Contacts of the helix formed by residues 258 - 276 (chain F) in PDB entry 5YWB
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 258 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252F LYS* 4.5 22.0 - - - +
253F LEU* 3.4 32.0 + - + +
254F PRO 3.2 15.6 + - - +
255F ILE* 4.1 12.2 + - - +
256F ALA 3.8 0.8 - - - -
257F MET* 1.3 79.4 - - - +
259F ALA* 1.3 66.6 + - - +
260F LEU* 3.1 12.3 + - + +
261F THR* 3.2 22.1 + - - +
262F ASN* 3.4 11.8 + - - -
1232F ASP* 4.3 18.8 + - - +
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Residues in contact with ALA 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257F MET 3.6 2.8 + - - -
258F ARG* 1.3 72.0 - - - +
260F LEU* 1.3 58.0 + - - +
262F ASN* 3.8 10.8 - - - +
263F TYR* 2.9 32.3 + - - +
389F GLY* 4.6 14.8 - - - +
390F ALA* 5.0 0.2 - - - -
393F THR* 4.2 4.1 - - + +
1228F LEU* 4.7 7.4 - - + -
1231F THR* 4.1 20.4 - - + +
1232F ASP* 3.2 22.9 + - - +
1235F ASN* 4.5 12.5 - - - +
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Residues in contact with LEU 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258F ARG* 3.1 9.1 - - + +
259F ALA* 1.3 78.8 - - - +
261F THR* 1.3 59.9 + - - +
263F TYR* 3.4 19.1 + - + +
264F GLN* 2.9 33.8 + - - +
1225F GLN* 5.5 5.4 - - - +
1228F LEU* 3.8 34.6 - - + +
1232F ASP* 4.9 1.6 + - - -
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Residues in contact with THR 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255F ILE 4.0 17.3 + - - +
256F ALA* 5.7 5.8 - - - -
258F ARG* 3.2 15.2 + - - +
260F LEU* 1.3 79.6 - - - +
262F ASN* 1.3 59.6 + - - +
264F GLN* 3.3 9.1 + - + +
265F ARG* 2.9 42.4 + - + +
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Residues in contact with ASN 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256F ALA 5.2 3.9 + - - +
257F MET* 4.2 5.9 + - - +
258F ARG 3.4 14.8 + - - -
259F ALA* 3.8 9.4 - - - +
260F LEU 3.3 0.6 - - - -
261F THR* 1.3 76.0 - - - +
263F TYR* 1.3 59.9 + - - +
265F ARG* 3.4 14.3 + - - +
266F LEU* 2.9 30.7 + - - +
386F ASN* 2.6 51.6 + - - +
389F GLY* 5.9 0.8 - - - -
390F ALA* 3.9 19.5 - - + +
1235F ASN* 5.9 1.8 - - - +
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Residues in contact with TYR 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259F ALA 2.9 18.7 + - - +
260F LEU* 3.7 19.7 - - + +
262F ASN* 1.3 76.0 - - - +
264F GLN* 1.3 64.2 + - - +
266F LEU* 3.7 4.6 - - + +
267F CYS* 2.9 57.8 + - + +
390F ALA* 4.1 3.9 - - - +
393F THR* 3.4 37.7 - - + +
394F LYS* 3.9 26.2 - - + -
397F ASN* 3.6 30.5 + - + -
1224F GLN* 4.7 7.9 - - - -
1228F LEU* 6.2 0.7 - - + -
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Residues in contact with GLN 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260F LEU* 2.9 24.0 + - - +
261F THR* 3.4 13.0 - - + +
262F ASN 3.2 0.2 - - - -
263F TYR* 1.3 84.9 - - - +
265F ARG* 1.3 63.8 + - - +
267F CYS* 3.8 5.0 - - - +
268F VAL* 2.9 41.4 + - + +
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Residues in contact with ARG 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261F THR* 2.9 32.1 + - + +
262F ASN* 3.8 13.8 + - - +
264F GLN* 1.3 74.1 - - - +
266F LEU* 1.3 58.1 + - - +
268F VAL* 3.3 8.1 + - - +
269F ALA* 2.9 29.5 + - + +
293F HIS* 6.3 1.3 - - + +
294F ALA* 3.8 34.1 + - + +
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Residues in contact with LEU 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262F ASN 2.9 18.1 + - - +
263F TYR* 3.7 4.5 - - + +
265F ARG* 1.3 77.7 - - - +
267F CYS* 1.3 57.7 + - - +
269F ALA* 3.3 4.1 + - + +
270F PHE* 2.8 29.5 + - - +
290F ALA* 4.8 10.5 - - + +
291F LEU* 3.8 26.5 - - + +
294F ALA* 4.7 17.5 - - + +
295F PHE* 6.4 0.2 - - + -
390F ALA* 3.8 33.2 - - + +
391F ILE* 4.3 11.2 - - + +
394F LYS* 3.6 35.7 - - + +
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Residues in contact with CYS 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263F TYR* 2.9 52.1 + - + +
264F GLN* 3.9 6.1 - - - +
266F LEU* 1.3 72.8 - - - +
268F VAL* 1.3 61.7 + - + +
270F PHE* 3.6 9.8 - - + +
271F ASP* 2.9 30.0 + - - +
394F LYS* 4.3 20.0 - - - +
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Residues in contact with VAL 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264F GLN* 2.9 38.2 + - + +
265F ARG* 3.7 7.2 - - - +
267F CYS* 1.3 77.7 - - + +
269F ALA* 1.3 58.8 + - - +
271F ASP* 3.3 6.9 + - - +
272F ALA* 3.0 29.3 + - + +
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Residues in contact with ALA 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265F ARG* 2.9 17.8 + - + +
266F LEU* 3.8 6.7 - - - +
268F VAL* 1.3 78.1 - - - +
270F PHE* 1.3 57.5 + - - +
272F ALA* 3.3 8.1 + - - +
273F GLN* 2.9 30.1 + - - +
290F ALA* 4.4 19.8 - - + +
293F HIS* 4.1 28.0 - - + +
294F ALA* 4.9 3.8 - - + -
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Residues in contact with PHE 270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266F LEU 2.8 17.2 + - - +
267F CYS* 3.3 9.2 + - - +
269F ALA* 1.3 77.2 - - - +
271F ASP* 1.3 59.9 + - + +
273F GLN* 3.3 8.0 + - + +
274F ALA* 2.9 38.2 + - + +
283F GLY 6.0 2.9 - - - -
286F ALA* 5.6 5.8 - - + -
287F ILE* 3.6 34.5 - - + -
290F ALA* 4.4 8.7 - - + +
394F LYS* 3.3 31.4 - - - +
614F LEU* 4.0 24.2 - - + -
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Residues in contact with ASP 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267F CYS 2.9 16.7 + - - +
268F VAL* 3.6 7.0 - - - +
270F PHE* 1.3 81.6 - - + +
272F ALA* 1.3 62.4 + - - +
274F ALA* 3.1 7.2 + - - +
275F ARG* 2.9 29.5 + - - +
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Residues in contact with ALA 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268F VAL* 3.0 19.4 + - + +
269F ALA* 3.3 7.8 + - - +
271F ASP* 1.3 78.1 - - - +
273F GLN* 1.3 60.8 + - - +
275F ARG* 3.6 26.7 + - - +
276F LYS* 3.4 20.6 + - - +
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Residues in contact with GLN 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269F ALA 2.9 17.9 + - - +
270F PHE* 3.6 8.3 - - + +
272F ALA* 1.3 75.1 - - - +
274F ALA* 1.3 64.9 + - - +
276F LYS* 3.4 24.8 + - - +
286F ALA* 3.7 38.0 - - + +
289F ARG* 3.6 26.2 - - - +
290F ALA* 4.4 7.2 + - + -
293F HIS* 6.0 0.9 - - - +
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Residues in contact with ALA 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270F PHE* 2.9 29.5 + - + +
271F ASP* 3.1 8.9 + - - +
273F GLN* 1.3 77.0 - - - +
275F ARG* 1.3 64.9 + - - +
276F LYS 3.3 4.5 + - - -
286F ALA* 6.2 1.6 - - - -
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Residues in contact with ARG 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271F ASP* 2.9 20.8 + - - +
272F ALA* 4.0 29.2 + - - +
273F GLN 3.4 0.2 - - - -
274F ALA* 1.3 77.2 - - - +
276F LYS* 1.3 64.8 + - - +
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Residues in contact with LYS 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272F ALA 3.4 12.4 + - - +
273F GLN* 3.7 24.9 - - - +
274F ALA 3.2 5.4 - - - +
275F ARG* 1.3 85.9 - - - +
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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
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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