Contacts of the helix formed by residues 261 - 277 (chain A) in PDB entry 3RK6
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 MET 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259A GLY 4.5 9.6 - - - +
260A LYS* 1.3 81.0 - - - +
262A ASP* 1.3 64.2 + - - +
263A MET 3.3 2.7 - - - -
264A GLU* 3.3 47.1 + - - +
265A GLU* 3.1 35.4 + - + +
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Residues in contact with ASP 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A ARG* 2.9 39.0 + - - +
255A TRP* 3.4 37.9 - - + -
260A LYS* 3.4 33.5 + - - +
261A MET* 1.3 78.0 + - - +
263A MET* 1.3 57.5 + - - +
265A GLU* 3.1 6.7 + - - +
266A ILE* 2.8 32.6 + - - +
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Residues in contact with MET 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A LEU* 4.8 11.9 - - + -
248A GLY 5.1 2.0 - - - +
252A GLU* 3.7 29.2 - - + +
255A TRP* 3.6 28.5 - - + +
260A LYS 5.2 0.6 + - - -
261A MET 3.3 0.6 - - - -
262A ASP* 1.3 78.0 - - - +
264A GLU* 1.3 53.6 + - - +
266A ILE* 3.3 20.1 + - + +
267A ILE* 2.8 63.3 + - + +
270A ILE* 5.2 1.8 - - + -
290A LEU* 6.3 0.7 - - + -
294A ARG* 3.1 48.5 - - + +
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Residues in contact with GLU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A MET* 3.3 46.4 + - + +
263A MET* 1.3 77.6 - - - +
265A GLU* 1.3 59.0 + - + +
267A ILE* 3.4 8.2 + - - +
268A GLN* 3.0 26.7 + - - +
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Residues in contact with GLU 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A ARG* 2.9 32.0 + - - +
261A MET* 3.1 28.6 + - + +
262A ASP* 3.1 9.4 + - - +
264A GLU* 1.3 73.6 - - + +
266A ILE* 1.3 60.5 + - - +
268A GLN* 3.2 8.0 + - - +
269A ARG* 3.0 34.7 + - - +
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Residues in contact with ILE 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A ARG* 3.3 34.3 - - - +
225A LEU* 4.0 22.9 - - + -
226A ASN* 4.0 9.0 - - - +
229A PHE* 4.2 12.8 - - + -
244A LEU* 4.2 11.9 - - + -
255A TRP* 4.5 11.2 - - + -
262A ASP 2.8 24.0 + - - +
263A MET* 3.5 19.7 - - + +
265A GLU* 1.3 70.1 - - - +
267A ILE* 1.3 60.9 + - - +
269A ARG* 3.1 7.3 + - - +
270A ILE* 2.9 47.3 + - + +
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Residues in contact with ILE 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A MET* 2.8 50.7 + - + +
264A GLU* 3.6 8.1 - - - +
265A GLU 3.3 0.2 - - - -
266A ILE* 1.3 73.1 - - - +
268A GLN* 1.3 57.2 + - - +
270A ILE* 3.3 11.4 + - + +
271A GLU* 2.9 50.6 + - - +
290A LEU 4.4 1.3 - - - +
291A VAL* 4.0 36.3 - - + +
294A ARG* 4.0 17.5 - - + +
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Residues in contact with GLN 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A GLU 3.0 13.8 + - - +
265A GLU* 3.2 9.4 + - - +
267A ILE* 1.3 76.1 - - - +
269A ARG* 1.3 59.2 + - + +
271A GLU* 3.4 22.7 + - - +
272A ASN* 2.9 58.9 + - - +
275A LEU* 5.2 2.4 - - - +
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Residues in contact with ARG 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A ARG* 3.3 14.5 - - - +
226A ASN* 3.2 58.2 + - - +
229A PHE* 4.2 22.0 - - + +
230A SER* 4.1 9.9 + - - -
265A GLU* 3.0 18.9 + - - +
266A ILE* 3.5 12.1 - - - +
268A GLN* 1.3 78.0 - - + +
270A ILE* 1.3 55.4 + - - +
272A ASN* 3.3 10.5 + - - +
273A VAL* 3.0 33.1 + - - +
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Residues in contact with ILE 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A PHE* 3.5 28.7 - - + -
244A LEU* 4.1 11.2 - - + -
263A MET* 5.2 0.9 - - + -
266A ILE* 2.9 37.7 + - + +
267A ILE* 3.6 20.0 - - + +
269A ARG* 1.3 73.3 - - - +
271A GLU* 1.3 64.9 + - - +
273A VAL* 3.3 10.1 + - - +
274A VAL* 3.0 23.4 + - + +
287A LEU* 3.7 28.3 - - + +
290A LEU* 4.7 13.2 - - + -
291A VAL* 3.7 21.8 - - + -
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Residues in contact with GLU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A ILE* 2.9 30.7 + - - +
268A GLN* 3.7 26.6 + - - +
270A ILE* 1.3 76.6 - - - +
272A ASN* 1.3 57.5 + - - +
274A VAL* 3.3 7.9 + - - +
275A LEU* 2.9 40.2 + - + +
288A LEU* 5.7 4.9 - - + -
291A VAL* 3.5 33.5 - - + +
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Residues in contact with ASN 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A GLN* 2.9 47.8 + - - +
269A ARG* 3.3 10.0 + - - +
271A GLU* 1.3 71.6 - - - +
273A VAL* 1.3 61.7 + - - +
275A LEU* 3.3 13.2 + - - +
276A ASP* 2.9 46.4 + - - +
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Residues in contact with VAL 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A PHE* 3.8 36.3 - - + +
232A PRO* 4.2 6.3 - - + -
237A LEU* 3.7 24.7 - - + -
269A ARG 3.0 18.4 + - - +
270A ILE* 3.4 8.1 - - - +
272A ASN* 1.3 76.8 - - - +
274A VAL* 1.3 59.7 + - - +
276A ASP* 5.2 0.2 - - - -
277A ALA* 2.8 45.8 + - + +
279A CYS* 4.3 2.9 - - - -
284A LYS* 3.7 2.1 + - - -
287A LEU* 3.6 24.9 - - + -
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Residues in contact with VAL 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A ILE* 3.0 19.0 + - + +
271A GLU* 3.3 8.7 + - - +
273A VAL* 1.3 76.0 - - - +
275A LEU* 1.3 61.5 + - + +
284A LYS* 2.8 60.0 + - + +
287A LEU* 3.9 18.4 - - + -
288A LEU* 3.9 37.0 - - + -
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Residues in contact with LEU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A GLN* 5.2 1.6 - - - +
271A GLU* 2.9 31.1 + - + +
272A ASN* 3.8 14.4 - - - +
274A VAL* 1.3 83.4 - - + +
276A ASP* 1.3 70.6 + - - +
284A LYS* 4.3 2.5 + - - -
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Residues in contact with ASP 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A ASN* 2.9 29.2 + - - +
273A VAL* 5.2 0.2 - - - -
275A LEU* 1.3 91.5 - - - +
277A ALA* 1.3 66.0 + - + +
278A ASN* 3.8 1.6 + - - +
284A LYS* 4.5 0.2 - - - -
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Residues in contact with ALA 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A PRO* 3.8 26.5 - - + +
273A VAL* 2.8 42.4 + - + +
276A ASP* 1.3 75.9 - - - +
278A ASN* 1.3 58.9 + - - +
279A CYS* 3.2 10.9 - - - +
284A LYS* 2.7 30.8 + - - -
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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