Contacts of the helix formed by residues 290 - 309 (chain A) in PDB entry 3KMU
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 290 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A VAL 3.4 3.2 + - - +
289A VAL* 1.3 78.2 - - - +
291A GLN* 1.3 59.6 + - - +
292A SER* 3.2 12.6 + - - -
293A GLN* 2.8 38.4 + - - +
294A ALA 3.0 21.5 + - - -
388A ARG* 3.5 4.3 + - - -
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Residues in contact with GLN 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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290A ASP* 1.3 74.3 - - - +
292A SER* 1.3 60.8 + - - +
294A ALA* 3.2 13.3 + - - +
295A VAL* 2.9 41.2 + - + +
385A LEU* 3.2 27.0 + - - +
386A VAL* 4.0 16.7 - - - +
388A ARG* 2.8 28.4 + - - +
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Residues in contact with SER 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ASP* 3.2 13.3 + - - -
291A GLN* 1.3 77.9 - - - +
293A GLN* 1.3 61.7 + - - +
295A VAL* 3.4 8.6 + - - +
296A LYS* 3.1 22.2 + - - +
451A ASP* 4.2 22.9 + - - -
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Residues in contact with GLN 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A VAL* 4.2 4.9 - - + -
290A ASP* 2.8 26.9 + - - +
292A SER* 1.3 78.5 - - - +
294A ALA* 1.3 56.0 + - - +
296A LYS* 3.2 17.0 + - - +
297A PHE* 2.8 60.0 + - + -
331A MSE 3.5 44.9 - - + +
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Residues in contact with ALA 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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289A VAL* 5.1 1.3 - - + +
290A ASP 3.0 13.3 + - - +
291A GLN* 3.2 24.8 + - - +
293A GLN* 1.3 72.1 - - - +
295A VAL* 1.3 65.2 + - - +
297A PHE* 3.2 9.3 + - - +
298A ALA* 3.0 22.4 + - - +
385A LEU* 3.7 29.3 - - + +
388A ARG* 3.8 17.5 - - - +
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Residues in contact with VAL 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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291A GLN* 2.9 25.5 + - + +
292A SER* 3.7 9.4 - - - +
293A GLN 3.3 0.2 - - - -
294A ALA* 1.3 75.9 - - + +
296A LYS* 1.3 57.2 + - - +
298A ALA* 3.2 8.5 + - - +
299A LEU* 3.0 26.7 + - + +
446A LEU* 4.1 10.9 - - + +
449A MSE 4.0 57.0 - - + +
450A GLN* 4.0 11.4 - - + +
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Residues in contact with LYS 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 SER 3.1 13.4 + - - +
293A GLN* 3.2 24.2 + - - +
295A VAL* 1.3 78.5 - - - +
297A PHE* 1.3 56.6 + - - +
299A LEU* 3.3 7.4 + - + +
300A ASP* 2.8 65.7 + - - +
303A ARG* 5.0 9.4 - - - +
331A MSE 5.3 1.3 - - - +
332A THR* 5.0 8.7 + - - +
450A GLN* 3.6 28.2 - - + +
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Residues in contact with PHE 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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277A LEU* 3.5 30.7 - - + -
280A VAL* 4.2 13.9 - - + -
281A LEU* 4.6 0.4 - - + -
289A VAL* 4.2 12.1 - - + -
293A GLN* 2.8 44.8 + - + -
294A ALA* 3.2 7.6 + - - +
296A LYS* 1.3 74.8 - - - +
298A ALA* 1.3 57.4 + - - +
300A ASP* 3.3 6.0 + - - +
301A MSE 2.9 45.7 + - + +
327A ILE* 3.8 26.0 - - + -
331A MSE 3.1 43.3 - - + -
333A ALA* 4.2 8.5 - - + -
385A LEU* 4.2 13.2 - - + -
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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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294A ALA 3.0 12.5 + - - +
295A VAL* 3.4 11.7 - - - +
297A PHE* 1.3 74.4 - - - +
299A LEU* 1.3 57.6 + - - +
301A MSE 3.4 13.1 + - - +
302A ALA* 2.9 30.5 + - - +
378A PHE* 3.4 7.3 - - + -
382A LEU* 4.1 20.6 - - + -
385A LEU* 4.1 7.0 - - + -
446A LEU* 3.9 21.5 - - + -
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Residues in contact with LEU 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 VAL 3.0 15.9 + - - +
296A LYS* 3.7 8.7 - - + +
298A ALA* 1.3 72.2 - - - +
300A ASP* 1.3 61.1 + - - +
302A ALA* 3.3 0.5 + - - +
303A ARG* 2.9 62.8 + - - +
443A VAL* 3.6 33.0 - - + +
446A LEU* 4.0 18.7 - - + +
447A GLU* 3.9 12.6 - - + +
450A GLN* 3.4 41.7 - - + +
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Residues in contact with ASP 300 (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 ASN* 3.2 39.1 + - - +
296A LYS* 2.8 52.3 + - - +
297A PHE* 3.5 5.1 - - - +
299A LEU* 1.3 77.4 - - - +
301A MSE 1.3 57.8 + - - +
303A ARG* 3.3 7.3 + - - -
304A GLY 3.0 23.9 + - - -
331A MSE 4.1 1.4 - - - +
332A THR* 3.4 10.8 - - - +
333A ALA* 2.9 32.2 + - + +
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Residues in contact with MSE 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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277A LEU* 4.0 19.7 - - + -
297A PHE* 2.9 26.1 + - + +
298A ALA* 3.9 14.8 - - - +
300A ASP* 1.3 75.9 - - - +
302A ALA* 1.3 57.5 + - - +
304A GLY 3.3 1.0 + - - -
305A MSE 2.8 37.5 + - + +
320A LEU* 5.0 1.6 - - + -
325A VAL* 3.7 43.1 - - + -
333A ALA* 4.0 6.5 - - + -
335A ILE* 4.1 15.3 - - + +
378A PHE* 4.0 12.6 - - + -
381A LEU* 4.0 25.1 - - + -
385A LEU* 4.0 17.9 - - + -
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Residues in contact with ALA 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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298A ALA 2.9 17.7 + - - +
299A LEU 3.7 4.0 - - - +
301A MSE 1.3 76.2 - - - +
303A ARG* 1.3 53.8 + - - +
305A MSE 3.4 0.2 + - - -
306A ALA* 2.8 36.4 + - - +
378A PHE* 3.9 9.3 - - + -
439A PHE* 3.7 15.1 - - + +
442A ILE* 4.1 11.7 - - + -
443A VAL* 3.7 15.0 - - + -
446A LEU* 3.7 20.2 - - + -
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Residues in contact with ARG 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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247A HIS* 3.6 21.5 - - + +
249A ASN* 3.5 22.4 + - - +
296A LYS* 5.0 7.1 - - - +
299A LEU* 2.9 43.2 + - + +
300A ASP* 3.6 8.8 + - - +
302A ALA* 1.3 74.8 - - - +
304A GLY* 1.3 63.4 + - - +
306A ALA* 3.4 3.9 + - - +
307A PHE 3.1 17.7 + - - -
443A VAL* 3.9 21.3 - - + +
447A GLU* 2.8 37.6 + - - +
450A GLN* 4.8 3.8 - - - +
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Residues in contact with GLY 304 (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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247A HIS* 4.1 7.2 - - - -
249A ASN* 3.8 28.9 - - - +
250A VAL* 4.0 2.5 - - - +
300A ASP 3.0 11.3 + - - -
301A MSE 3.7 2.9 - - - -
303A ARG* 1.3 77.6 - - - +
305A MSE 1.3 56.1 + - - +
307A PHE* 3.2 4.4 + - - +
308A LEU* 2.9 31.9 + - - +
335A ILE* 4.2 9.6 - - - -
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Residues in contact with MSE 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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301A MSE 2.8 26.1 + - - +
304A GLY* 1.3 70.1 - - - +
306A ALA* 1.3 62.4 + - - +
308A LEU* 3.2 7.2 + - + +
309A HIS* 2.8 63.4 + - + +
318A HIS* 3.6 32.1 - - + +
320A LEU* 3.9 20.2 - - + -
335A ILE* 4.0 18.8 - - + -
374A ASP* 3.6 23.8 - - + +
439A PHE* 3.6 32.1 - - + -
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Residues in contact with ALA 306 (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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302A ALA 2.8 19.2 + - - +
303A ARG* 3.7 7.9 - - - +
305A MSE 1.3 75.1 - - - +
307A PHE* 1.3 61.5 + - - +
309A HIS* 3.3 12.3 + - - +
310A THR* 3.2 19.9 + - - +
439A PHE* 3.7 19.0 - - + +
440A ASP* 4.0 22.2 - - + +
443A VAL* 4.5 3.8 - - + -
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Residues in contact with PHE 307 (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 ILE* 3.7 25.6 - - + -
246A SER* 3.4 25.4 - - - -
247A HIS* 3.5 41.1 - + + +
250A VAL* 4.1 9.2 - - + -
303A ARG 3.1 8.7 + - - +
304A GLY 3.4 7.0 - - - +
306A ALA* 1.3 79.3 - - - +
308A LEU* 1.3 64.2 + - + +
310A THR* 2.6 42.8 + - + -
311A LEU* 3.8 22.3 + - + +
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Residues in contact with LEU 308 (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 ILE* 3.8 28.9 - - + -
250A VAL* 4.0 14.6 - - + -
304A GLY 2.9 21.2 + - - +
305A MSE 3.2 11.4 + - + +
307A PHE* 1.3 78.2 - - + +
309A HIS* 1.3 63.2 + - + +
310A THR 3.1 0.2 - - - -
311A LEU* 3.1 36.4 + - + +
314A LEU* 3.7 8.3 - - - +
315A ILE* 5.3 5.9 + - + +
318A HIS* 4.1 15.0 - - + +
335A ILE* 3.9 20.2 - - + -
337A MSE 3.7 26.5 - - + -
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Residues in contact with HIS 309 (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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305A MSE 2.8 29.3 + - + +
306A ALA* 3.7 8.3 - - - +
307A PHE 3.1 0.4 - - - -
308A LEU* 1.3 78.3 - - + +
310A THR* 1.3 57.7 + - - +
311A LEU 3.3 0.4 - - - -
314A LEU* 3.7 13.0 - - + +
371A ARG* 2.9 88.8 + - + +
374A ASP* 2.8 24.7 + - - -
438A LYS* 5.8 7.2 + - - +
439A PHE* 3.5 32.2 + + - +
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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
------------------------------------------------------------
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