Contacts of the helix formed by residues 401 - 420 (chain A) in PDB entry 2I6W
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 ALA 401 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A GLY 3.0 19.9 + - - +
398A MET 3.7 4.7 - - - +
399A VAL 2.9 0.6 - - - -
400A LEU* 1.3 75.4 - - - +
402A ILE* 1.3 54.7 + - - +
403A GLY 2.8 6.3 - - - -
404A LEU* 2.6 35.3 + - + +
405A LEU* 3.1 14.0 + - + +
453A PHE* 6.1 0.2 - - - -
474A ILE* 3.9 31.0 - - + +
477A ALA* 4.5 12.8 - - + -
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Residues in contact with ILE 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU* 3.8 26.9 - - + +
347A ALA* 5.0 17.3 - - + +
348A ILE* 6.1 4.9 - - + -
351A VAL* 5.7 0.7 - - + -
372A VAL* 4.4 11.0 - - + -
376A LEU* 4.2 8.1 - - + -
398A MET 3.0 14.5 + - - +
399A VAL* 2.6 46.7 + - + +
401A ALA* 1.3 70.5 - - - +
403A GLY* 1.3 55.3 + - - +
404A LEU 3.3 0.2 - - - -
405A LEU* 3.3 17.9 - - + -
406A VAL* 2.9 42.3 + - + +
982A PHE* 4.8 1.8 - - + -
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Residues in contact with GLY 403 (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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399A VAL 3.8 3.2 + - - -
400A LEU 4.9 0.4 - - - -
401A ALA 2.8 1.6 + - - -
402A ILE* 1.3 77.4 - - - +
404A LEU* 1.3 55.2 + - - +
405A LEU 3.1 4.9 - - - -
406A VAL* 3.2 19.1 - - - +
407A ASP* 3.3 14.6 - - - +
937A LEU* 4.0 13.7 - - - +
978A THR* 4.1 2.4 - - - +
982A PHE* 3.3 37.9 - - - -
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Residues in contact with LEU 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A LEU 4.9 0.6 + - - +
401A ALA* 2.6 21.4 + - + +
403A GLY* 1.3 72.0 - - - +
405A LEU* 1.3 60.3 + - + +
407A ASP* 4.3 6.0 - - - +
408A ASP* 3.0 23.0 - - - +
449A LEU* 3.2 38.1 - - + -
453A PHE* 3.6 33.4 - - + -
474A ILE* 4.2 7.4 - - + -
478A MET* 5.6 7.9 - - + +
481A SER* 3.9 6.2 + - - -
933A THR* 4.2 13.2 - - - +
937A LEU* 4.5 19.9 - - + +
940A LYS* 4.4 22.7 - - + -
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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
----------------------------------------------------------
372A VAL* 4.2 14.4 - - + -
375A VAL* 3.6 15.3 - - + -
376A LEU* 3.8 30.5 - - + -
398A MET 4.6 1.6 - - - +
401A ALA* 3.1 12.2 + - + +
402A ILE* 3.3 28.9 - - + +
404A LEU* 1.3 79.3 - - + +
406A VAL* 1.3 72.4 + - - +
407A ASP 2.9 2.2 + - - -
408A ASP* 3.3 14.2 + - - +
409A ALA* 3.7 7.5 + - - +
477A ALA* 3.2 22.9 - - + +
478A MET* 4.8 1.1 - - - +
481A SER* 3.2 33.1 - - - +
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Residues in contact with VAL 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A VAL* 4.0 32.3 - - + -
355A MET* 6.3 0.2 - - - -
368A PRO* 6.0 2.7 - - + -
372A VAL* 3.8 16.6 - - + +
402A ILE* 2.9 34.5 + - + +
403A GLY* 3.2 18.2 - - - +
405A LEU* 1.3 75.3 - - - +
407A ASP* 1.3 77.5 + - - +
409A ALA* 3.0 23.6 - - - +
410A ILE* 3.4 15.5 + - + +
978A THR* 4.4 10.3 - - + +
981A ALA* 5.2 2.2 - - + -
982A PHE* 4.9 10.1 - - + +
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Residues in contact with ASP 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A GLY 3.3 17.5 - - - +
404A LEU* 4.3 8.3 - - - +
405A LEU 2.9 1.1 + - - +
406A VAL* 1.3 83.6 - - - +
408A ASP* 1.3 55.1 + - - +
409A ALA 2.7 12.1 + - - -
410A ILE* 3.0 10.8 + - - +
411A VAL* 2.8 27.3 + - - +
937A LEU* 5.7 2.7 - - + -
940A LYS* 3.2 44.4 + - + +
941A ASN* 4.9 5.7 - - - +
944A LEU* 5.4 3.6 - - - +
978A THR* 2.8 39.4 + - + +
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Residues in contact with ASP 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 LEU 3.0 23.0 - - - +
405A LEU 3.3 6.0 + - - +
407A ASP* 1.3 77.9 - - - +
409A ALA* 1.3 64.5 + - - +
411A VAL* 3.5 9.4 - - - +
412A VAL* 3.3 25.3 + - - +
442A LEU* 3.2 20.0 - - + +
445A ILE* 3.8 6.9 - - - +
478A MET* 6.0 0.5 - - - +
481A SER* 3.9 13.4 + - - +
482A VAL* 4.9 6.1 - - - +
485A ALA* 3.9 24.6 - - + +
489A THR* 4.9 0.2 - - - +
940A LYS* 3.2 31.3 + - - -
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Residues in contact with ALA 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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367A ILE* 6.0 1.1 - - + -
368A PRO* 4.0 27.6 - - + -
371A ALA* 4.7 12.3 - - + -
405A LEU 3.7 4.5 + - - +
406A VAL* 3.0 17.2 + - - +
407A ASP 2.7 4.9 + - - -
408A ASP* 1.3 72.3 - - - +
410A ILE* 1.3 60.8 + - - +
412A VAL* 3.0 13.9 + - - +
413A VAL* 2.6 27.0 - - + +
485A ALA* 5.2 1.3 - - - +
489A THR* 4.8 11.2 - - + +
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Residues in contact with ILE 410 (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* 6.3 0.2 - - + -
355A MET* 3.2 30.7 - - + -
359A LEU* 6.3 0.2 - - + -
368A PRO* 5.2 0.2 - - + -
406A VAL* 3.5 20.0 - - + +
407A ASP 3.0 2.9 + - - +
409A ALA* 1.3 74.3 - - + +
411A VAL* 1.3 54.3 + - - +
413A VAL* 2.7 13.6 + - + +
414A GLU* 2.6 42.4 + - + +
974A PRO* 4.7 4.5 - - + -
977A MET* 3.3 42.0 - - + +
978A THR* 3.6 39.5 - - - +
981A ALA* 4.8 5.8 - - + -
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Residues in contact with VAL 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ASP* 2.8 40.6 - - - +
408A ASP* 3.5 12.8 - - - +
410A ILE* 1.3 75.9 - - + +
412A VAL* 1.3 58.7 + - + +
413A VAL 3.2 2.3 + - - -
414A GLU* 4.5 4.4 - - - +
415A ASN* 2.9 32.8 + - + +
438A ILE* 3.7 30.9 - - + +
442A LEU* 4.9 2.5 - - + -
940A LYS* 5.7 0.7 - - - +
944A LEU* 4.1 25.4 - - + -
948A PHE* 5.7 4.0 - - + -
974A PRO* 5.0 9.4 - - + -
978A THR* 5.0 2.2 - - - +
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Residues in contact with VAL 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 ASP 3.3 18.6 - - - +
409A ALA 3.0 4.5 + - - +
411A VAL* 1.3 80.0 - - + +
413A VAL* 1.3 58.4 + - - +
416A VAL* 2.8 20.5 - - - +
435A MET* 3.1 32.3 - - + -
438A ILE* 3.8 14.4 - - + -
442A LEU* 3.9 28.0 - - + -
485A ALA* 4.4 9.6 - - + +
489A THR* 4.1 13.9 - - + -
490A PRO* 4.1 4.3 - - + -
493A CYS* 3.7 17.6 - - - -
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Residues in contact with VAL 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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355A MET* 5.9 0.9 - - + -
359A LEU* 4.9 17.0 - - + -
364A ALA* 5.3 6.1 - - + +
367A ILE* 4.4 28.9 - - + -
368A PRO* 4.2 17.7 - - + -
409A ALA* 2.6 33.9 - - - +
410A ILE* 2.7 11.8 + - + +
411A VAL 3.0 0.2 - - - -
412A VAL* 1.3 82.0 - - + +
414A GLU* 1.3 55.7 + - - +
415A ASN 3.2 1.1 - - - -
416A VAL* 3.0 9.8 + - - +
417A GLU* 2.7 32.8 + - + +
489A THR* 5.3 2.5 - - + -
493A CYS* 4.9 6.7 - - + -
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Residues in contact with GLU 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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359A LEU* 5.3 4.5 - - + -
410A ILE* 2.6 29.2 + - + +
411A VAL 4.5 1.1 - - - +
413A VAL* 1.3 70.5 - - + +
415A ASN* 1.3 62.8 + - - +
416A VAL 2.9 5.4 - - - -
417A GLU* 3.2 14.1 - - + +
418A ARG* 2.5 68.1 + - - +
948A PHE* 5.9 1.0 - - - -
973A ARG* 3.5 28.8 - - - -
974A PRO* 3.5 44.4 - - + +
977A MET* 4.5 4.5 - - + -
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Residues in contact with ASN 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 VAL* 2.9 20.8 + - + +
413A VAL 3.2 0.6 - - - -
414A GLU* 1.3 91.7 + - - +
416A VAL* 1.3 56.6 + - - +
418A ARG* 2.9 35.9 + - - +
419A VAL* 3.0 14.6 - - - +
434A SER* 3.0 32.0 + - - +
437A GLN* 3.4 25.3 + - - +
438A ILE* 3.3 15.4 - - + +
948A PHE* 3.8 18.5 - - + -
970A MET* 5.4 1.9 - - - +
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Residues in contact with VAL 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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412A VAL 2.8 29.8 - - - +
413A VAL* 3.1 6.7 - - - +
415A ASN* 1.3 77.0 - - - +
417A GLU* 1.3 64.9 + - - +
418A ARG 2.7 5.7 + - - -
419A VAL* 2.7 18.5 + - - +
420A MET* 2.9 31.9 + - + +
427A PRO 5.2 0.7 - - - +
430A ALA* 3.9 29.2 - - + -
431A THR* 3.9 17.0 - - + +
434A SER* 3.5 20.4 - - - -
493A CYS* 4.8 8.5 - - + +
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Residues in contact with GLU 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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359A LEU* 3.9 33.6 - - + +
361A ASN* 5.4 3.3 - - - +
364A ALA* 5.1 6.2 - - - +
413A VAL* 2.7 12.7 + - + +
414A GLU* 3.2 25.6 - - + +
416A VAL* 1.3 75.7 - - - +
418A ARG* 1.3 60.9 + - - +
420A MET* 3.4 31.5 + - - +
421A ALA* 5.1 0.2 - - - +
498A LYS 5.5 1.8 - - - +
499A PRO 4.8 8.1 - - - +
973A ARG* 5.7 6.5 - - - +
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Residues in contact with ARG 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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414A GLU* 2.5 52.3 + - - +
415A ASN* 2.9 38.0 + - - +
416A VAL 2.7 0.6 + - - -
417A GLU* 1.3 70.6 - - - +
419A VAL* 1.3 66.5 + - - +
420A MET 2.4 30.4 + - - +
421A ALA* 3.2 10.8 + - - +
422A GLU* 3.5 39.2 + - + +
437A GLN* 5.4 2.0 - - - -
948A PHE* 5.4 0.6 - - - -
969A ARG 4.5 1.6 + - - -
970A MET* 2.8 56.9 + - - +
971A ARG* 4.7 0.4 - - - +
973A ARG* 5.5 2.6 - - - +
974A PRO* 4.9 1.4 - - - +
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Residues in contact with VAL 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 ASN 3.0 24.5 - - - +
416A VAL* 2.7 14.3 + - - +
418A ARG* 1.3 84.2 - - + +
420A MET* 1.3 56.7 + - - +
421A ALA 3.1 6.3 + - - -
422A GLU* 3.5 12.0 + - - +
423A GLU* 3.4 38.2 + - + +
426A PRO* 5.1 1.8 - - + -
430A ALA* 4.3 19.3 - - + +
433A LYS* 4.0 32.8 - - + -
434A SER 5.0 2.0 - - - +
437A GLN* 4.7 12.6 - - - +
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Residues in contact with MET 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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416A VAL* 2.9 51.3 + - + +
417A GLU* 3.4 25.4 - - - +
418A ARG 2.4 9.9 + - - +
419A VAL* 1.3 67.7 - - - +
421A ALA* 1.3 65.4 + - - +
424A GLY* 4.5 11.4 - - - -
426A PRO* 4.5 11.4 - - + -
427A PRO* 4.4 17.3 - - + -
430A ALA* 4.4 12.3 - - + -
493A CYS 6.1 0.2 - - - +
498A LYS 4.8 4.5 - - - +
499A PRO* 3.9 44.5 - - + +
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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