Contacts of the helix formed by residues 259 - 274 (chain A) in PDB entry 3QN3
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 SER 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A GLY 4.8 4.0 - - - -
250A LYS* 3.7 21.7 - - - +
251A TYR* 4.4 1.8 - - - -
257A ALA 4.0 0.8 + - - -
258A PHE* 1.3 79.0 - - - +
260A SER* 1.3 63.9 + - - +
261A GLU* 3.3 17.1 + - - +
262A ALA* 3.1 24.7 + - - +
263A LEU* 3.0 18.9 + - - +
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Residues in contact with SER 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A PHE* 5.2 0.5 - - - -
249A GLY 5.0 4.9 + - - -
251A TYR* 3.7 14.9 - - - -
259A SER* 1.3 73.4 - - - +
261A GLU* 1.3 72.3 + - - +
263A LEU* 3.3 2.4 + - - +
264A ILE* 3.1 29.3 + - - +
283A LEU* 4.2 5.8 - - - +
287A ASP* 2.5 33.8 + - - -
290A GLY* 4.1 17.3 - - - -
293A LYS* 4.8 2.2 - - - -
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Residues in contact with GLU 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A SER* 3.4 16.0 + - - +
260A SER* 1.3 83.4 + - - +
262A ALA* 1.3 62.6 + - - +
264A ILE* 3.3 13.7 + - + +
265A GLU* 3.2 24.9 + - - +
293A LYS* 2.3 41.8 + - - +
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Residues in contact with ALA 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A PHE* 3.9 19.9 - - + -
259A SER* 3.1 22.3 + - - +
261A GLU* 1.3 80.0 - - - +
263A LEU* 1.3 61.2 + - - +
265A GLU* 3.2 6.7 + - - +
266A ARG* 3.0 21.5 + - - +
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Residues in contact with LEU 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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245A PHE* 4.5 2.9 - - + -
251A TYR* 3.5 42.6 - - + -
253A MET* 3.5 33.4 - - + -
258A PHE* 3.9 10.7 - - + -
259A SER 3.0 17.4 + - - +
260A SER* 3.8 4.7 - - - +
262A ALA* 1.3 75.2 - - - +
264A ILE* 1.3 62.9 + - - +
266A ARG* 3.3 11.9 - - + +
267A TYR* 3.0 49.3 + - + +
282A GLY 3.7 14.8 - - - +
283A LEU* 4.0 5.6 - - + -
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Residues in contact with ILE 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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260A SER 3.1 20.1 + - - +
261A GLU* 3.3 11.2 + - + +
263A LEU* 1.3 77.2 - - - +
265A GLU* 1.3 61.2 + - + +
267A TYR* 2.9 12.2 + - - +
268A VAL* 2.9 25.3 + - + +
283A LEU* 4.2 8.5 - - + -
290A GLY* 3.8 10.5 - - - +
293A LYS* 3.8 14.6 - - + +
294A LEU* 3.4 47.1 - - + +
297A LYS* 3.7 33.7 - - + -
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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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261A GLU 3.2 12.4 + - - +
262A ALA* 3.9 8.1 - - - +
264A ILE* 1.3 80.5 - - + +
266A ARG* 1.3 62.3 + - - +
268A VAL* 3.2 14.0 + - - +
269A GLU* 3.0 25.3 + - - +
297A LYS* 3.2 36.0 + - + +
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Residues in contact with ARG 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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214A ASN* 5.4 0.4 - - - +
215A THR* 3.9 21.8 - - - +
253A MET* 4.7 4.3 - - + -
254A GLU* 2.9 40.0 + - - +
256A LYS* 5.7 0.4 - - - +
258A PHE* 4.3 15.3 - - + -
262A ALA 3.0 13.9 + - - +
263A LEU* 3.3 22.4 - - + +
265A GLU* 1.3 76.7 - - - +
267A TYR* 1.3 58.5 + - + +
269A GLU* 3.2 35.4 + - - +
270A LEU* 3.0 59.3 + - + +
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Residues in contact with TYR 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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161A PHE* 4.3 12.3 - + - -
238A LEU* 5.9 1.3 - - + -
240A VAL* 3.3 30.1 - - + +
263A LEU* 3.0 44.6 + - + +
264A ILE* 2.9 9.1 + - - +
266A ARG* 1.3 76.9 - - + +
268A VAL* 1.3 63.1 + - - +
270A LEU* 3.8 13.4 - - + +
271A CYS* 3.0 29.3 + - - -
279A ILE* 3.9 23.8 - - + -
282A GLY* 2.5 48.9 + - - -
283A LEU* 4.5 3.8 - - + -
294A LEU* 4.0 20.6 - - + -
298A LEU* 3.8 15.7 - - + -
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Residues in contact with VAL 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ILE 2.9 17.7 + - - +
265A GLU* 3.2 23.1 + - - +
267A TYR* 1.3 77.2 - - - +
269A GLU* 1.3 56.8 + - - +
271A CYS* 3.3 2.1 + - - +
272A ALA* 2.9 31.6 + - + +
297A LYS* 3.7 40.8 - - + +
298A LEU* 4.0 23.3 - - + -
301A LYS* 4.7 5.4 + - - +
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Residues in contact with GLU 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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265A GLU 3.0 12.3 + - - +
266A ARG* 3.2 44.4 + - - +
268A VAL* 1.3 75.1 - - - +
270A LEU* 1.3 64.8 + - - +
272A ALA* 3.0 9.4 + - - +
273A LYS* 3.0 23.5 + - - +
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Residues in contact with LEU 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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161A PHE* 4.4 24.9 - - + -
214A ASN* 6.1 0.7 - - + -
215A THR* 3.7 24.5 - - + -
218A ILE* 4.7 5.8 - - + -
238A LEU* 5.5 1.8 - - + -
254A GLU* 5.5 0.2 - - - +
266A ARG* 3.0 57.6 + - + +
267A TYR* 3.8 13.5 - - + +
269A GLU* 1.3 79.0 - - + +
271A CYS* 1.3 58.7 + - - +
273A LYS* 3.2 4.7 + - + -
274A TYR* 2.9 48.4 + - + +
276A ILE* 4.0 18.6 - - + -
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Residues in contact with CYS 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 TYR 3.0 26.3 + - - +
268A VAL* 3.8 4.7 - - - +
270A LEU* 1.3 74.0 - - - +
272A ALA* 1.3 60.7 - - - +
274A TYR 3.0 19.5 - - - +
276A ILE* 4.0 20.1 - - - +
279A ILE* 3.9 13.5 - - - -
298A LEU* 4.6 7.6 - - + -
301A LYS* 4.0 19.3 + - - +
302A ILE* 3.8 39.7 - - + -
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Residues in contact with ALA 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 VAL* 2.9 16.7 + - + +
269A GLU* 3.4 11.4 - - - +
271A CYS* 1.3 77.9 - - - +
273A LYS* 1.3 59.5 + - - +
301A LYS* 4.0 11.3 - - - +
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Residues in contact with LYS 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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215A THR* 6.0 0.4 - - + -
219A ASP* 4.7 2.2 + - - -
269A GLU 3.0 14.6 + - - +
270A LEU* 3.8 6.3 - - + +
272A ALA* 1.3 80.1 - - - +
274A TYR* 1.3 102.6 + - + +
275A PRO* 4.7 1.2 - - - +
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Residues in contact with TYR 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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215A THR* 3.7 15.6 - - + +
218A ILE* 3.6 41.3 - - + -
219A ASP* 2.7 32.5 + - - -
222A MET* 4.3 14.4 - - + -
270A LEU* 2.9 42.0 + - + +
271A CYS* 3.0 20.3 - - - +
272A ALA 5.3 0.2 - - - -
273A LYS* 1.3 118.6 - - + +
275A PRO* 1.3 66.1 - - + +
276A ILE* 2.9 22.9 + - + +
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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