Contacts of the helix formed by residues 286 - 306 (chain A) in PDB entry 3N2Q
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 ASN 286 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A PHE* 6.2 1.1 - - + -
284A LYS 3.4 8.1 + - - +
285A TYR* 1.3 71.9 - - - +
287A GLY* 1.3 60.4 + - - +
289A THR* 4.4 2.8 + - - -
290A GLU* 3.2 39.8 + - + +
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Residues in contact with GLY 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A TYR* 3.6 32.4 + - - -
286A ASN* 1.3 80.0 + - - +
288A LYS* 1.3 64.0 + - - -
289A THR* 3.5 2.9 - - - -
290A GLU* 4.2 0.6 - - - +
291A LEU* 3.5 18.9 + - - +
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Residues in contact with LYS 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A TYR* 3.9 11.4 + - - +
287A GLY* 1.3 71.2 - - - -
289A THR* 1.3 58.5 + - + +
291A LEU* 3.1 6.5 + - + -
292A MSE 2.7 48.7 + - + +
339A PHE* 4.0 49.3 - - + +
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Residues in contact with THR 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ASN 4.4 4.2 + - - -
287A GLY* 4.8 0.3 - - - -
288A LYS* 1.3 79.6 + - + +
290A GLU* 1.3 78.0 + - - +
292A MSE 3.2 13.5 + - - +
293A ALA* 3.3 14.0 + - - +
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Residues in contact with GLU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A PHE* 3.3 37.7 - - + +
286A ASN* 3.2 47.8 + - + +
287A GLY 3.9 2.4 + - - +
288A LYS 3.3 0.4 - - - -
289A THR* 1.3 86.1 + - - +
291A LEU* 1.3 64.1 + - - +
292A MSE 3.3 0.3 + - - -
293A ALA* 3.3 6.7 + - - +
294A LEU 3.1 17.5 + - - -
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Residues in contact with LEU 291 (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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255A PHE* 5.2 1.3 - - - -
283A ILE* 4.8 8.1 - - + -
285A TYR* 4.2 11.2 - - + +
287A GLY 3.5 12.6 + - - +
288A LYS* 3.1 11.3 + - + +
290A GLU* 1.3 79.4 - - - +
292A MSE 1.3 57.6 + - - +
294A LEU* 3.6 10.9 + - + +
295A THR* 3.0 32.8 + - - +
316A ILE* 3.8 37.5 - - + -
323A GLU* 3.8 31.2 - - + +
324A ALA* 4.2 4.7 - - + -
339A PHE* 3.6 31.2 - - + -
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Residues in contact with MSE 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LYS* 2.7 33.3 + - + +
289A THR* 3.4 12.6 - - - +
290A GLU 3.2 0.2 - - - -
291A LEU* 1.3 70.7 - - - +
293A ALA* 1.3 65.6 + - - +
295A THR* 2.5 29.0 + - - +
296A GLN* 3.0 9.9 + - + +
337A VAL* 6.4 0.2 - - - -
339A PHE* 3.7 28.4 - - + -
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Residues in contact with ALA 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A PHE* 4.7 9.9 - - + -
289A THR 3.3 9.1 + - - +
290A GLU* 3.6 10.3 - - - +
292A MSE 1.3 77.1 - - - +
294A LEU* 1.3 57.2 - - - +
296A GLN* 3.4 14.8 + - - +
297A LEU* 3.0 28.3 + - - +
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Residues in contact with LEU 294 (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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252A ILE* 4.3 22.2 - - + +
255A PHE* 3.7 52.4 - - + -
261A ILE* 4.9 2.7 - - + -
281A ILE* 4.3 17.5 - - + -
283A ILE* 4.6 11.0 - - + -
290A GLU 3.1 12.7 + - - +
291A LEU* 3.7 14.4 - - + +
293A ALA* 1.3 74.8 - - - +
295A THR* 1.3 60.8 + - - +
297A LEU* 3.4 4.7 + - + +
298A ALA* 3.0 26.6 + - + +
316A ILE* 4.3 28.5 - - + -
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Residues in contact with THR 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A LEU* 3.0 17.0 + - + +
292A MSE 2.5 29.7 + - - +
294A LEU* 1.3 76.4 - - - +
296A GLN* 1.3 55.8 + - - +
299A ALA* 2.9 31.7 + - - +
316A ILE* 4.1 19.7 - - + -
324A ALA* 4.2 11.7 - - + -
326A ILE* 3.4 17.0 - - + +
337A VAL* 3.8 31.9 - - + +
339A PHE* 4.1 8.7 - - + -
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Residues in contact with GLN 296 (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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292A MSE 3.0 13.1 + - + +
293A ALA* 3.5 16.5 - - - +
294A LEU 3.2 0.2 - - - -
295A THR* 1.3 75.4 + - - +
297A LEU* 1.3 70.2 + - + +
299A ALA* 4.0 4.8 - - - +
300A GLN* 3.2 31.9 + - - +
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Residues in contact with LEU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A GLU* 3.8 26.3 - - + +
252A ILE* 4.0 9.8 - - - +
254A GLY* 3.8 7.2 - - - -
255A PHE* 3.5 40.8 - - + +
293A ALA 3.0 17.3 + - - +
294A LEU* 3.4 5.6 + - + +
296A GLN* 1.3 80.7 - - + +
298A ALA* 1.3 62.1 + - - +
300A GLN* 3.9 4.0 + - - +
301A GLY* 3.2 18.4 + - - -
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Residues in contact with ALA 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A PHE* 3.3 10.7 - - + -
252A ILE* 3.8 19.9 - - + +
294A LEU* 3.0 19.6 + - + +
295A THR* 4.5 0.2 - - - -
297A LEU* 1.3 75.4 - - - +
299A ALA* 1.3 64.9 + - - +
301A GLY 3.1 0.9 + - - -
302A MSE 3.0 23.5 + - - +
314A LEU* 3.9 20.9 - - + -
316A ILE* 5.4 1.8 - - + -
326A ILE* 3.7 18.4 - - + -
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Residues in contact with ALA 299 (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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295A THR 2.9 20.8 + - - +
296A GLN* 4.0 5.4 - - - +
298A ALA* 1.3 74.0 - - - +
300A GLN* 1.3 64.1 + - - +
302A MSE 3.0 16.6 + - - +
303A LEU* 3.4 9.5 + - - +
326A ILE* 4.0 23.5 - - + +
335A PRO* 3.8 26.1 - - + +
337A VAL* 5.2 6.1 - - + -
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Residues in contact with GLN 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A GLN* 3.2 22.0 + - - +
297A LEU* 4.0 4.7 - - - +
299A ALA* 1.3 78.1 - - - +
301A GLY* 1.3 57.9 + - - +
303A LEU* 3.2 19.5 + - - +
304A ASP* 2.9 61.4 + - - +
334A LYS* 5.7 4.9 - - - +
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Residues in contact with GLY 301 (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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248A PHE* 3.5 18.0 - - - -
251A GLU* 4.6 15.9 - - - -
297A LEU 3.2 10.8 + - - -
298A ALA 3.1 7.5 + - - -
300A GLN* 1.3 75.7 - - - +
302A MSE 1.3 62.7 + - - +
304A ASP* 3.9 7.4 - - - -
305A LYS* 3.2 28.4 + - - +
306A LEU* 4.2 0.3 + - - +
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Residues in contact with MSE 302 (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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248A PHE* 3.9 8.5 - - + -
279A MSE 4.1 6.5 - - + -
298A ALA 3.0 17.4 + - - +
299A ALA* 3.0 7.6 + - - +
301A GLY* 1.3 77.2 - - - +
303A LEU* 1.3 58.6 + - - +
306A LEU* 3.0 44.6 + - + +
312A VAL* 3.8 25.8 - - + +
314A LEU* 3.2 48.0 - - + +
326A ILE* 3.6 37.9 - - + +
328A LYS* 4.6 24.2 - - + +
335A PRO* 4.7 2.5 - - + -
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Residues in contact with LEU 303 (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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299A ALA 3.4 5.4 + - - +
300A GLN* 3.2 23.5 + - - +
302A MSE 1.3 80.6 - - - +
304A ASP* 1.3 67.7 + - - +
305A LYS 3.5 0.2 + - - -
306A LEU 4.3 6.2 - - - +
328A LYS* 4.2 16.8 - - + -
332A SER 4.6 4.0 - - - +
333A ASP 4.4 13.5 - - - +
334A LYS* 4.3 15.9 - - + +
335A PRO* 3.7 35.7 - - + -
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Residues in contact with ASP 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A GLU* 5.5 4.1 - - - +
300A GLN* 2.9 42.3 + - - +
301A GLY* 4.3 5.6 - - - +
302A MSE 3.3 0.2 - - - -
303A LEU* 1.3 79.8 - - - +
305A LYS* 1.3 81.9 + - + +
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Residues in contact with LYS 305 (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 LYS* 3.5 33.4 - - - +
247A ASN* 3.5 39.0 - - + +
248A PHE* 3.8 15.0 - - - +
251A GLU* 3.9 28.7 + - + -
301A GLY 3.2 17.0 + - - +
304A ASP* 1.3 101.5 + - + +
306A LEU* 1.3 60.8 + - + +
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Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LYS* 4.1 15.9 - - + +
245A ILE* 4.3 6.5 - - + +
248A PHE* 4.0 22.4 - - + -
274A MSE 5.8 0.4 - - + -
277A LEU* 3.5 32.5 - - + -
279A MSE 4.3 9.0 - - + -
301A GLY 4.3 2.7 - - - +
302A MSE 3.0 35.8 + - + +
303A LEU* 4.3 6.2 - - - +
305A LYS* 1.3 86.9 - - - +
307A PRO* 1.4 75.6 - - + +
308A LYS* 3.3 3.3 + - - -
312A VAL* 3.8 29.8 - - + -
328A LYS* 5.4 1.6 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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