Contacts of the helix formed by residues 380 - 393 (chain A) in PDB entry 1KNU
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 380 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A LYS* 4.6 3.6 - - - -
378A GLU 4.0 0.2 + - - -
379A LEU* 1.3 77.0 - - - +
381A ASP* 1.3 66.0 + - - +
382A SER* 2.5 29.8 + - - -
383A ASP* 2.9 22.9 + - - +
384A LEU* 3.0 14.6 + - - +
424A ASN* 2.7 28.7 + - - +
425A HIS* 4.7 1.8 + - - +
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Residues in contact with ASP 381 (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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219A TYR* 3.6 20.2 + - + +
222A TYR* 2.6 45.5 + - + -
223A ILE* 5.2 0.6 - - + +
229A THR* 3.2 12.0 - - + +
230A LYS* 2.8 24.7 + - - +
231A ALA* 3.0 31.7 + - - +
380A ASP* 1.3 73.9 - - - +
382A SER* 1.3 57.0 + - - +
384A LEU* 3.2 5.1 + - - +
385A ALA* 3.0 30.3 + - - +
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Residues in contact with SER 382 (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 ALA 5.5 0.5 - - - +
219A TYR* 3.5 40.8 + - - +
380A ASP* 2.5 27.1 + - - -
381A ASP* 1.3 75.2 - - - +
383A ASP* 1.3 61.2 + - - +
385A ALA* 3.9 5.2 + - - +
386A ILE* 3.7 18.0 - - - +
420A GLN* 3.0 27.5 + - - -
424A ASN* 3.7 2.3 + - - -
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Residues in contact with ASP 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A LEU* 3.8 13.3 - - + -
380A ASP 2.9 22.6 + - - +
382A SER* 1.3 79.2 + - - +
384A LEU* 1.3 68.0 + - - +
386A ILE* 3.2 7.3 + - - +
387A PHE* 3.2 20.1 + - - +
417A LEU* 4.1 5.2 - - + +
420A GLN* 3.0 31.9 + - - +
421A LEU* 3.7 19.8 - - + +
424A ASN* 3.2 13.4 + - - +
425A HIS* 2.8 31.1 - - - -
435A LEU* 6.0 0.2 - - + -
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Residues in contact with LEU 384 (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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222A TYR* 3.6 24.7 - - + +
230A LYS* 4.3 12.6 - - + +
328A THR* 4.2 18.2 - - + +
329A MET* 5.7 4.7 - - + -
332A SER* 3.7 22.7 - - - +
374A PHE* 4.1 28.3 - - + -
379A LEU* 4.3 12.8 - - + +
380A ASP 3.0 17.0 + - - +
381A ASP* 3.6 12.3 - - - +
383A ASP* 1.3 74.1 - - - +
385A ALA* 1.3 67.2 + - - +
386A ILE 2.9 0.3 + - - -
387A PHE* 3.0 8.7 + - + -
388A ILE* 2.8 33.5 + - + +
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Residues in contact with ALA 385 (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 ALA 5.5 0.2 - - - +
218A LEU* 3.8 20.2 - - + +
219A TYR* 3.8 12.3 - - - +
222A TYR* 3.8 20.5 - - + -
299A TYR* 2.6 30.1 + - - +
381A ASP 3.0 16.7 + - - +
382A SER 4.0 5.6 - - - +
383A ASP 3.4 0.2 - - - -
384A LEU* 1.3 76.6 - - - +
386A ILE* 1.3 62.8 + - + +
388A ILE* 3.7 2.0 + - - +
389A ALA* 3.3 12.3 + - - +
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Residues in contact with ILE 386 (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 ALA* 3.8 26.0 - - + +
218A LEU* 4.2 20.6 - - + -
382A SER 3.7 12.1 - - - +
383A ASP 3.2 4.2 + - - +
384A LEU 3.1 0.6 - - - -
385A ALA* 1.3 77.1 - - + +
387A PHE* 1.3 60.4 + - - +
389A ALA* 2.9 22.0 + - - +
390A VAL* 2.9 12.7 + - + +
413A LEU* 3.7 18.6 - - + +
416A ALA* 3.9 11.7 - - + +
417A LEU* 3.5 25.6 - - + +
420A GLN* 3.6 36.6 - - + -
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Residues in contact with PHE 387 (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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328A THR* 3.7 28.9 - - + -
374A PHE* 4.0 15.0 - + - -
379A LEU* 5.6 0.2 - - + -
383A ASP 3.2 11.3 + - - +
384A LEU* 3.0 13.8 + - + +
386A ILE* 1.3 77.0 - - - +
388A ILE* 1.3 59.6 + - - +
390A VAL* 3.2 7.0 + - + +
391A ILE* 3.1 50.2 + - + +
417A LEU* 4.0 15.8 - - + +
435A LEU* 3.7 53.8 - - + -
436A LEU* 5.2 5.2 - - + -
438A LYS* 5.2 1.3 - - + -
439A MET* 3.9 24.7 - - + -
442A LEU* 4.4 6.3 - - + -
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Residues in contact with ILE 388 (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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222A TYR* 4.1 13.7 - - + -
226A PHE* 5.0 1.6 - - + -
296A ILE* 5.4 0.4 - - + -
299A TYR* 3.8 23.3 - - + -
325A ILE* 3.7 28.0 - - + -
328A THR* 4.7 13.7 - - + -
329A MET* 3.4 46.9 - - + -
384A LEU* 2.8 24.1 + - + +
385A ALA 3.8 3.8 - - - +
387A PHE* 1.3 76.5 - - + +
389A ALA* 1.3 62.6 + - - +
391A ILE* 3.4 10.7 + - + +
392A ILE* 3.2 23.6 + - + +
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Residues in contact with ALA 389 (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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218A LEU* 4.4 3.6 - - + -
299A TYR* 4.2 6.5 - - - +
303A ILE* 3.8 27.1 - - + -
385A ALA 3.3 11.7 + - - +
386A ILE* 2.9 13.6 + - - +
388A ILE* 1.3 78.3 - - - +
390A VAL* 1.3 63.5 + - - +
392A ILE 3.8 0.4 + - - -
393A LEU* 3.4 17.8 + - - +
413A LEU* 3.2 35.4 - - + +
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Residues in contact with VAL 390 (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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386A ILE 2.9 16.3 + - - +
387A PHE* 3.2 12.5 + - + +
389A ALA* 1.3 75.8 - - - +
391A ILE* 1.3 68.6 + - + +
393A LEU 3.3 7.6 + - - +
394A SER* 3.8 1.0 + - - -
410A GLN* 3.2 28.7 - - + +
413A LEU* 3.9 25.8 - - + -
414A LEU* 4.0 35.0 - - + +
417A LEU* 4.3 14.1 - - + -
436A LEU* 4.9 8.1 - - + -
439A MET* 4.9 10.8 - - + -
437B GLN* 5.4 3.4 - - - +
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Residues in contact with ILE 391 (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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321A GLY* 4.2 1.6 - - - +
324A GLU* 3.4 36.1 - - + +
325A ILE* 4.0 15.0 - - + -
328A THR* 4.1 12.6 - - + +
387A PHE* 3.1 45.0 + - + +
388A ILE* 3.6 11.7 - - - +
389A ALA 3.4 0.2 - - - -
390A VAL* 1.3 77.6 - - - +
392A ILE* 1.3 61.4 + - - +
394A SER* 2.7 24.3 + - - -
397A ARG* 3.2 12.0 + - - +
439A MET* 3.5 21.8 - - + -
442A LEU* 4.1 10.8 - - + -
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Residues in contact with ILE 392 (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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296A ILE* 4.2 9.9 - - + -
299A TYR* 4.5 8.1 - - + -
300A ALA* 3.7 25.1 - - + -
303A ILE* 3.9 13.7 - - + -
306A PHE* 3.8 23.1 - - + -
317A LEU* 3.3 33.7 - - + +
318A LEU* 5.3 5.4 - - + +
321A GLY* 5.1 3.8 - - - -
325A ILE* 3.2 31.9 - - + -
388A ILE 3.2 9.0 + - - +
389A ALA 4.0 1.8 - - - +
390A VAL 3.3 0.2 - - - -
391A ILE* 1.3 78.7 - - - +
393A LEU* 1.3 77.7 + - + +
394A SER* 3.0 7.1 + - - -
397A ARG* 4.9 1.8 + - - +
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Residues in contact with LEU 393 (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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303A ILE* 4.0 16.8 - - + -
306A PHE* 4.2 11.4 - - + -
309A LEU* 4.2 17.7 - - + -
317A LEU* 4.5 4.3 - - + -
389A ALA 3.4 17.2 + - - +
390A VAL 3.3 3.9 + - - +
391A ILE 3.3 0.8 - - - -
392A ILE* 1.3 93.7 - - + +
394A SER* 1.3 53.0 + - - +
395A GLY 3.8 1.6 + - - -
406A ILE* 4.0 17.3 - - + +
409A ILE* 3.7 43.5 - - + -
410A GLN* 2.5 47.3 - - + +
413A LEU* 4.0 2.2 - - + -
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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
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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