Contacts of the helix formed by residues 396 - 421 (chain A) in PDB entry 2M6B
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 396 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A TRP* 3.3 35.4 - - + -
394A LYS* 3.1 27.6 - - - +
395A ILE* 1.3 87.9 - - - +
397A LYS* 1.3 58.6 + - - +
398A ILE* 2.9 10.3 - - + +
399A SER* 2.8 37.4 + - - +
400A ARG* 3.7 2.6 + - - +
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Residues in contact with LYS 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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300A GLU* 3.6 26.7 + - - -
391A ARG* 5.9 4.7 - - - +
394A LYS* 5.6 0.6 - - - +
395A ILE* 3.2 15.6 - - + +
396A ASP* 1.3 77.2 - - - +
398A ILE* 1.3 55.2 + - - +
400A ARG* 2.8 45.5 + - + +
401A ILE* 3.2 24.5 + - + +
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Residues in contact with ILE 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A TRP* 3.6 51.3 - - + +
240A ILE* 5.6 0.9 - - - +
242A PHE* 3.5 33.4 - - + -
243A TRP* 3.4 35.4 - - + -
300A GLU* 4.1 19.9 + - + +
394A LYS* 5.8 1.6 - - + -
396A ASP* 2.9 7.3 + - - +
397A LYS* 1.3 78.2 - - - +
399A SER* 1.3 64.7 + - - +
401A ILE* 3.8 6.9 - - - +
402A GLY* 2.9 25.5 + - - -
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Residues in contact with SER 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ILE* 4.9 19.1 + - - +
243A TRP* 4.9 6.1 - - - +
396A ASP* 2.8 21.2 + - - +
398A ILE* 1.3 85.2 - - - +
400A ARG* 1.3 61.4 + - - +
402A GLY* 4.3 0.9 - - - +
403A PHE* 2.9 49.7 + - - +
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Residues in contact with ARG 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A ILE* 5.4 14.6 + - - +
396A ASP 3.7 2.3 + - - -
397A LYS* 2.8 30.9 + - + +
399A SER* 1.3 78.4 - - - +
401A ILE* 1.3 59.5 + - + +
403A PHE* 3.8 4.6 - - - +
404A PRO* 2.9 23.6 - - - +
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Residues in contact with ILE 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A TRP* 3.3 33.0 - - + -
300A GLU* 4.2 13.2 - - - +
397A LYS* 3.6 31.0 - - + +
398A ILE* 3.8 3.6 - - - +
400A ARG* 1.3 78.4 - - + +
402A GLY* 1.3 66.1 + - - +
403A PHE 3.2 0.7 - - - -
404A PRO* 3.4 9.0 - - - +
405A LEU* 3.1 29.5 + - + +
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Residues in contact with GLY 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A TRP* 3.8 19.7 - - - -
240A ILE* 5.1 7.5 - - - +
398A ILE 2.9 22.5 + - - -
399A SER* 3.8 1.6 - - - -
400A ARG 3.4 0.2 - - - -
401A ILE* 1.3 78.1 - - - +
403A PHE* 1.3 55.5 + - - +
405A LEU* 3.8 4.7 - - - +
406A ALA* 2.7 38.3 + - - +
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Residues in contact with PHE 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ILE* 5.4 10.1 - - + +
399A SER* 2.9 33.7 + - - +
400A ARG* 3.8 4.0 - - - +
402A GLY* 1.3 77.6 - - - +
404A PRO* 1.3 66.2 - - + +
406A ALA* 3.8 3.1 - - - +
407A PHE* 3.1 29.7 + - + +
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Residues in contact with PRO 404 (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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400A ARG 2.9 23.8 - - - +
401A ILE* 3.4 11.7 - - - +
403A PHE* 1.3 92.3 - - + +
405A LEU* 1.3 57.1 + - - +
407A PHE* 4.1 10.8 - - + +
408A LEU* 3.3 27.2 + - - +
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Residues in contact with LEU 405 (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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239A TRP* 4.8 20.4 - - + -
296A SER* 3.5 28.3 - - - +
401A ILE* 3.1 20.7 + - + +
402A GLY* 4.0 4.3 - - - +
403A PHE 3.2 0.6 - - - -
404A PRO* 1.3 78.0 - - + +
406A ALA* 1.3 65.5 + - + +
408A LEU* 3.8 7.8 + - + +
409A ILE* 3.4 39.6 + - + +
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Residues in contact with ALA 406 (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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236A ILE* 2.9 56.5 - - + +
240A ILE* 5.5 4.5 - - + -
402A GLY 2.7 20.7 + - - +
403A PHE* 3.8 3.6 - - - +
405A LEU* 1.3 78.6 - - + +
407A PHE* 1.3 58.6 + - - +
409A ILE 3.4 0.2 + - - -
410A PHE* 3.0 21.0 + - - +
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Residues in contact with PHE 407 (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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403A PHE* 3.1 16.3 + - + +
404A PRO* 4.3 11.0 - - + +
406A ALA* 1.3 75.5 - - - +
408A LEU* 1.3 74.9 + - + +
410A PHE* 3.6 5.1 + - + +
411A ASN* 3.1 38.3 + - + +
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Residues in contact with LEU 408 (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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404A PRO 3.3 19.4 + - - +
405A LEU* 4.0 7.6 - - + +
406A ALA 3.3 0.6 - - - -
407A PHE* 1.3 90.7 - - + +
409A ILE* 1.3 58.8 + - + +
411A ASN* 3.6 3.5 + - - +
412A LEU* 2.8 56.9 + - + +
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Residues in contact with ILE 409 (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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232A LEU* 3.8 25.1 - - + +
235A VAL* 5.3 13.5 - - + -
236A ILE* 4.2 15.7 - - + -
292A LEU* 6.3 2.9 - - + -
405A LEU* 3.4 36.6 + - + +
406A ALA 3.8 3.4 - - - +
407A PHE 3.3 0.4 - - - -
408A LEU* 1.3 79.5 - - + +
410A PHE* 1.3 67.6 + - - +
412A LEU* 2.9 23.6 + - + +
413A PHE* 2.9 20.1 + - + +
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Residues in contact with PHE 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ILE* 5.2 9.4 - - + -
232A LEU* 4.8 10.3 - - + -
233A LEU* 3.8 43.5 - - + -
236A ILE* 4.1 18.6 - - + -
406A ALA 3.0 16.8 + - - +
407A PHE* 4.0 7.4 - - + +
409A ILE* 1.3 77.9 - - + +
411A ASN* 1.3 56.7 + - - +
413A PHE* 3.9 2.6 + - - +
414A TYR* 3.0 38.1 + + + +
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Residues in contact with ASN 411 (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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407A PHE* 3.1 37.0 + - + +
408A LEU* 3.7 3.8 - - + +
409A ILE 3.1 0.4 - - - -
410A PHE* 1.3 75.5 - - - +
412A LEU* 1.3 60.3 + - - +
413A PHE 3.4 0.9 - - - -
414A TYR* 3.9 13.3 - - - +
415A TRP* 3.3 38.0 + - - +
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Residues in contact with LEU 412 (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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408A LEU* 2.8 51.0 + - + +
409A ILE* 2.9 14.1 + - + +
411A ASN* 1.3 81.0 - - - +
413A PHE* 1.3 61.7 + - + +
415A TRP* 4.3 1.4 - - - +
416A ILE* 3.2 25.6 + - - +
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Residues in contact with PHE 413 (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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228A TYR* 3.5 28.7 - + - -
232A LEU* 3.3 42.6 - - + -
285A ILE* 3.8 30.3 - - + -
289A VAL* 4.1 20.2 - - + -
409A ILE* 2.9 18.7 + - + +
410A PHE* 4.6 2.0 - - - +
412A LEU* 1.3 81.1 - - + +
414A TYR* 1.3 60.0 + - - +
415A TRP 3.4 0.4 - - - -
416A ILE* 3.6 9.4 - - + -
417A ILE* 2.9 60.0 + - + +
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Residues in contact with TYR 414 (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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229A ILE* 5.1 16.2 - - + -
410A PHE* 3.0 32.7 + + + +
411A ASN* 4.2 12.3 - - - +
412A LEU 3.5 0.2 - - - -
413A PHE* 1.3 78.4 - - - +
415A TRP* 1.3 65.0 + + - +
417A ILE* 4.7 3.1 - - - -
418A TYR* 3.4 60.1 + + + +
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Residues in contact with TRP 415 (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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411A ASN* 3.3 31.9 + - - +
412A LEU* 4.9 1.3 - - - +
414A TYR* 1.3 82.6 - + - +
416A ILE* 1.3 58.6 + - + +
417A ILE 3.5 0.2 - - - -
418A TYR* 5.1 1.5 - - - +
419A LYS* 2.9 55.9 + - + +
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Residues in contact with ILE 416 (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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285A ILE* 5.5 6.3 - - + -
412A LEU 3.2 21.8 + - - +
413A PHE* 3.4 22.7 - - + +
415A TRP* 1.3 81.1 - - + +
417A ILE* 1.3 67.9 + - + +
418A TYR 3.5 0.2 - - - -
419A LYS* 3.2 33.2 - - - +
420A ILE* 2.9 50.1 + - + +
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Residues in contact with ILE 417 (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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225A ILE* 3.7 37.7 - - + +
228A TYR* 4.1 28.0 - - + -
229A ILE* 5.3 8.5 - - + +
232A LEU* 5.6 0.9 - - + -
413A PHE* 2.9 50.6 + - + +
414A TYR* 4.4 3.4 - - - +
415A TRP 3.5 0.2 - - - -
416A ILE* 1.3 78.0 - - + +
418A TYR* 1.3 72.8 + - + +
419A LYS 3.1 5.6 + - - -
420A ILE* 4.3 2.9 - - - +
421A VAL* 3.0 32.2 + - + +
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Residues in contact with TYR 418 (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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225A ILE* 6.2 3.1 - - + -
229A ILE* 6.2 2.9 - - + -
414A TYR* 3.4 62.7 + + + +
415A TRP* 4.5 1.8 - - - +
417A ILE* 1.3 88.5 - - + +
419A LYS* 1.3 57.8 + - - +
421A VAL* 4.6 2.9 - - + -
422A ARG* 4.4 0.9 - - - +
434A HIS* 3.5 54.6 - - + +
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Residues in contact with LYS 419 (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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415A TRP* 2.9 46.8 + - + +
416A ILE* 3.2 33.3 - - - +
417A ILE 3.1 0.6 - - - -
418A TYR* 1.3 79.5 - - - +
420A ILE* 1.3 63.6 + - - +
421A VAL 3.2 1.3 - - - -
422A ARG* 2.9 24.3 + - - +
423A ARG* 2.8 34.9 + - + +
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Residues in contact with ILE 420 (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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281A LYS* 3.8 33.9 - - + +
416A ILE* 2.9 45.4 + - + +
417A ILE* 4.3 3.8 - - - +
419A LYS* 1.3 80.1 - - - +
421A VAL* 1.3 64.3 + - + +
423A ARG* 4.4 4.0 - - + +
424A GLU* 2.9 59.2 + - + +
425A ASP* 4.1 9.6 - - - +
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Residues in contact with VAL 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A TYR* 6.2 0.2 - - + -
225A ILE* 3.7 30.1 - - + -
417A ILE* 3.0 20.9 - - + +
418A TYR* 4.9 3.6 - - + +
419A LYS 3.2 0.6 - - - -
420A ILE* 1.3 78.0 - - + +
422A ARG* 1.3 56.6 + - - +
425A ASP* 2.8 50.4 - - + +
426A GLU* 3.0 1.2 + - - -
428A GLU* 4.0 5.6 - - - +
429A HIS* 3.3 38.6 - - + +
434A HIS 3.7 8.3 - - - +
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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