Contacts of the helix formed by residues 272 - 288 (chain A) in PDB entry 4NQJ
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 ASP 272 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A LYS* 2.6 34.0 + - - -
263A GLN* 5.1 2.3 + - - +
268A ASP 3.4 6.5 - - - +
271A LYS* 1.3 87.9 - - + +
273A ILE* 1.3 64.0 + - - +
274A THR* 3.1 5.8 - - - -
275A THR* 2.3 40.0 + - + +
276A LEU* 3.3 6.9 + - - +
162B GLU* 5.2 1.6 - - - -
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Residues in contact with ILE 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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260A LYS* 3.8 34.1 - - + +
269A PHE* 3.7 11.9 - - + +
270A LEU* 3.2 20.1 + - + +
271A LYS 3.5 0.2 - - - -
272A ASP* 1.3 81.9 + - - +
274A THR* 1.3 60.1 + - + +
275A THR 3.3 0.2 + - - -
276A LEU* 3.3 8.4 + - + +
277A LEU* 2.9 43.4 + - + +
159B PHE* 4.2 13.9 - - + -
160C PHE* 3.9 53.8 - - + -
164C LEU* 4.5 7.2 - - + -
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Residues in contact with THR 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LYS 4.8 1.2 + - - -
272A ASP 4.4 2.6 - - - -
273A ILE* 1.3 78.5 - - + +
275A THR* 1.3 61.4 + - - +
277A LEU* 3.9 8.5 - - + +
278A HIS* 3.0 28.4 + - - +
159B PHE* 3.4 50.3 - - + +
162B GLU* 3.1 34.0 + - + +
163B GLU* 3.6 21.0 - - + +
166B ILE* 3.5 11.5 - - - +
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Residues in contact with THR 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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272A ASP* 2.3 40.0 + - + +
274A THR* 1.3 77.7 - - - +
276A LEU* 1.3 56.8 + - - +
278A HIS* 3.2 5.1 + - - +
279A SER* 2.9 30.1 + - - -
162B GLU* 3.7 21.8 - - - +
166B ILE* 4.4 13.2 - - + -
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Residues in contact with LEU 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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256A SER* 3.8 32.1 - - - +
257A ILE* 5.1 0.9 - - - -
260A LYS* 3.5 46.4 - - + -
272A ASP* 3.3 5.9 + - - +
273A ILE* 3.7 11.7 - - + +
275A THR* 1.3 80.8 + - - +
277A LEU* 1.3 58.2 + - + +
279A SER* 2.7 31.9 + - - +
280A LEU* 2.9 27.0 + - + +
164C LEU* 4.1 15.0 - - + -
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Residues in contact with LEU 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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273A ILE* 2.9 33.5 + - + +
274A THR* 3.9 7.9 - - - +
276A LEU* 1.3 78.7 - - + +
278A HIS* 1.3 58.3 + - - +
280A LEU* 3.4 10.1 + - + +
281A GLU* 2.9 28.4 + - - +
159B PHE* 5.6 2.0 - - + -
163B GLU* 5.5 6.7 - - - +
160C PHE* 4.0 31.2 - - + +
163C GLU* 4.2 26.5 - - + +
164C LEU* 4.1 26.7 - - + -
167C GLN* 5.0 3.2 - - + +
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Residues in contact with HIS 278 (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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274A THR 3.0 18.2 + - - +
275A THR* 3.2 4.9 + - - +
277A LEU* 1.3 76.3 - - - +
279A SER* 1.3 61.8 + - - +
281A GLU* 3.2 13.8 + - - -
282A GLN* 2.8 62.5 + - + +
166B ILE* 3.5 40.9 - - + +
170B GLN* 4.0 19.5 + - + +
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Residues in contact with SER 279 (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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253A MET* 4.5 1.0 - - - +
256A SER* 5.3 0.3 + - - -
275A THR 2.9 13.4 + - - -
276A LEU* 2.7 20.4 + - - +
278A HIS* 1.3 76.9 + - - +
280A LEU* 1.3 74.5 + - - +
282A GLN* 3.1 6.7 + - - +
283A GLY* 2.6 35.2 + - - -
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Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A MET* 3.1 33.9 - - + +
256A SER* 4.0 12.6 - - - +
257A ILE* 3.8 30.5 - - + -
276A LEU* 2.9 27.7 + - + +
277A LEU* 3.5 8.3 - - + +
279A SER* 1.3 91.7 + - - +
281A GLU* 1.3 57.8 + - - +
284A MET* 2.8 30.7 + - - +
164C LEU* 4.1 17.3 - - + -
167C GLN* 3.2 27.4 - - + +
171C LEU* 4.7 1.6 - - + -
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Residues in contact with GLU 281 (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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277A LEU 2.9 17.8 + - - +
278A HIS* 3.6 20.0 - - - +
280A LEU* 1.3 77.0 - - - +
282A GLN* 1.3 68.5 + - - +
284A MET* 3.5 6.4 + - - +
285A LYS* 3.2 32.8 + - + +
170B GLN* 4.5 7.6 + - - +
167C GLN* 4.4 4.4 + - - +
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Residues in contact with GLN 282 (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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278A HIS* 2.8 50.6 + - + +
279A SER* 3.6 5.4 - - - +
281A GLU* 1.3 78.7 - - - +
283A GLY* 1.3 66.2 + - - +
285A LYS* 3.1 34.4 + - - +
286A VAL* 3.4 15.7 + - - +
170B GLN* 3.8 20.3 + - - +
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Residues in contact with GLY 283 (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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249A LEU* 3.9 12.1 - - - +
253A MET* 3.6 21.3 - - - -
279A SER 2.6 20.6 + - - -
282A GLN* 1.3 72.6 - - - +
284A MET* 1.3 59.3 + - - +
286A VAL* 3.3 10.4 - - - +
287A LEU* 3.3 23.6 + - - +
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Residues in contact with MET 284 (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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253A MET* 3.5 20.2 - - + -
280A LEU 2.8 16.6 + - - +
281A GLU* 4.1 6.3 - - - +
282A GLN 3.2 0.4 - - - -
283A GLY* 1.3 70.1 - - - +
285A LYS* 1.3 63.9 + - - +
287A LEU* 3.6 10.2 + - + +
288A ALA* 3.1 22.0 + - - +
290A ARG* 5.4 1.0 + - - -
167C GLN* 3.3 36.6 - - - +
170C GLN* 3.7 25.1 - - + +
171C LEU* 3.5 27.8 - - + -
174C THR* 4.8 7.9 - - - -
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Residues in contact with LYS 285 (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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281A GLU* 3.2 25.4 + - + +
282A GLN* 3.1 29.5 + - - +
284A MET* 1.3 73.4 - - - +
286A VAL* 1.3 67.9 + - + +
288A ALA* 3.3 15.8 + - + +
289A THR* 3.4 14.6 - - - +
170B GLN* 4.7 10.3 - - - +
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Residues in contact with VAL 286 (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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246A GLN* 3.5 18.5 + - + +
249A LEU* 3.9 21.1 - - + -
282A GLN 3.6 13.5 - - - +
283A GLY* 3.3 10.3 + - - +
285A LYS* 1.3 78.1 - - + +
287A LEU* 1.3 65.0 + - + +
289A THR* 2.7 34.4 + - - +
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Residues in contact with LEU 287 (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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246A GLN* 3.8 24.4 - - + +
249A LEU* 3.5 33.9 - - + -
250A ALA* 3.9 14.8 - - + -
253A MET* 4.2 8.5 - - - -
283A GLY 3.3 3.7 + - - +
284A MET* 3.7 14.6 - - + +
285A LYS 3.4 0.2 - - - -
286A VAL* 1.3 80.3 - - + +
288A ALA* 1.3 54.4 + - - +
289A THR 3.3 0.9 + - - -
290A ARG* 2.6 39.5 + - - +
171C LEU* 3.9 28.9 - - + -
174C THR* 3.9 25.1 - - + -
178C LEU* 4.2 9.4 - - + -
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Residues in contact with ALA 288 (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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284A MET 3.1 13.8 + - - +
285A LYS* 3.5 14.1 - - + +
286A VAL 3.0 1.2 + - - -
287A LEU* 1.3 76.4 - - - +
289A THR* 1.3 58.8 + - - +
290A ARG* 3.2 23.1 + - - +
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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