Contacts of the helix formed by residues 279 - 299 (chain A) in PDB entry 3MEK
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 279 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A GLY* 1.3 70.9 - - - -
280A GLU* 1.3 66.3 + - - +
281A GLN* 3.0 16.8 + - - +
282A VAL* 2.9 52.5 + - + +
283A TRP* 3.1 15.1 + - - -
318A GLU* 4.6 14.4 + - + +
319A ARG 5.4 2.4 + - - -
320A LEU* 3.8 5.7 - - - +
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Residues in contact with GLU 280 (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 GLY 3.3 4.8 + - - -
279A ASP* 1.3 74.1 + - - +
281A GLN* 1.3 63.8 + - - +
283A TRP* 3.4 32.7 + - + +
284A LYS* 2.9 56.7 + - + +
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Residues in contact with GLN 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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279A ASP* 3.0 17.5 + - - +
280A GLU* 1.3 78.9 - - - +
282A VAL* 1.3 63.1 + - + +
284A LYS* 3.5 7.3 + - - +
285A GLU* 3.3 31.3 + - - +
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Residues in contact with VAL 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ASP* 2.9 33.2 + - + +
281A GLN* 1.3 76.6 - - + +
283A TRP* 1.3 59.0 + - - +
285A GLU* 3.1 18.4 + - - +
286A VAL* 3.0 30.4 + - + +
318A GLU* 3.6 43.3 - - + +
319A ARG 4.8 0.4 - - - -
320A LEU* 3.7 25.8 - - + +
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Residues in contact with TRP 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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276A LEU* 3.2 45.0 + - + -
277A THR 3.9 7.0 - - - -
278A GLY 3.9 2.0 + - - -
279A ASP 3.1 27.5 + - - -
280A GLU* 3.4 29.0 - - + +
282A VAL* 1.3 73.3 - - - +
284A LYS* 1.3 101.0 + - + +
286A VAL* 3.8 2.8 - - - +
287A GLN* 2.9 36.3 + - - +
320A LEU* 3.7 18.8 - - + -
324A ASN* 3.3 33.7 - - - +
326A TYR* 3.7 26.7 - + + -
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Residues in contact with LYS 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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280A GLU* 2.9 55.8 + - + +
281A GLN* 3.6 7.9 - - - +
283A TRP* 1.3 108.3 - - + +
285A GLU* 1.3 59.4 + - + +
287A GLN* 3.4 15.8 + - - +
288A GLU* 3.0 27.0 + - - +
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Residues in contact with GLU 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 GLN* 3.3 20.4 - - - +
282A VAL* 3.1 16.8 + - - +
284A LYS* 1.3 73.0 - - + +
286A VAL* 1.3 61.6 + - + +
288A GLU* 3.3 7.7 + - - +
289A SER* 2.9 35.0 + - - +
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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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282A VAL* 3.0 22.6 + - + +
283A TRP* 3.9 7.0 - - - +
285A GLU* 1.3 74.0 - - + +
287A GLN* 1.3 60.4 - - - +
289A SER* 3.2 7.7 + - - -
290A LEU* 2.9 28.5 + - + +
312A ILE* 3.8 25.8 - - + -
320A LEU* 3.8 17.5 - - + -
326A TYR* 3.9 19.7 - - + +
327A GLN* 4.4 1.8 - - - +
330A VAL* 3.6 30.5 - - + -
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Residues in contact with GLN 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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248A GLU* 3.2 11.5 + - - -
283A TRP* 2.9 24.5 + - - +
284A LYS* 3.6 23.3 + - - +
286A VAL* 1.3 76.3 - - - +
288A GLU* 1.3 64.6 + - - +
290A LEU* 3.4 15.0 + - - +
291A LYS* 3.7 10.4 + - - +
326A TYR* 3.2 48.0 + - + +
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Residues in contact with GLU 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 LYS 3.0 13.8 + - - +
285A GLU* 3.5 11.2 - - - +
286A VAL 3.2 0.2 - - - -
287A GLN* 1.3 76.9 - - - +
289A SER* 1.3 63.0 + - - +
291A LYS* 2.7 60.5 + - - +
292A LYS* 4.1 1.6 + - - +
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Residues in contact with SER 289 (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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285A GLU* 2.9 18.7 + - - +
286A VAL* 3.6 4.0 - - - -
288A GLU* 1.3 75.7 - - - +
290A LEU* 1.3 57.6 + - - +
292A LYS* 3.2 9.3 + - - +
293A ILE* 3.0 28.6 + - - +
308A MSE 3.7 16.7 - - - +
312A ILE* 4.1 21.9 - - - +
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Residues in contact with LEU 290 (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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286A VAL* 2.9 16.7 + - + +
287A GLN* 3.5 8.1 - - + +
288A GLU 3.2 0.2 - - - -
289A SER* 1.3 73.1 - - - +
291A LYS* 1.3 59.7 + - - +
293A ILE* 4.0 18.6 - - + -
294A GLU* 2.8 53.8 + - + +
326A TYR* 3.6 48.5 - - + +
329A LYS* 3.9 27.8 - - + +
330A VAL* 3.9 24.5 - - + +
333A CYS* 4.8 2.0 - - - -
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Residues in contact with LYS 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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287A GLN* 3.7 8.8 + - + +
288A GLU* 2.7 49.6 + - - +
290A LEU* 1.3 77.5 - - - +
292A LYS* 1.3 62.1 + - - +
294A GLU* 4.2 8.2 + - - +
295A GLU* 3.2 23.2 + - - +
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Residues in contact with LYS 292 (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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288A GLU 4.1 1.0 + - - +
289A SER* 3.2 11.3 + - - +
291A LYS* 1.3 77.8 - - - +
293A ILE* 1.3 63.2 + - - +
295A GLU* 3.3 9.0 + - - +
296A LEU* 3.0 31.0 + - + +
308A MSE 3.8 20.0 - - + -
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Residues in contact with ILE 293 (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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289A SER 3.0 23.4 + - - +
290A LEU* 3.8 13.5 - - + +
292A LYS* 1.3 74.1 - - - +
294A GLU* 1.3 57.4 + - - +
296A LEU* 3.2 11.2 + - + +
297A LYS* 2.9 26.9 + - - +
305A VAL* 3.8 8.6 - - + +
308A MSE 3.7 34.5 - - + +
309A CYS* 3.9 27.8 - - - -
312A ILE* 3.9 27.8 - - + -
330A VAL* 4.4 6.7 - - + -
333A CYS* 3.9 22.7 - - + -
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Residues in contact with GLU 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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290A LEU* 2.8 45.1 + - + +
291A LYS* 4.2 7.0 + - - +
293A ILE* 1.3 69.7 - - - +
295A GLU* 1.3 61.1 + - - +
297A LYS* 3.3 10.0 + - + +
298A ALA* 2.8 30.9 + - - +
329A LYS* 4.0 28.4 + - - +
333A CYS* 4.9 9.8 - - - -
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Residues in contact with GLU 295 (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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42A LYS* 4.8 8.1 + - - -
291A LYS 3.2 18.9 + - - +
292A LYS* 3.4 8.1 - - - +
294A GLU* 1.3 76.1 - - - +
296A LEU* 1.3 67.5 + - + +
298A ALA* 3.2 11.8 + - - +
299A HIS* 3.0 50.5 + - - +
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Residues in contact with LEU 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 LYS* 3.0 20.6 + - + +
293A ILE* 3.2 8.5 + - - +
295A GLU* 1.3 79.0 - - + +
297A LYS* 1.3 63.7 + - - +
299A HIS* 3.1 9.4 + - + -
301A LYS* 3.0 44.8 + - + +
304A GLN* 3.9 37.7 - - + +
305A VAL* 3.6 13.5 - - + +
308A MSE 3.7 27.1 - - - -
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Residues in contact with LYS 297 (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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190A MSE 4.8 4.9 + - - -
191A GLN* 2.8 55.6 + - - +
192A GLU* 5.5 1.8 - - - +
293A ILE 2.9 14.0 + - - +
294A GLU* 3.5 12.8 - - + +
296A LEU* 1.3 74.8 - - - +
298A ALA* 1.3 58.2 + - - +
300A TRP* 2.9 15.7 + - - +
301A LYS 4.8 0.4 - - - +
302A TRP* 4.0 14.2 - - + -
305A VAL* 3.4 13.4 - - + +
332A ASP* 5.0 6.8 + - - -
333A CYS* 3.6 31.6 - - + +
336A ASP* 4.0 28.0 + - - -
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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
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41A CYS* 5.5 3.0 - - - -
43A GLY* 3.2 24.8 - - - +
44A SER* 3.9 2.1 + - - -
191A GLN* 4.3 5.1 + - - +
192A GLU 5.5 2.9 - - - +
294A GLU 2.8 17.1 + - - +
295A GLU* 3.2 11.2 + - - +
297A LYS* 1.3 75.6 - - - +
299A HIS* 1.3 65.0 + - + +
300A TRP* 3.4 9.0 + - - -
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Residues in contact with HIS 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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42A LYS* 4.2 23.6 + - + +
43A GLY* 3.7 31.0 + - - +
47A VAL* 5.0 4.2 - - - +
295A GLU* 3.0 45.9 + - - +
296A LEU* 3.1 8.6 + - - +
297A LYS 3.1 1.0 - - - -
298A ALA* 1.3 80.9 - - + +
300A TRP* 1.3 70.3 + - - +
301A LYS* 3.1 31.3 + - + +
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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