Contacts of the helix formed by residues 272 - 286 (chain A) in PDB entry 6M0X
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 SER 272 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268A ALA* 3.6 9.6 - - - +
269A ALA 2.6 28.8 + - - -
270A LYS 3.8 0.3 - - - +
271A ALA* 1.3 79.4 - - - +
273A TYR* 1.3 64.6 + - - +
274A THR* 4.0 0.5 + - - -
275A ALA* 3.3 15.4 + - - +
276A GLN* 3.0 25.7 + - - +
372A LEU 4.6 0.2 - - - -
373A ASP* 3.5 27.6 - - - +
376A ALA* 3.5 14.7 - - - +
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Residues in contact with TYR 273 (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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271A ALA 3.9 0.6 + - - -
272A SER* 1.3 71.9 - - - +
274A THR* 1.3 61.7 + - - +
276A GLN* 3.1 9.6 + - - +
277A GLU* 2.9 37.6 + - + +
305A ILE* 5.1 1.0 - - - +
309A LYS* 2.9 28.5 + - - -
350A PHE* 3.7 22.5 - + - -
353A TYR* 3.8 30.1 - + - -
369A ARG* 3.0 48.5 - - + +
372A LEU* 4.3 23.6 + - + +
373A ASP* 2.8 16.8 + - - +
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Residues in contact with THR 274 (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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272A SER* 3.4 0.6 - - - -
273A TYR* 1.3 77.1 - - - +
275A ALA* 1.3 57.5 + - - +
278A PHE* 3.1 24.3 + - - +
369A ARG* 3.1 20.0 + - - +
373A ASP* 2.3 33.3 + - - -
429A VAL* 3.4 25.6 - - + +
432A MET* 3.6 20.0 - - + -
433A MET* 3.4 28.9 - - - -
436A ILE* 3.5 6.4 - - + +
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Residues in contact with ALA 275 (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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268A ALA* 4.4 2.0 - - + -
269A ALA 3.4 13.7 - - - +
270A LYS 4.0 6.5 - - - +
272A SER* 3.3 19.0 + - - +
273A TYR 3.2 0.8 - - - -
274A THR* 1.3 77.1 - - - +
276A GLN* 1.3 61.6 + - - +
278A PHE* 4.0 0.9 - - - +
279A ASN* 3.0 36.2 + - - -
425A HIS* 3.9 16.9 - - + -
432A MET* 3.6 23.1 - - + -
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Residues in contact with GLN 276 (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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270A LYS 3.7 12.6 - - - +
271A ALA 3.1 15.9 + - - -
272A SER 3.0 22.6 + - - +
273A TYR* 3.1 10.2 + - - +
275A ALA* 1.3 75.2 - - - +
277A GLU* 1.3 63.9 + - - +
279A ASN* 3.7 6.9 - - - +
280A LEU* 3.2 24.4 + - - +
348A HIS* 5.1 2.1 - - - +
350A PHE* 3.3 37.7 + - + -
351A GLU 3.6 0.7 + - - +
352A ALA* 3.0 37.5 + - + +
353A TYR* 3.2 16.5 + - - +
356A MET* 6.0 0.4 - - - -
372A LEU* 6.3 0.8 - - - +
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Residues in contact with GLU 277 (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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273A TYR* 2.9 27.4 + - + +
276A GLN* 1.3 75.9 - - - +
278A PHE* 1.3 65.9 + - - +
280A LEU* 4.1 0.5 - - - +
281A LEU* 3.0 35.3 + - + +
305A ILE* 4.4 5.5 - - + +
350A PHE* 3.8 16.3 - - + -
369A ARG* 2.3 36.7 + - - +
436A ILE* 3.7 28.2 - - + +
440A TYR* 2.9 34.4 + - - +
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Residues in contact with PHE 278 (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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274A THR 3.1 17.9 + - - +
275A ALA 4.0 0.2 - - - +
277A GLU* 1.3 76.4 - - - +
279A ASN* 1.3 66.0 + - - +
281A LEU* 3.8 3.0 - - - +
282A ASN* 3.1 28.2 + - + +
425A HIS* 3.7 17.0 - + - -
427A PHE* 3.6 22.9 - + - -
432A MET* 3.5 35.4 - - + -
435A LEU* 3.9 24.9 - - + -
436A ILE* 3.7 15.6 - - + +
439A LEU* 3.8 21.5 - - + +
446A GLN* 3.9 17.7 - - + -
4B C 3.5 23.8 - - - -
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Residues in contact with ASN 279 (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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270A LYS* 5.0 7.1 + - - +
275A ALA* 3.0 28.1 + - - +
276A GLN* 3.7 7.3 - - - +
277A GLU 3.2 0.2 - - - -
278A PHE* 1.3 81.4 - - - +
280A LEU* 1.3 57.7 + - - +
282A ASN* 4.1 2.8 - - - +
283A ASP* 3.1 21.8 + - - +
348A HIS* 3.3 48.7 + - + +
425A HIS* 2.8 34.8 + - - -
4B C 4.3 1.1 + - - -
5B U 3.3 15.0 + - - +
6B A 4.9 2.6 + - - -
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Residues in contact with LEU 280 (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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276A GLN 3.2 13.2 + - - +
277A GLU 4.3 1.3 - - - +
279A ASN* 1.3 76.7 - - - +
281A LEU* 1.3 63.3 + - + +
283A ASP* 3.1 1.8 + - + +
284A LEU* 2.8 51.4 + - + +
304A ILE* 5.6 2.7 - - + +
305A ILE* 5.0 8.1 - - + -
308A VAL* 4.3 16.6 - - + -
319A LEU* 4.7 8.5 - - + -
347A ILE* 3.5 26.5 - - + -
348A HIS* 3.0 39.2 - - + +
349A THR* 4.6 1.1 - - - -
350A PHE* 4.2 25.1 - - + -
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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
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277A GLU* 3.0 22.8 + - + +
278A PHE* 3.8 4.5 - - - +
280A LEU* 1.3 75.6 - - - +
282A ASN* 1.3 61.8 + - - +
284A LEU* 3.2 10.6 + - + +
285A ASN* 2.9 31.1 + - - +
301A LYS* 5.1 4.7 - - + -
305A ILE* 3.3 35.0 - - + -
436A ILE* 3.4 45.8 - - + +
439A LEU* 3.7 22.2 - - + +
440A TYR* 3.7 24.9 - - + +
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Residues in contact with ASN 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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278A PHE* 3.1 24.7 + - + +
279A ASN* 4.3 2.7 - - - +
281A LEU* 1.3 76.0 - - - +
283A ASP* 1.3 70.2 + - - +
285A ASN* 3.6 2.8 + - - +
286A ASN* 2.8 45.3 + - - +
439A LEU* 4.3 12.2 - - + +
445A GLU* 3.3 13.1 + - - +
446A GLN* 2.9 48.2 - - - +
4B C 4.4 14.5 + - - +
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Residues in contact with ASP 283 (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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279A ASN 3.1 18.8 + - - +
280A LEU* 3.1 12.2 + - + +
282A ASN* 1.3 83.2 - - - +
284A LEU* 1.3 62.9 + - - +
286A ASN* 3.4 13.0 + - - +
287A LEU* 3.5 15.2 + - - +
336A GLY 4.8 1.0 - - - +
337A TYR* 6.0 0.2 - - - -
338A ARG* 3.7 26.4 + - - -
347A ILE* 2.9 24.9 - - + +
348A HIS* 2.9 36.6 + - - -
5B U 5.6 2.1 - - - +
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Residues in contact with LEU 284 (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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280A LEU* 2.8 40.4 + - + +
281A LEU* 3.2 8.0 + - + +
283A ASP* 1.3 73.5 - - - +
285A ASN* 1.3 62.4 + - - +
287A LEU* 2.9 46.7 + - + +
296A LEU* 4.0 16.0 + - + +
301A LYS* 4.2 33.0 - - + +
304A ILE* 4.5 27.6 - - + -
305A ILE* 4.9 5.8 - - + -
319A LEU* 5.3 0.4 - - + -
323A ILE* 4.8 6.7 - - + -
347A ILE* 4.0 19.5 - - + -
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Residues in contact with ASN 285 (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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281A LEU 2.9 18.7 + - - +
282A ASN 4.3 3.1 - - - +
284A LEU* 1.3 77.2 - - - +
286A ASN* 1.3 59.0 + - - +
287A LEU 3.0 13.5 - - - +
295A LYS* 5.4 6.6 - - - +
296A LEU* 5.9 2.5 - - - +
301A LYS* 3.3 24.5 - - - +
439A LEU* 3.2 26.6 + - - +
442A THR 3.3 2.8 + - - -
443A SER* 3.3 42.9 - - - +
444A GLU 3.3 15.7 + - - +
445A GLU* 4.6 3.6 - - - +
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Residues in contact with ASN 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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282A ASN* 2.8 40.3 + - - +
283A ASP* 3.8 7.1 + - - +
284A LEU 3.2 1.0 - - - -
285A ASN* 1.3 72.7 - - - +
287A LEU* 1.3 64.3 + - - +
288A THR* 4.6 3.5 - - - +
336A GLY* 2.9 25.0 - - - +
445A GLU* 3.1 32.1 + - - +
3B G 5.9 1.0 - - - +
4B C 5.4 2.8 + - - -
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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