Contacts of the helix formed by residues 379 - 397 (chain A) in PDB entry 1YCH
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 ARG 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375A GLN 5.9 0.9 - - - -
377A VAL* 4.4 9.0 - - + +
378A PRO* 1.3 76.2 - - - +
380A GLY* 1.3 66.2 + - - +
381A GLU* 2.4 36.9 + - - +
382A ASP* 2.4 65.2 + - - +
383A LEU* 3.1 15.9 + - - +
385A ARG* 3.9 8.5 - - - +
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Residues in contact with GLY 380 (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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379A ARG* 1.3 72.9 - - - +
381A GLU* 1.3 60.8 + - - +
383A LEU* 3.3 8.0 + - - +
384A GLN* 3.0 27.2 + - - +
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Residues in contact with GLU 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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379A ARG* 2.4 51.7 - - + +
380A GLY* 1.3 71.2 + - - -
382A ASP* 1.3 56.0 + - - +
384A GLN* 3.3 8.7 - - - +
385A ARG* 2.7 54.8 + - - +
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Residues in contact with ASP 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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373A THR 4.9 1.3 - - - +
374A VAL* 3.6 34.1 - - + +
375A GLN 5.3 0.9 + - - -
378A PRO* 3.9 4.3 - - + +
379A ARG* 2.4 68.0 + - - +
381A GLU* 1.3 84.3 + - - +
383A LEU* 1.3 61.0 + - - +
385A ARG* 2.9 29.1 + - - +
386A CYS* 3.1 26.7 + - - -
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Residues in contact with LEU 383 (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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268A LYS* 3.6 39.5 - - + +
269A MET* 4.2 6.7 - - + -
272A ALA* 3.6 15.3 - - + +
378A PRO* 3.7 27.6 - - + +
379A ARG 3.1 13.6 + - - +
380A GLY* 3.8 8.1 - - - +
382A ASP* 1.3 73.5 - - - +
384A GLN* 1.3 60.0 + - - +
386A CYS* 3.3 4.0 + - - +
387A TYR* 2.8 28.9 + - - +
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Residues in contact with GLN 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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380A GLY 3.0 14.5 + - - +
381A GLU* 3.3 14.1 - - - +
383A LEU* 1.3 75.9 - - - +
385A ARG* 1.3 58.9 + - - +
387A TYR* 3.1 20.4 + - - +
388A GLU* 2.9 63.5 + - + +
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Residues in contact with ARG 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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372A PRO* 6.1 6.6 - - + +
373A THR 4.9 9.3 + - - +
374A VAL* 5.6 0.4 - - - +
379A ARG* 3.9 5.1 - - - +
381A GLU* 2.7 30.8 + - - +
382A ASP* 2.9 50.4 + - - +
384A GLN* 1.3 73.1 - - - +
386A CYS* 1.3 62.6 + - - +
388A GLU* 3.0 10.7 + - + +
389A LEU* 2.9 33.0 + - + +
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Residues in contact with CYS 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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269A MET* 3.9 36.3 - - - -
272A ALA* 3.6 13.9 - - + -
273A LEU* 3.5 22.1 - - + +
372A PRO* 4.1 21.7 - - - +
374A VAL* 5.7 1.8 - - - -
382A ASP 3.1 16.8 + - - -
383A LEU* 3.5 9.0 - - - +
385A ARG* 1.3 77.1 - - - +
387A TYR* 1.3 63.9 + - - +
389A LEU* 3.0 11.8 + - - +
390A GLY* 2.9 21.1 + - - -
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Residues in contact with TYR 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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272A ALA* 3.6 13.4 + - + +
275A ASP* 3.8 19.1 - - + -
276A GLY* 3.3 30.5 - - - -
279A ALA* 3.3 22.7 - - + +
383A LEU 2.8 14.5 + - - +
384A GLN* 3.3 22.0 - - - +
386A CYS* 1.3 78.3 - - - +
388A GLU* 1.3 79.2 + - - +
390A GLY 3.3 1.2 + - - -
391A ARG* 3.0 43.5 + - - +
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Residues in contact with GLU 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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384A GLN* 2.9 43.2 + - + +
385A ARG* 3.0 12.3 + - + +
387A TYR* 1.3 90.6 - - - +
389A LEU* 1.3 52.9 + - + +
391A ARG* 3.0 15.5 - - - +
392A LYS* 2.7 33.3 + - - +
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Residues in contact with LEU 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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273A LEU* 4.1 8.3 - - + -
340A LEU* 4.3 7.9 - - + -
367A ILE* 4.2 23.3 - - + -
368A ALA* 4.4 14.1 - - + -
371A GLY 5.5 0.2 - - - -
372A PRO* 3.2 36.8 - - + -
385A ARG* 2.9 22.2 + - + +
386A CYS* 3.0 9.4 + - - +
388A GLU* 1.3 75.1 - - + +
390A GLY* 1.3 61.0 + - - +
392A LYS* 3.1 18.5 + - + +
393A ILE* 2.9 34.4 + - - +
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Residues in contact with GLY 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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273A LEU* 3.6 29.7 - - - +
276A GLY 3.6 7.2 - - - -
277A LEU* 3.5 17.4 - - - +
386A CYS 2.9 11.8 + - - -
387A TYR 3.7 2.5 - - - -
388A GLU 3.3 0.2 - - - -
389A LEU* 1.3 76.1 - - - +
391A ARG* 1.3 56.2 + - - +
393A ILE* 3.6 2.9 + - - -
394A ALA* 3.0 28.8 + - - +
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Residues in contact with ARG 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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276A GLY 3.7 14.5 - - - -
279A ALA* 4.2 13.1 + - - +
280A GLY* 3.5 23.7 - - - -
387A TYR* 3.0 40.9 + - - +
388A GLU* 3.0 25.6 - - - +
390A GLY* 1.3 78.7 - - - +
392A LYS* 1.3 59.7 + - - +
394A ALA* 3.3 5.1 - - - +
395A ALA* 3.1 23.5 + - - +
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Residues in contact with LYS 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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367A ILE* 3.6 40.8 + - + +
368A ALA* 5.4 1.8 - - - +
388A GLU 2.7 12.2 + - - +
389A LEU* 3.1 20.6 + - + +
391A ARG* 1.3 73.4 - - - +
393A ILE* 1.3 66.4 + - + +
395A ALA* 3.0 23.9 + - + +
396A ARG* 3.1 8.0 + - + +
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Residues in contact with ILE 393 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A LEU* 5.3 0.2 - - + -
277A LEU* 3.8 8.1 - - + -
306A ALA* 3.8 13.9 - - + -
308A LEU* 3.4 34.8 - - + -
338A VAL* 4.9 8.3 - - + -
339A GLY* 4.9 2.7 - - - +
340A LEU* 4.1 9.2 - - + -
367A ILE* 3.6 37.5 - - + -
389A LEU 2.9 21.5 + - - +
390A GLY* 3.9 7.0 - - - +
392A LYS* 1.3 74.6 - - - +
394A ALA* 1.3 57.3 + - - +
396A ARG* 3.2 7.5 + - - +
397A ILE* 2.9 48.7 + - + +
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Residues in contact with ALA 394 (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 16.2 - - + +
280A GLY* 3.6 40.0 - - - +
282A CYS* 4.6 4.7 - - + -
390A GLY 3.0 15.2 + - - +
391A ARG* 3.3 10.8 - - - +
392A LYS 3.1 0.2 - - - -
393A ILE* 1.3 75.9 - - - +
395A ALA* 1.3 58.8 + - - +
397A ILE* 3.4 8.1 + - - +
398A ALA* 3.0 25.8 + - - +
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Residues in contact with ALA 395 (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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391A ARG* 3.1 12.6 + - - +
392A LYS* 3.0 14.7 + - + +
394A ALA* 1.3 80.7 - - - +
396A ARG* 1.3 60.1 + - - +
398A ALA* 3.2 19.3 - - - +
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Residues in contact with ARG 396 (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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338A VAL* 3.9 24.7 - - + +
365A GLU* 2.5 47.4 + - - +
366A LEU 5.5 0.4 + - - -
367A ILE* 4.1 31.7 - - + +
392A LYS 3.1 9.2 + - - +
393A ILE* 3.2 9.2 + - - +
395A ALA* 1.3 76.9 - - - +
397A ILE* 1.3 58.0 + - + +
398A ALA* 2.8 14.8 + - - +
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Residues in contact with ILE 397 (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 ALA* 3.5 29.8 - - + -
254A LYS 4.0 7.0 - - - +
255A ALA* 4.1 3.6 - - + -
277A LEU* 4.2 1.6 - - + -
282A CYS* 3.6 25.6 - - - -
305A ARG* 3.1 38.0 + - + +
306A ALA* 3.3 32.3 - - + -
338A VAL* 5.6 4.9 - - + -
393A ILE* 2.9 30.8 + - + +
394A ALA* 3.7 5.6 - - - +
396A ARG* 1.3 74.0 - - + +
398A ALA* 1.3 64.9 + - - +
399A ASP 3.0 3.2 + - - -
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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