Contacts of the helix formed by residues 251 - 269 (chain B) in PDB entry 6R6H
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 PHE 251 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242B GLY 4.3 4.5 - - - -
245B HIS* 3.3 37.0 - - + -
246B LEU* 3.8 10.8 - - + -
249B GLY* 3.0 35.8 + - - -
250B GLU* 1.3 76.9 - - - +
252B GLU* 1.3 58.5 + - - +
254B ALA* 3.2 12.8 - - + -
255B HIS* 2.2 43.1 + - + +
258B PHE* 4.4 8.1 - + - -
279B TYR* 5.5 4.3 - + - -
283B ALA* 3.4 45.5 - - + +
286B LEU* 5.5 12.8 - - + -
287B MET* 5.2 6.5 - - + -
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Residues in contact with GLU 252 (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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250B GLU* 3.2 15.7 + - - +
251B PHE* 1.3 80.3 - - - +
253B LYS* 1.3 78.5 + - + +
255B HIS* 3.0 34.8 + - + +
256B THR* 3.0 10.4 + - - +
287B MET* 5.5 12.8 - - + +
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Residues in contact with LYS 253 (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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250B GLU* 4.2 5.5 + - + +
252B GLU* 1.3 91.7 - - + +
254B ALA* 1.3 59.2 + - - +
256B THR* 2.4 51.1 + - - +
257B ASP* 2.8 25.0 + - - +
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Residues in contact with ALA 254 (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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245B HIS* 3.3 42.0 + - + +
250B GLU* 3.4 3.5 - - - +
251B PHE* 3.1 29.3 + - + +
252B GLU 3.1 0.6 - - - +
253B LYS* 1.3 77.7 - - - +
255B HIS* 1.3 58.4 + - - +
257B ASP* 3.0 14.6 + - - +
258B PHE* 2.8 32.1 + - + -
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Residues in contact with HIS 255 (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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251B PHE* 2.2 36.7 + - + +
252B GLU* 3.0 38.7 + - + +
254B ALA* 1.3 65.9 - - - +
256B THR* 1.3 85.7 + - + +
258B PHE* 3.1 13.4 + - + +
259B PHE* 2.9 26.0 + - - +
280B LEU* 3.3 11.5 - - + +
283B ALA* 5.4 0.2 - - + -
284B ASN* 3.2 28.4 + - - +
287B MET* 4.4 25.2 - - + +
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Residues in contact with THR 256 (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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252B GLU 3.0 12.7 + - - +
253B LYS* 2.4 61.5 + - - +
255B HIS* 1.3 91.9 + - + +
257B ASP* 1.3 59.2 + - - +
259B PHE* 3.2 11.2 + - - +
260B GLU* 3.0 32.4 + - - +
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Residues in contact with ASP 257 (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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238B ARG* 4.2 33.7 + - + +
245B HIS* 4.7 10.1 + - + -
253B LYS* 2.8 30.1 + - - +
254B ALA* 3.1 14.9 - - - +
256B THR* 1.3 76.3 + - - +
258B PHE* 1.3 59.5 + - - +
260B GLU* 3.9 6.5 - - - +
261B ALA* 2.8 34.2 + - - +
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Residues in contact with PHE 258 (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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238B ARG* 4.8 8.5 - - + -
239B GLU* 5.6 3.8 - - - -
242B GLY* 3.4 32.3 - - - -
245B HIS* 4.9 0.9 - + - -
251B PHE* 4.4 18.8 - + - -
254B ALA* 2.8 34.8 + - + -
255B HIS* 3.1 5.8 + - - +
257B ASP* 1.3 76.8 - - - +
259B PHE* 1.3 55.5 + - - +
261B ALA* 4.3 3.8 - - + -
262B PHE* 2.8 64.0 + + + -
276B CYS* 4.7 1.8 - - + -
279B TYR* 3.9 26.0 - + - -
280B LEU* 3.2 44.4 - - + -
283B ALA* 4.7 1.3 - - + -
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Residues in contact with PHE 259 (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 2.9 12.0 + - - +
256B THR* 3.2 13.2 + - - +
258B PHE* 1.3 77.6 - - - +
260B GLU* 1.3 84.8 + - + +
262B PHE* 3.8 4.6 - - - +
263B LYS* 2.9 56.4 + - + +
280B LEU* 4.2 5.5 - - + +
296B SER* 3.2 43.1 - - - -
297B GLN* 4.2 20.9 - - + -
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Residues in contact with GLU 260 (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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238B ARG* 4.9 8.7 - - - +
256B THR* 3.0 16.6 + - - +
257B ASP* 3.9 7.0 - - - +
259B PHE* 1.3 92.6 - - + +
261B ALA* 1.3 58.0 + - - +
263B LYS* 2.6 42.9 + - - +
264B ASN* 2.9 27.9 + - - +
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Residues in contact with ALA 261 (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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234B MET* 6.1 0.2 - - - -
235B GLY* 3.2 37.9 - - - +
238B ARG* 4.3 11.1 - - + +
257B ASP 2.8 24.2 + - - +
258B PHE* 3.8 7.0 - - + +
260B GLU* 1.3 73.1 - - - +
262B PHE* 1.3 66.4 + - + +
264B ASN* 3.3 6.8 + - - +
265B TYR* 2.8 27.5 + - - +
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Residues in contact with PHE 262 (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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258B PHE* 2.8 44.6 + + - +
259B PHE* 3.8 4.3 - - - +
261B ALA* 1.3 79.5 - - + +
263B LYS* 1.3 61.8 + - - +
265B TYR* 3.5 7.8 - - + +
266B ASP* 2.9 31.2 + - - +
273B ARG* 3.1 38.9 + - - +
276B CYS* 3.0 38.6 - - + -
277B LEU* 3.7 4.9 - - + -
280B LEU* 3.3 35.9 - - + -
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Residues in contact with LYS 263 (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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259B PHE* 2.9 52.1 + - + +
260B GLU* 2.6 46.5 + - - +
262B PHE* 1.3 75.9 - - - +
264B ASN* 1.3 57.4 + - - +
266B ASP* 3.4 4.5 + - - +
267B GLU* 2.9 43.3 + - - +
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Residues in contact with ASN 264 (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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232B LEU* 2.6 46.6 + - - +
233B ILE* 3.8 1.7 - - - +
234B MET* 3.2 31.7 - - + +
235B GLY 4.2 2.0 - - - +
260B GLU 2.9 10.0 + - - +
261B ALA* 3.6 10.3 - - - +
263B LYS* 1.3 80.0 - - - +
265B TYR* 1.3 56.8 + - - +
267B GLU* 3.0 24.1 + - - +
268B SER* 2.9 23.2 + - - -
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Residues in contact with TYR 265 (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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235B GLY 6.6 0.2 - - - -
236B VAL* 5.5 12.6 - - + -
261B ALA 2.8 17.0 + - - +
262B PHE* 3.5 12.3 - + + +
263B LYS 3.1 0.6 - - - -
264B ASN* 1.3 73.6 - - - +
266B ASP* 1.3 51.9 - - - +
267B GLU 3.1 0.7 - - - -
268B SER* 2.3 22.1 + - - -
269B GLY 2.2 60.5 + - - +
270B SER* 3.5 0.7 - - - -
271B PRO* 2.9 23.3 - - + +
272B ARG* 2.2 45.9 + - + +
273B ARG* 3.2 47.1 - - + -
276B CYS* 4.4 6.5 - - - -
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Residues in contact with ASP 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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262B PHE 2.9 15.4 + - - +
263B LYS* 3.7 4.7 - - - +
265B TYR* 1.3 76.1 - - - +
267B GLU* 1.3 61.7 + - + +
268B SER 3.2 0.9 + - - -
269B GLY* 3.4 18.1 + - - -
273B ARG* 4.9 6.2 - - - +
302B TYR* 4.9 17.8 + - - -
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Residues in contact with GLU 267 (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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232B LEU* 5.8 5.4 - - + +
263B LYS* 2.9 38.9 + - - +
264B ASN* 3.0 35.1 - - - +
265B TYR 3.1 0.2 - - - -
266B ASP* 1.3 75.2 - - + +
268B SER* 1.3 55.6 + - - +
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Residues in contact with SER 268 (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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232B LEU* 5.2 8.7 - - - -
233B ILE* 5.7 9.2 - - - -
264B ASN 2.9 10.6 + - - -
265B TYR* 2.3 52.6 + - - -
266B ASP 3.9 0.4 - - - -
267B GLU* 1.3 72.5 - - - +
269B GLY* 1.3 54.6 + - - -
271B PRO* 5.2 1.6 - - - +
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Residues in contact with GLY 269 (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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265B TYR* 2.2 51.0 + - - +
266B ASP* 3.4 14.9 + - - -
268B SER* 1.3 71.8 + - - +
270B SER* 1.3 61.2 + - - -
271B PRO* 3.6 8.3 - - - -
273B ARG* 4.4 0.7 - - - -
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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