Contacts of the helix formed by residues 273 - 285 (chain B) in PDB entry 6R7H
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 ARG 273 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262B PHE* 3.7 27.8 - - + -
265B TYR* 3.7 16.6 - - - +
266B ASP* 3.5 32.1 - - - +
269B GLY* 3.0 28.2 + - - +
270B SER* 4.3 2.3 - - - +
271B PRO 3.2 0.4 - - - -
272B ARG* 1.3 77.9 - - - +
274B THR* 1.3 76.1 + - - +
275B THR 3.4 1.3 - - - -
276B CYS* 3.6 2.0 + - - +
277B LEU* 3.5 22.6 + - - +
298B GLU 3.7 18.0 + - - -
299B ALA* 4.9 0.6 - - - +
302B TYR* 4.2 25.7 - - - +
308B ILE* 3.4 30.7 - - - +
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Residues in contact with THR 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B SER* 5.2 9.4 - - - -
271B PRO* 4.0 6.1 + - - +
273B ARG* 1.3 90.6 + - - +
275B THR* 1.3 64.6 + - - +
277B LEU* 3.3 18.2 + - + +
278B LYS* 3.9 20.7 + - - +
307B GLU* 4.2 29.0 + - + +
308B ILE* 4.2 23.5 - - + +
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Residues in contact with THR 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B GLN* 5.9 4.5 - - - +
271B PRO 3.4 20.8 + - - +
272B ARG* 4.1 14.8 - - + +
274B THR* 1.3 78.9 - - - +
276B CYS* 1.3 67.3 + - - +
277B LEU 3.4 0.6 + - - -
278B LYS* 3.9 14.9 + - - +
279B TYR* 3.3 34.5 + - - -
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Residues in contact with CYS 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B GLU* 3.5 31.2 - - - -
258B PHE* 5.5 4.3 - - + +
261B ALA* 6.0 1.8 - - + -
262B PHE* 4.4 17.4 - - + +
265B TYR* 3.6 22.2 - - + -
272B ARG 3.6 22.0 - - - +
273B ARG* 3.6 6.0 + - - +
274B THR 3.2 0.8 - - - -
275B THR* 1.3 82.0 - - - +
277B LEU* 1.3 63.2 + - - +
278B LYS 3.4 0.7 - - - -
279B TYR* 3.6 11.1 + - - +
280B LEU* 3.5 18.9 + - - +
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Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B PHE* 3.7 28.9 - - + -
273B ARG* 3.5 15.4 + - - +
274B THR* 3.3 13.7 + - + +
276B CYS* 1.3 78.1 - - - +
278B LYS* 1.3 64.1 + - + +
280B LEU* 3.3 17.5 + - + -
281B VAL* 3.4 23.4 + - + +
294B PHE* 4.3 16.4 - - + -
299B ALA* 3.8 26.7 - - + -
308B ILE* 3.8 28.5 - - + -
311B MET* 5.2 10.8 - - + -
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Residues in contact with LYS 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B THR* 3.9 22.5 + - - +
275B THR* 3.9 10.5 + - - +
276B CYS 3.4 0.6 - - - -
277B LEU* 1.3 77.4 - - + +
279B TYR* 1.3 69.2 + - + +
281B VAL* 3.5 10.8 - - - +
282B LEU* 3.3 23.7 + - - +
307B GLU* 3.6 25.5 + - - +
308B ILE* 5.4 0.4 - - - +
311B MET* 3.6 44.8 - - + +
336B ASN* 3.5 32.1 + - - +
337B ILE* 5.4 1.1 - - - -
340B ASP* 5.9 7.6 - - + +
343B ILE* 4.5 14.7 - - + +
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Residues in contact with TYR 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B GLU* 4.7 7.2 - - + -
243B LYS* 3.7 34.8 + - + -
246B LEU* 6.0 0.9 - - + +
258B PHE* 3.3 46.5 - + + -
275B THR* 3.3 33.7 + - - -
276B CYS* 3.6 12.2 + - - +
277B LEU 3.3 0.8 - - - -
278B LYS* 1.3 83.2 - - + +
280B LEU* 1.3 62.5 + - - +
282B LEU* 4.0 7.5 - - + +
283B ALA 3.7 12.0 + - - -
340B ASP* 3.2 38.0 + - - -
342B PHE* 3.9 20.4 - + + +
343B ILE* 4.9 7.6 - - + -
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Residues in contact with LEU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B HIS* 4.2 14.4 - - + +
258B PHE* 3.7 14.1 - - + +
259B PHE* 3.6 59.0 - - + +
262B PHE* 4.0 35.2 - - + -
276B CYS 3.5 10.7 + - - +
277B LEU* 3.3 15.0 + - + +
278B LYS 3.3 0.8 - - - -
279B TYR* 1.3 79.2 - - - +
281B VAL* 1.3 66.0 + - + +
282B LEU 3.5 0.3 + - - -
283B ALA* 3.7 2.3 + - - +
284B ASN* 3.6 17.5 + - - +
296B SER* 5.7 1.3 - - - +
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Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LEU* 3.4 29.8 - - + +
278B LYS* 3.5 13.5 - - - +
280B LEU* 1.3 78.7 - - + +
282B LEU* 1.3 65.3 + - + +
284B ASN* 3.6 7.8 + - - +
285B MET* 3.3 32.6 + - + +
293B PRO 3.8 22.4 - - - +
294B PHE* 4.8 6.3 - - + -
311B MET* 4.3 25.8 - - + +
314B LEU* 5.8 1.6 - - + -
315B VAL* 4.2 18.7 - - + +
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Residues in contact with LEU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B LEU* 3.9 21.1 - - + -
278B LYS 3.3 17.7 + - - +
279B TYR* 4.1 9.2 - - + +
280B LEU 3.2 1.0 - - - -
281B VAL* 1.3 82.2 - - + +
283B ALA* 1.3 60.5 + - - +
284B ASN 3.5 0.3 + - - -
285B MET* 3.7 13.8 + - + +
286B LEU* 3.6 29.7 + - + +
314B LEU* 5.4 2.0 - - + -
343B ILE* 3.8 32.5 - - + -
346B HIS* 4.2 19.3 - - + +
347B ILE* 6.2 2.2 - - + -
350B LEU* 4.0 28.5 - - + -
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Residues in contact with ALA 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B LEU* 4.0 25.1 - - + -
251B PHE 4.2 6.6 - - - +
255B HIS* 4.3 29.1 - - + +
258B PHE* 4.4 6.1 - - + -
279B TYR 3.7 12.6 + - - +
280B LEU 3.7 5.3 + - - +
281B VAL 3.4 0.2 - - - -
282B LEU* 1.3 78.3 - - - +
284B ASN* 1.3 62.7 + - - +
286B LEU* 3.6 8.9 + - - +
287B MET* 3.4 20.3 - - - +
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Residues in contact with ASN 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B HIS* 3.1 29.8 + - + +
280B LEU 3.6 10.5 + - - +
281B VAL* 3.6 11.8 + - - +
282B LEU 3.3 0.8 - - - -
283B ALA* 1.3 79.6 - - - +
285B MET* 1.3 60.2 + - + +
286B LEU 3.5 0.7 + - - -
287B MET* 3.6 25.0 + - - +
289B SER 3.1 22.6 + - - +
290B GLY* 4.2 7.5 - - - -
292B ASN* 3.2 37.4 + - - +
295B ASP* 5.0 4.9 + - - -
315B VAL* 6.0 0.8 - - + +
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Residues in contact with MET 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B VAL* 3.3 26.5 + - + +
282B LEU* 3.7 7.6 + - + +
283B ALA 3.4 0.4 - - - -
284B ASN* 1.3 77.7 - - + +
286B LEU* 1.3 60.6 + - - +
287B MET 3.4 0.8 + - - -
288B LYS 4.0 3.4 + - - -
289B SER 4.8 0.2 - - - -
290B GLY* 4.1 15.9 - - - +
314B LEU* 3.9 37.7 - - + +
315B VAL* 4.0 19.7 - - + -
318B TYR* 3.1 64.2 + - + -
326B PHE* 4.9 0.7 - - - -
350B LEU* 3.8 30.5 - - + +
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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