Contacts of the helix formed by residues 376 - 398 (chain A) in PDB entry 4YON
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 THR 376 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A ASN* 3.5 18.2 - - - +
374A ALA* 3.8 0.9 - - - +
375A LYS* 1.3 88.9 - - + +
377A ALA* 1.3 63.1 + - - +
378A GLU* 3.6 9.6 + - - +
379A GLU* 3.1 24.7 + - - +
380A LYS 3.1 17.5 + - - -
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Residues in contact with ALA 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A ASN* 3.4 19.2 + - - +
376A THR* 1.3 72.2 - - - +
378A GLU* 1.3 60.4 + - - +
380A LYS* 3.3 7.6 + - + +
381A GLN* 3.0 29.2 + - - +
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Residues in contact with GLU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A THR* 3.2 9.6 + - - +
377A ALA* 1.3 80.0 - - - +
379A GLU* 1.3 57.4 + - - +
381A GLN* 3.3 9.5 + - - +
382A LYS* 3.0 29.1 + - + +
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Residues in contact with GLU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A GLY* 5.5 2.1 - - - -
277A THR 4.0 19.9 + - - +
278A LEU* 4.6 2.4 - - - +
374A ALA* 3.4 10.2 - - + +
375A LYS* 2.9 41.7 + - - +
376A THR* 3.1 21.1 + - - +
378A GLU* 1.3 75.0 - - - +
380A LYS* 1.3 66.2 + - - +
382A LYS* 3.3 23.3 + - - +
383A TRP* 3.1 40.9 + - + +
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Residues in contact with LYS 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ASN* 2.8 27.0 + - - +
341A VAL 3.2 11.7 + - - -
343A ASP* 4.8 3.8 + - - -
357A ASN* 3.5 28.9 - - - +
358A GLY 2.8 26.9 + - - +
359A TRP* 3.7 24.9 - - + -
374A ALA* 3.7 1.7 - - + +
376A THR 3.1 13.2 + - - +
377A ALA* 3.5 10.3 - - - +
379A GLU* 1.3 77.0 - - - +
381A GLN* 1.3 62.8 + - - +
383A TRP* 3.2 3.1 + - - +
384A LEU* 3.0 39.5 + - + +
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Residues in contact with GLN 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ALA 3.0 17.7 + - - +
378A GLU* 3.6 9.1 - - - +
380A LYS* 1.3 78.5 - - - +
382A LYS* 1.3 56.6 + - - +
384A LEU* 4.2 4.7 - - - +
385A ASP* 2.9 58.5 + - - +
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Residues in contact with LYS 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LEU* 4.1 31.9 - - + +
275A GLN 5.1 4.4 + - - -
378A GLU* 3.0 15.5 + - + +
379A GLU* 3.5 32.2 + - - +
380A LYS 3.2 0.2 - - - -
381A GLN* 1.3 77.8 - - - +
383A TRP* 1.3 64.6 + - - +
385A ASP* 3.7 6.2 + - - +
386A ALA* 3.1 23.2 + - - +
389A ARG* 5.3 0.5 + - - -
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Residues in contact with TRP 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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274A LEU* 3.5 33.4 - - + +
275A GLN 4.0 3.3 + - - -
276A GLY* 3.6 30.2 - - - -
278A LEU* 3.8 32.6 - - + +
291A PHE* 3.4 39.9 - + + -
292A PHE 4.4 0.4 - - - -
293A LEU* 4.1 20.2 - - + -
298A LEU* 4.3 9.6 - - + -
359A TRP* 3.6 26.9 - + + -
379A GLU* 3.1 33.5 + - + +
380A LYS 3.7 2.7 - - - +
382A LYS* 1.3 80.5 - - - +
384A LEU* 1.3 60.4 + - - +
386A ALA* 3.3 2.6 + - - +
387A ILE* 3.0 47.1 + - + +
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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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338A VAL* 3.7 32.5 - - + -
340A ASN* 4.6 10.8 - - + +
359A TRP* 3.7 27.1 - - + +
380A LYS* 3.0 43.7 + - + +
381A GLN* 4.2 4.3 - - - +
383A TRP* 1.3 74.3 - - - +
385A ASP* 1.3 68.4 + - - +
387A ILE* 3.4 6.8 + - + +
388A ILE* 3.1 36.3 + - + +
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Residues in contact with ASP 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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381A GLN* 2.9 48.3 + - - +
382A LYS* 3.8 6.5 + - - +
384A LEU* 1.3 79.3 - - - +
386A ALA* 1.3 57.4 + - - +
388A ILE* 3.7 10.1 - - - +
389A ARG* 2.9 51.5 + - - +
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Residues in contact with ALA 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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273A LEU* 5.2 5.2 - - + +
274A LEU* 3.8 23.3 - - + -
293A LEU* 3.7 14.2 - - + +
382A LYS 3.1 17.1 + - - +
383A TRP 3.6 4.3 - - - +
384A LEU 3.2 0.2 - - - -
385A ASP* 1.3 76.5 - - - +
387A ILE* 1.3 61.3 + - - +
389A ARG* 3.3 17.3 + - - +
390A GLU* 2.9 30.0 + - - +
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Residues in contact with ILE 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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293A LEU* 4.1 18.4 - - + -
298A LEU* 6.1 3.4 - - + -
336A MET* 3.8 25.8 - - + -
338A VAL* 4.1 22.7 - - + -
359A TRP* 4.4 11.9 - - - +
361A ILE* 4.2 23.6 - - + -
383A TRP* 3.0 36.1 + - + +
384A LEU* 3.8 13.0 - - + +
385A ASP 3.3 0.2 - - - -
386A ALA* 1.3 72.9 - - - +
388A ILE* 1.3 66.5 + - + +
390A GLU* 3.5 5.1 + - - +
391A ARG* 3.2 30.6 + - - +
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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
----------------------------------------------------------
338A VAL* 5.6 7.2 - - + -
384A LEU* 3.1 28.0 + - + +
385A ASP* 3.7 10.1 - - - +
387A ILE* 1.3 78.2 - - + +
389A ARG* 1.3 59.0 + - - +
391A ARG* 3.3 15.2 + - - +
392A GLU* 2.9 41.6 + - + +
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Residues in contact with ARG 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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382A LYS 5.3 0.4 + - - -
385A ASP* 2.9 36.6 + - - +
386A ALA* 3.6 33.1 - - - +
388A ILE* 1.3 80.2 - - - +
390A GLU* 1.3 62.4 + - - +
392A GLU* 3.4 5.9 + - - +
393A GLN* 3.0 51.9 + - + +
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Residues in contact with GLU 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LEU* 3.6 31.1 - - + +
293A LEU* 4.3 8.9 - - + +
294A PHE 3.6 9.6 - - - +
295A ASP* 3.8 5.5 - - + +
296A ASN 2.8 24.1 + - - -
333A THR* 2.9 24.1 + - - +
336A MET* 5.8 0.7 - - - +
386A ALA 2.9 17.8 + - - +
387A ILE* 3.8 6.0 - - - +
389A ARG* 1.3 75.2 - - - +
391A ARG* 1.3 58.8 + - - +
393A GLN* 4.1 5.0 - - - +
394A ARG* 3.0 57.9 + - - +
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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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333A THR 5.4 0.4 + - - -
336A MET* 3.3 26.4 + - - +
337A GLU* 3.9 15.8 - - - +
338A VAL* 4.2 19.4 - - - +
387A ILE* 3.2 19.4 + - - +
388A ILE* 3.7 16.4 - - - +
389A ARG 3.3 0.2 - - - -
390A GLU* 1.3 79.4 + - - +
392A GLU* 1.3 63.0 + - - +
394A ARG* 3.4 26.6 + - - +
395A GLU* 2.9 58.6 + - + +
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Residues in contact with GLU 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ILE* 2.9 34.4 + - + +
389A ARG* 3.7 7.2 - - + +
391A ARG* 1.3 79.6 - - + +
393A GLN* 1.3 58.9 + - + +
395A GLU* 3.4 17.0 + - - +
396A SER* 2.9 34.7 + - - +
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Residues in contact with GLN 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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271A GLN* 5.3 6.9 + - - -
273A LEU* 5.3 7.6 - - - +
389A ARG* 3.0 41.2 + - + +
390A GLU* 4.1 4.4 - - - +
392A GLU* 1.3 77.1 - - + +
394A ARG* 1.3 57.8 + - - +
396A SER* 3.3 7.2 + - - -
397A LEU* 3.0 37.4 + - + +
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Residues in contact with ARG 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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295A ASP* 6.6 0.2 - - + -
296A ASN* 3.4 26.2 - - - +
332A ASN* 5.8 0.2 - - - -
333A THR* 3.3 27.2 + - - -
334A GLU* 3.6 28.6 - - - +
390A GLU* 3.0 47.6 + - - +
391A ARG* 3.5 29.4 - - - +
392A GLU 3.3 0.2 - - - -
393A GLN* 1.3 78.0 - - - +
395A GLU* 1.3 69.4 + - - +
397A LEU* 3.5 11.1 + - - +
398A LYS* 3.3 33.1 + - - +
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Residues in contact with GLU 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* 2.9 44.7 + - + +
392A GLU* 3.8 17.5 - - - +
394A ARG* 1.3 84.6 + - - +
396A SER* 1.3 64.4 + - - +
398A LYS* 3.3 31.0 + - + +
399A LEU 3.7 10.9 - - - +
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Residues in contact with SER 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A GLU* 2.9 24.9 + - - +
393A GLN* 3.3 8.7 + - - -
395A GLU* 1.3 73.8 - - - +
397A LEU* 1.3 60.2 + - - +
398A LYS 3.0 1.6 - - - -
399A LEU* 2.9 25.2 + - - +
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Residues in contact with LEU 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A GLN* 3.0 22.3 + - + +
394A ARG* 3.8 9.6 - - - +
395A GLU 3.4 0.2 - - - -
396A SER* 1.3 75.6 - - - +
398A LYS* 1.3 57.2 + - - +
399A LEU* 3.0 18.3 + - - +
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Residues in contact with LYS 398 (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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334A GLU* 4.5 19.4 + - - +
394A ARG* 3.3 26.6 + - - +
395A GLU* 3.4 26.4 - - - +
396A SER 3.0 1.2 - - - -
397A LEU* 1.3 76.2 - - - +
399A LEU* 1.3 72.6 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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