.9 40.2 + - + -
321A ALA* 4.0 4.9 + - + +
325A VAL 5.7 0.2 - - - +
400A ILE* 3.5 29.2 - - + -
401A GLY* 4.5 12.3 - - - -
403A ARG* 4.2 8.3 + - - +
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Residues in contact with GLU 302 (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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298A ASP* 3.1 19.6 + - - +
299A GLY* 3.8 7.4 - - - +
300A GLU 3.2 0.2 - - - -
301A ILE* 1.3 77.6 - - + +
303A GLY* 1.3 59.0 + - - +
304A LYS* 3.4 38.5 + - + +
319A ALA* 4.0 10.5 - - - +
403A ARG* 3.6 49.1 + - + +
406A LYS* 3.7 22.4 - - - +
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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