Contacts of the helix formed by residues 264 - 279 (chain D) in PDB entry 1M7X
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 264 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262D TRP 3.9 0.2 + - - -
263D LEU* 1.3 74.2 - - - +
265D TYR* 1.3 55.2 + - - +
266D ARG* 3.5 9.4 + - - +
267D GLU* 2.8 35.7 + - - +
268D LEU* 2.7 37.0 + - - +
312D PHE* 3.2 16.6 - - - +
317D ASP* 6.0 1.3 - - - -
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Residues in contact with TYR 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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250D LEU* 4.0 17.9 - - + -
264D SER* 1.3 71.6 - - - +
266D ARG* 1.3 58.5 + - - +
268D LEU* 3.3 7.7 + - + +
269D ALA* 2.9 28.6 + - - +
289D ILE* 4.6 3.7 + - + +
308D PRO* 4.0 4.1 - - + +
309D THR* 2.7 49.7 + - - +
312D PHE* 2.8 42.9 + + + +
313D GLY 3.5 10.8 - - - -
314D THR 3.6 13.2 - - - -
317D ASP* 3.5 27.6 - - + +
318D PHE* 3.4 46.2 - + + -
321D PHE* 3.6 11.6 - + + -
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Residues in contact with ARG 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D SER* 3.1 7.7 + - - +
265D TYR* 1.3 80.0 - - - +
267D GLU* 1.3 60.7 + - - +
269D ALA* 3.5 12.4 + - - +
270D ASP* 3.0 18.9 + - - +
316D ASP 5.0 2.6 + - - -
317D ASP* 3.0 35.0 + - + +
320D TYR* 3.7 55.6 - - + +
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Residues in contact with GLU 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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256D HIS* 2.8 41.8 + - - -
262D TRP 4.1 0.7 - - - +
263D LEU* 3.3 8.0 - - + -
264D SER* 2.8 39.4 + - - +
266D ARG* 1.3 73.6 - - - +
268D LEU* 1.3 63.1 - - - +
270D ASP* 2.4 25.6 - - - +
271D GLN* 3.2 30.1 + - - +
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Residues in contact with LEU 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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250D LEU* 3.7 52.9 - - + +
253D TRP* 4.0 20.6 - - + -
254D ARG 5.5 0.7 - - - +
263D LEU* 3.7 37.2 - - + +
264D SER 2.7 24.9 + - - +
265D TYR* 3.6 10.3 - - + +
267D GLU* 1.3 72.3 - - - +
269D ALA* 1.3 57.7 + - - +
272D LEU* 2.9 37.8 + - + +
273D VAL 3.3 2.6 + - - -
312D PHE* 4.6 4.9 - - + -
321D PHE* 3.7 15.1 - - + -
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Residues in contact with ALA 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D TYR 2.9 16.9 + - - +
266D ARG 3.7 7.6 - - - +
267D GLU 3.1 0.6 - - - -
268D LEU* 1.3 78.9 - - - +
270D ASP* 1.3 58.0 + - - +
271D GLN 3.5 0.2 - - - -
273D VAL* 3.4 23.0 - - - +
274D PRO* 3.7 2.8 - - - +
320D TYR* 4.1 13.5 - - + -
321D PHE* 3.6 21.7 - - + -
324D ALA* 3.9 23.6 - - + +
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Residues in contact with ASP 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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266D ARG 3.0 12.6 - - - +
267D GLU* 2.4 35.2 - - - +
269D ALA* 1.3 74.9 - - + +
271D GLN* 1.3 69.5 + - - +
274D PRO* 3.4 20.1 - - - +
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Residues in contact with GLN 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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727C ALA* 3.8 31.1 - - + +
728C GLU* 5.3 3.1 + - - +
253D TRP* 3.7 10.2 - - + -
254D ARG* 3.4 30.4 + - - +
256D HIS* 5.2 2.6 + - - -
263D LEU* 3.4 28.9 - - + +
267D GLU* 3.2 30.7 + - - +
269D ALA 3.5 0.4 - - - -
270D ASP* 1.3 92.2 + - - +
272D LEU* 1.3 65.0 + - - +
273D VAL 3.5 0.7 - - - -
274D PRO* 3.6 2.3 - - - +
275D TYR* 3.2 24.6 + - - +
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Residues in contact with LEU 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D TYR* 3.9 20.2 - - + -
248D VAL* 4.0 15.3 - - + -
250D LEU* 3.6 31.2 - - + -
253D TRP* 3.5 44.8 - - + +
268D LEU* 2.9 27.0 + - + +
271D GLN* 1.3 73.0 - - - +
273D VAL* 1.3 57.9 + - - +
275D TYR* 3.2 2.6 + - + +
276D ALA* 2.9 27.4 + - - +
284D LEU* 4.3 15.3 - - + -
286D LEU* 5.0 0.2 - - + -
321D PHE* 4.0 14.8 - - + -
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Residues in contact with VAL 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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268D LEU 3.3 1.0 + - - -
269D ALA* 3.4 17.3 - - - +
272D LEU* 1.3 79.7 - - - +
274D PRO* 1.3 72.9 - - + +
275D TYR 3.2 0.2 + - - -
276D ALA* 3.3 1.5 + - - -
277D LYS* 3.0 22.0 + - - +
284D LEU* 4.6 5.6 - - + -
321D PHE* 3.8 28.0 - - + -
324D ALA* 3.8 10.5 - - + +
325D ALA* 3.9 26.5 - - + +
328D ALA* 3.5 29.2 - - + -
330D LEU* 3.8 9.4 - - + +
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Residues in contact with PRO 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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612C HIS* 3.3 28.9 - - + +
269D ALA 3.7 2.7 - - - +
270D ASP* 3.4 38.4 - - - +
271D GLN 3.6 5.4 - - - +
273D VAL* 1.3 99.3 - - + +
275D TYR* 1.3 54.9 + - - +
277D LYS* 3.5 7.9 + - + +
278D TRP* 2.9 22.7 + - - +
328D ALA* 5.7 0.2 - - + -
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Residues in contact with TYR 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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246D TYR* 3.4 31.0 - + - -
253D TRP* 3.8 17.5 - + + -
254D ARG* 4.8 7.9 - - - +
271D GLN 3.2 19.9 + - - +
272D LEU 3.2 3.8 + - - +
273D VAL 3.1 0.2 - - - -
274D PRO* 1.3 77.1 - - - +
276D ALA* 1.3 69.6 + - - +
278D TRP* 3.2 9.3 + + - +
279D MET* 3.0 43.6 + - + +
571D GLU* 2.7 26.7 + - - +
586D TRP* 3.6 17.7 - + - -
600D GLN* 3.0 31.8 + - - -
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Residues in contact with ALA 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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246D TYR* 4.1 21.5 - - + -
272D LEU 2.9 16.1 + - - +
273D VAL* 3.9 4.0 - - - +
275D TYR* 1.3 81.7 - - - +
277D LYS* 1.3 60.7 + - - +
279D MET 3.4 4.0 + - - -
281D PHE* 3.3 43.3 + - + +
284D LEU* 4.4 11.9 - - + -
330D LEU* 4.3 14.1 - - + -
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Residues in contact with LYS 277 (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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612C HIS* 4.6 28.8 + - + +
273D VAL 3.0 16.5 + - - +
274D PRO* 3.7 6.7 - - + +
276D ALA* 1.3 79.3 - - - +
278D TRP* 1.3 60.0 + - - +
280D GLY* 3.4 12.0 + - - -
281D PHE 4.6 2.5 - - - +
328D ALA* 3.4 37.7 + - + +
330D LEU* 4.2 17.4 - - + +
611D ARG* 5.3 1.7 + - - -
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Residues in contact with TRP 278 (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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605C ASP* 6.3 0.4 - - - -
608C LEU* 3.4 29.8 - - + -
609C THR* 3.8 30.1 - - + -
612C HIS* 3.7 35.9 - + + +
613C HIS* 5.7 0.7 - + - -
678C ILE 6.0 1.6 - - - -
274D PRO 2.9 17.9 + - - +
275D TYR* 3.2 9.8 + + - +
277D LYS* 1.3 76.3 - - - +
279D MET* 1.3 70.8 + - + +
280D GLY* 3.2 2.3 + - - -
604D ARG* 3.0 68.6 + - - +
608D LEU* 5.6 0.3 - - - +
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Residues in contact with MET 279 (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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275D TYR* 3.0 38.5 + - + +
277D LYS 3.2 0.4 - - - -
278D TRP* 1.3 85.2 - - + +
280D GLY* 1.3 56.9 + - - +
281D PHE* 3.4 25.4 - - + -
571D GLU* 4.5 7.9 - - + -
600D GLN* 3.0 51.6 - - + +
603D VAL* 3.8 16.6 - - + -
604D ARG* 3.2 47.0 - - - +
607D ASN* 3.0 19.4 + - - +
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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