Contacts of the helix formed by residues 265 - 279 (chain B) in PDB entry 4HRE
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 ASN 265 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261B GLN* 2.8 17.3 + - - +
264B GLN* 1.3 77.6 - - + +
266B LYS* 1.3 58.0 + - - +
267B PRO* 3.0 15.5 - - - +
268B LEU* 2.6 49.0 + - + +
269B TYR* 3.0 21.8 + - - +
306B GLU* 3.0 30.7 + - - -
309B ARG* 5.3 0.4 - - - +
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Residues in contact with LYS 266 (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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133B CYS 5.6 0.4 - - - -
134B SER* 3.1 32.3 + - - +
135B ARG 5.0 0.4 - - - -
136B THR* 3.9 21.8 - - - +
139B GLU* 5.3 0.4 + - - -
222B VAL* 6.5 0.2 - - - -
262B CYS* 3.6 36.3 + - - +
265B ASN* 1.3 68.1 - - - +
267B PRO* 1.4 77.5 - - + +
269B TYR* 2.9 17.5 + - - +
270B PHE* 3.0 32.4 + - + -
295B ARG* 4.0 21.7 - - - +
299B ASP* 4.5 0.7 - - - +
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Residues in contact with PRO 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ASN* 3.0 14.8 - - - +
266B LYS* 1.4 89.5 - - + +
268B LEU* 1.3 50.7 + - - +
270B PHE* 3.3 2.6 + - + -
271B ALA* 2.7 33.3 + - - +
299B ASP* 4.2 14.3 - - + +
302B LYS* 3.6 46.0 - - + +
303B ILE* 3.8 23.4 - - + +
306B GLU* 3.9 10.5 - - + -
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Residues in contact with LEU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B GLN* 6.1 0.4 - - - +
265B ASN* 2.6 39.5 + - + +
267B PRO* 1.3 70.0 - - - +
269B TYR* 1.3 65.6 + - - +
271B ALA* 3.8 7.6 - - + -
272B ASP* 2.9 46.4 + - - +
306B GLU* 3.8 24.1 - - + +
309B ARG* 4.5 7.0 - - - +
310B LYS* 4.0 30.7 - - + +
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Residues in contact with TYR 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B GLU* 3.4 30.8 - - + +
133B CYS* 5.4 0.6 - - + +
134B SER* 4.6 2.2 - - - -
258B ASN* 2.5 47.1 + - + +
261B GLN* 3.9 40.4 - - + -
262B CYS* 3.5 23.3 - - - -
265B ASN 3.0 13.6 + - - +
266B LYS* 2.9 14.2 + - - +
268B LEU* 1.3 79.1 - - - +
270B PHE* 1.3 94.0 + + - +
272B ASP* 3.2 2.8 + - - +
273B ARG* 2.9 46.2 + - + +
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Residues in contact with PHE 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B GLU* 4.3 18.8 - - + -
134B SER* 3.6 24.2 - - - -
135B ARG* 4.2 2.5 - - - -
266B LYS* 3.0 41.1 + - + -
267B PRO 3.8 1.1 - - - +
269B TYR* 1.3 94.7 - + - +
271B ALA* 1.3 64.1 + - - +
273B ARG* 2.9 5.5 + - - +
274B LEU* 2.7 29.4 + - - +
291B ILE* 3.9 27.4 - - + -
294B SER* 5.2 0.7 - - - -
295B ARG* 3.4 47.8 - - + -
299B ASP* 3.8 10.5 - - - -
303B ILE* 3.7 19.5 - - + -
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Residues in contact with ALA 271 (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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267B PRO 2.7 21.9 + - - +
268B LEU* 3.6 15.0 - - + +
269B TYR 3.3 0.2 - - - -
270B PHE* 1.3 73.1 - - - +
272B ASP* 1.3 57.8 + - - +
274B LEU* 3.2 3.8 + - - +
275B TYR* 2.9 24.8 + - - +
303B ILE* 3.7 28.8 - - - +
306B GLU* 4.1 2.2 - - + -
307B PHE* 3.4 30.6 - - + +
311B TYR* 4.5 3.1 - - + -
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Residues in contact with ASP 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B GLN* 4.1 14.7 - - - +
268B LEU* 2.9 40.3 + - - +
269B TYR* 3.5 4.9 - - - +
271B ALA* 1.3 72.4 - - - +
273B ARG* 1.3 58.4 + - + +
275B TYR* 3.4 1.4 + - - +
276B ASP* 3.0 39.1 + - - +
310B LYS* 2.6 40.3 + - - +
311B TYR* 2.7 21.2 + - - +
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Residues in contact with ARG 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ASP* 3.6 28.9 + - - +
129B ILE* 5.9 0.2 - - - +
130B GLU* 2.6 36.7 + - - +
254B ASN* 5.8 0.8 + - - -
258B ASN* 3.7 16.5 + - - +
269B TYR* 2.9 52.1 + - + +
270B PHE* 2.9 11.7 + - - +
272B ASP* 1.3 71.4 - - + +
274B LEU* 1.3 66.4 + - - +
276B ASP* 3.5 13.1 + - - +
277B SER* 3.3 21.0 + - - -
287B VAL* 4.0 17.6 - - + +
290B ARG* 3.1 15.2 - - - +
291B ILE* 3.6 16.2 - - + -
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Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B PHE 2.7 11.9 + - - +
271B ALA* 3.4 7.2 - - - +
273B ARG* 1.3 74.1 - - - +
275B TYR* 1.3 64.4 + - - +
277B SER* 2.5 20.9 + - - -
278B MET* 3.4 14.6 - - + +
288B LEU* 3.6 32.3 - - + +
291B ILE* 3.5 41.5 - - + -
292B MET* 4.5 4.7 - - - -
300B MET* 5.3 0.4 - - - -
303B ILE* 3.6 31.9 - - + -
307B PHE* 4.2 7.6 - - + -
315B LEU* 3.7 25.8 - - + -
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Residues in contact with TYR 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ALA 2.9 8.9 + - - +
272B ASP 3.8 1.3 - - - +
274B LEU* 1.3 75.1 - - - +
276B ASP* 1.3 71.8 + - - +
277B SER 3.2 0.7 + - - -
278B MET* 3.3 12.6 + - - +
279B LYS* 3.4 45.5 + - + +
307B PHE* 3.6 12.2 - + + -
311B TYR* 3.3 66.4 - + + +
318B TYR* 3.9 34.8 - + - -
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Residues in contact with ASP 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ASP* 3.0 27.9 + - - +
273B ARG* 3.7 14.3 - - - +
274B LEU 3.2 0.2 - - - -
275B TYR* 1.3 83.3 - - - +
277B SER* 1.3 61.9 + - - +
278B MET 3.5 0.2 + - - -
279B LYS* 3.6 35.6 + - - +
284B ARG* 3.2 15.9 + - - -
311B TYR* 4.9 1.6 + - - -
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Residues in contact with SER 277 (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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273B ARG 3.3 11.8 + - - -
274B LEU* 2.5 25.8 + - - +
276B ASP* 1.3 80.3 - - - +
278B MET* 1.3 61.1 + - - +
283B THR* 3.1 6.8 - - - -
284B ARG* 2.6 65.8 + - - +
287B VAL* 4.4 11.1 - - - +
288B LEU* 4.1 11.0 - - - +
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Residues in contact with MET 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 LEU 3.4 21.5 - - - +
275B TYR 3.3 5.3 + - - +
277B SER* 1.3 85.9 - - - +
279B LYS* 1.3 61.3 + - - +
280B GLY 3.5 4.5 + - - +
282B GLY 3.6 9.8 - - - +
283B THR* 4.4 1.8 - - + -
288B LEU* 4.0 32.5 - - + -
307B PHE* 4.9 2.5 - - + -
315B LEU* 3.5 32.5 - - + -
318B TYR* 3.8 33.9 - - + +
319B ILE* 4.2 4.5 - - + +
322B ASP* 2.9 52.2 - - + +
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Residues in contact with LYS 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B TYR* 3.4 49.5 + - + +
276B ASP* 3.6 36.4 + - - +
277B SER 3.7 1.4 - - - -
278B MET* 1.3 74.6 - - - +
280B GLY* 1.3 68.5 + - - +
284B ARG* 3.9 1.3 - - - +
318B TYR* 5.9 2.9 - - - -
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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
------------------------------------------------------------
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