Contacts of the helix formed by residues 362 - 384 (chain A) in PDB entry 2ADS
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 TYR 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A VAL* 1.3 86.8 - - + +
363A LYS* 1.3 63.8 + - - +
364A LYS* 3.5 3.3 + - + +
365A LEU* 3.6 28.3 + - + +
366A GLU* 3.4 16.4 + - - +
427A TYR* 3.0 51.5 + + + +
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Residues in contact with LYS 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A VAL 3.3 5.9 + - - +
362A TYR* 1.3 71.5 - - - +
364A LYS* 1.3 68.0 + - + +
366A GLU* 3.1 35.2 + - - +
367A TRP* 3.5 20.6 - - + +
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Residues in contact with LYS 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A TYR* 3.4 2.5 - - + -
363A LYS* 1.3 79.2 - - + +
365A LEU* 1.3 69.1 + - + +
366A GLU 3.4 0.7 + - - -
367A TRP* 3.5 25.8 + - - +
368A ARG* 4.1 9.2 + - - +
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Residues in contact with LEU 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A SER* 6.0 0.7 - - - +
362A TYR* 3.8 26.5 - - + +
363A LYS 3.2 1.0 - - - -
364A LYS* 1.3 80.3 - - + +
366A GLU* 1.3 64.3 + - - +
367A TRP 3.2 0.2 - - - -
368A ARG* 3.2 60.5 + - - +
369A LYS* 3.5 13.7 + - - +
425A GLU* 4.8 7.6 - - - +
427A TYR* 3.4 37.0 - - + +
462A LYS* 4.5 11.2 - - - +
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Residues in contact with GLU 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A SER* 3.1 32.7 - - - +
361A VAL* 4.6 2.3 + - - +
362A TYR 3.4 17.5 - - - +
363A LYS* 3.1 27.1 + - - +
365A LEU* 1.3 78.7 - - - +
367A TRP* 1.3 63.8 + - + +
369A LYS* 3.0 22.5 + - - +
370A GLU* 3.0 19.2 + - + +
394A LEU* 3.4 25.2 - - - +
396A LEU* 5.7 0.2 - - - +
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Residues in contact with TRP 367 (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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363A LYS* 3.5 31.1 + - + +
364A LYS* 3.6 16.8 - - - +
365A LEU 3.2 0.8 - - - -
366A GLU* 1.3 78.7 - - + +
368A ARG* 1.3 56.6 + - + +
370A GLU* 3.2 15.5 + - + +
371A GLU* 2.9 43.5 + - + +
374A LYS* 6.2 2.9 - - - -
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Residues in contact with ARG 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A LYS* 4.2 9.8 + - - +
365A LEU* 3.4 44.4 - - - +
366A GLU 3.2 0.2 - - - -
367A TRP* 1.3 76.9 - - + +
369A LYS* 1.3 58.3 + - + +
371A GLU* 3.4 14.9 + - - +
372A PHE* 3.0 28.3 + - - +
461A LEU* 5.6 5.5 - - + +
462A LYS* 3.7 22.6 - - - +
466A LEU* 6.2 0.3 - - - +
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Residues in contact with LYS 369 (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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358A SER* 4.8 7.2 - - - -
359A VAL 3.2 16.0 + - - +
360A SER* 2.9 27.4 + - - +
365A LEU* 3.6 17.7 - - - +
366A GLU* 3.0 9.8 + - - +
368A ARG* 1.3 75.9 - - + +
370A GLU* 1.3 62.9 + - - +
372A PHE* 3.4 6.6 + - - +
373A LEU* 2.8 30.4 + - - +
423A PHE* 4.5 27.6 - - + -
425A GLU* 2.9 30.5 + - - +
427A TYR* 5.2 0.2 + - - -
458A ASN* 3.0 30.4 - - - +
461A LEU* 5.1 7.4 - - + -
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Residues in contact with GLU 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ILE* 6.2 0.2 - - - +
366A GLU* 3.0 21.3 + - + +
367A TRP* 3.5 20.4 - - + +
369A LYS* 1.3 76.5 - - - +
371A GLU* 1.3 60.7 + - + +
373A LEU* 3.2 14.5 + - - +
374A LYS* 2.9 50.8 + - - +
392A LYS* 2.9 35.5 + - - +
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Residues in contact with GLU 371 (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 TRP* 2.9 34.8 + - + +
368A ARG* 3.6 14.0 + - - +
370A GLU* 1.3 76.9 - - + +
372A PHE* 1.3 62.0 + - - +
374A LYS* 3.2 16.5 + - + +
375A GLU* 3.1 29.7 + - - +
466A LEU* 6.5 0.9 - - + -
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Residues in contact with PHE 372 (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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368A ARG 3.0 17.5 + - - +
369A LYS* 3.7 6.1 - - - +
371A GLU* 1.3 76.6 - - - +
373A LEU* 1.3 62.0 + - - +
375A GLU* 3.2 20.5 + - - +
376A LEU* 3.0 52.3 + - + +
423A PHE* 3.9 27.8 - + - -
456A ILE* 4.7 10.5 - - + -
461A LEU* 3.6 31.9 - - + -
466A LEU* 4.1 14.6 - - + -
469A VAL* 3.6 31.4 - - + -
470A LEU* 3.6 23.1 - - + -
473A VAL* 4.7 3.8 - - + -
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Residues in contact with LEU 373 (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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354A VAL* 5.7 0.7 - - + -
356A ILE* 3.3 37.7 - - + -
369A LYS 2.8 18.6 + - - +
370A GLU* 3.4 15.9 - - - +
372A PHE* 1.3 77.2 - - - +
374A LYS* 1.3 59.7 + - + +
376A LEU* 3.1 11.5 + - + +
377A ILE* 2.9 44.0 + - + +
387A LEU* 5.5 1.1 - - + -
389A ILE* 4.3 8.1 - - + -
392A LYS* 4.2 19.7 - - - +
421A ILE* 4.5 17.0 - - + -
423A PHE* 4.5 14.6 - - + -
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Residues in contact with LYS 374 (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 TRP* 6.2 2.8 - - - -
370A GLU* 2.9 35.9 + - - +
371A GLU* 3.2 14.7 + - + +
373A LEU* 1.3 76.2 - - + +
375A GLU* 1.3 57.9 + - + +
377A ILE* 3.9 10.4 - - + +
378A ASN* 2.9 34.0 + - - +
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Residues in contact with GLU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A GLU* 3.1 20.5 + - - +
372A PHE* 3.2 23.7 + - + +
374A LYS* 1.3 73.5 - - + +
376A LEU* 1.3 64.5 + - - +
378A ASN* 4.0 4.2 - - - +
379A PHE* 2.9 29.1 + - - +
466A LEU* 4.5 22.7 - - - +
467A LYS* 5.4 2.3 - - - +
470A LEU* 3.5 37.0 - - + +
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Residues in contact with LEU 376 (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 PHE* 3.0 61.2 + - + +
373A LEU* 3.1 13.2 + - + +
375A GLU* 1.3 75.7 - - - +
377A ILE* 1.3 64.2 + - - +
379A PHE* 3.7 0.4 - - - +
380A LEU* 2.9 38.8 + - + +
387A LEU* 4.4 9.2 - - + -
421A ILE* 4.4 21.3 - - + -
423A PHE* 5.2 1.8 - - + -
456A ILE* 4.8 6.3 - - + -
470A LEU* 3.8 17.5 - - + +
473A VAL* 4.4 20.9 - - + -
474A ALA* 5.2 5.6 - - + +
477A VAL* 4.9 10.5 - - + -
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Residues in contact with ILE 377 (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 LEU* 2.9 41.3 + - + +
374A LYS* 3.9 9.6 - - + +
376A LEU* 1.3 74.6 - - - +
378A ASN* 1.3 59.9 + - - +
380A LEU* 3.8 1.2 - - - +
381A LYS* 2.9 67.2 + - + +
387A LEU* 3.9 26.2 - - + +
389A ILE* 4.0 26.9 - - + -
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Residues in contact with ASN 378 (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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374A LYS 2.9 19.8 + - - +
375A GLU* 4.0 3.9 - - - +
377A ILE* 1.3 78.8 - - - +
379A PHE* 1.3 58.0 + - - +
381A LYS* 3.1 7.7 + - - +
382A ASN* 2.9 59.9 + - - +
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Residues in contact with PHE 379 (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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341A GLU* 5.6 9.0 - - + -
375A GLU 2.9 21.3 + - - +
376A LEU 3.7 1.3 - - - +
378A ASN* 1.3 76.2 - - - +
380A LEU* 1.3 63.4 + - + +
382A ASN* 3.4 15.4 + - + +
383A LYS* 3.3 60.2 + - + +
470A LEU* 4.0 16.8 - - + -
471A LEU* 3.4 39.9 - - + -
474A ALA* 3.5 32.3 - - + -
670A PHE* 6.0 1.6 - + - -
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Residues in contact with LEU 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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376A LEU* 2.9 27.2 + - + +
377A ILE 4.0 1.6 - - - +
379A PHE* 1.3 77.3 - - + +
381A LYS* 1.3 61.3 + - - +
383A LYS* 3.4 6.4 + - + +
384A GLY 2.9 8.8 + - - -
385A ILE* 2.8 38.1 + - + +
387A LEU* 3.6 27.4 - - + -
474A ALA* 3.9 23.3 - - + +
477A VAL* 3.9 22.0 - - + -
478A LEU* 3.5 42.8 - - + -
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Residues in contact with LYS 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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377A ILE* 2.9 43.0 + - + +
378A ASN* 3.1 6.5 + - - +
380A LEU* 1.3 74.9 - - - +
382A ASN* 1.3 66.8 + - - +
383A LYS 3.1 0.2 - - - -
384A GLY* 3.0 14.9 + - - +
385A ILE 3.2 15.5 - - - +
386A LYS* 4.0 15.9 - - + +
387A LEU 3.8 24.1 + - - +
388A LYS* 4.9 4.9 - - - +
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Residues in contact with ASN 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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378A ASN* 2.9 48.5 + - - +
379A PHE* 3.5 14.7 - - + +
381A LYS* 1.3 77.5 - - - +
383A LYS* 1.3 62.7 + - + +
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Residues in contact with LYS 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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340A LEU* 3.6 27.6 + - - +
341A GLU* 4.5 19.1 - - - +
343A CYS* 5.0 2.5 - - - +
344A ARG* 5.0 8.3 - - - +
345A PRO* 4.2 27.6 - - + +
379A PHE* 3.3 53.7 + - + +
380A LEU* 3.4 12.1 - - + +
381A LYS 3.1 0.2 - - - -
382A ASN* 1.3 81.2 - - + +
384A GLY* 1.3 56.5 + - - +
385A ILE 3.9 0.4 - - - +
471A LEU 5.2 2.8 + - - -
475A GLU* 5.6 0.8 - - - +
478A LEU* 3.4 34.4 - - + +
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Residues in contact with GLY 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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344A ARG* 6.4 0.9 - - - -
347A VAL* 5.9 4.0 - - - -
350A ASP* 3.7 9.9 - - - +
380A LEU 2.9 3.2 + - - -
381A LYS* 3.0 12.9 + - - -
382A ASN 4.6 0.2 - - - -
383A LYS* 1.3 77.6 - - - +
385A ILE* 1.3 70.4 + - - +
386A LYS* 3.4 20.3 + - - +
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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
------------------------------------------------------------
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