Contacts of the helix formed by residues 411 - 433 (chain A) in PDB entry 4Z1H
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 ILE 411 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A LEU* 5.8 1.3 - - + -
378A ASP* 4.5 13.1 - - + +
379A ILE* 3.8 26.1 - - + +
396A ILE* 4.2 24.5 - - + -
397A PRO* 5.1 13.0 - - + -
408A SER* 3.4 30.7 - - - +
409A ALA 4.1 0.8 - - - -
410A LEU* 1.3 86.8 - - - +
412A ARG* 1.3 62.5 + - - +
413A LYS 3.8 1.3 - - - -
414A LEU* 3.3 31.8 - - + +
415A ARG* 3.2 24.2 + - - +
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Residues in contact with ARG 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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409A ALA 3.5 20.0 + - - +
410A LEU* 3.3 31.4 - - + +
411A ILE* 1.3 79.9 - - - +
413A LYS* 1.3 59.4 + - - +
414A LEU 2.9 4.9 - - - -
415A ARG* 2.8 52.0 + - - +
416A ASP* 2.9 20.2 + - - +
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Residues in contact with LYS 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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336A PRO 5.6 3.2 + - - -
337A LEU* 4.2 26.8 - - + +
410A LEU* 3.8 22.4 - - + +
412A ARG* 1.3 74.8 - - - +
414A LEU* 1.3 61.3 + - + +
416A ASP* 4.0 10.3 - - - +
417A VAL* 3.4 24.3 + - - +
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Residues in contact with LEU 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A LEU* 4.6 17.2 - - + +
339A ILE* 3.6 35.0 - - + -
365A LEU* 4.7 3.6 - - + -
379A ILE* 4.0 14.4 - - + -
391A VAL* 4.6 11.9 - - + -
393A SER* 4.7 8.7 - - - +
396A ILE* 4.2 15.7 - - + -
411A ILE* 3.3 34.5 - - + +
413A LYS* 1.3 78.8 - - + +
415A ARG* 1.3 61.2 + - - +
416A ASP 3.2 0.2 + - - -
417A VAL* 3.2 7.2 - - - +
418A LEU* 2.9 45.5 + - + +
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Residues in contact with ARG 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ASP* 3.0 28.5 + - - +
379A ILE 3.3 19.5 + - - +
380A LEU 3.6 23.1 + - - -
381A PRO* 3.7 22.9 - - + +
411A ILE* 3.2 8.2 + - - +
412A ARG* 2.8 52.0 + - - +
414A LEU* 1.3 75.5 - - - +
416A ASP* 1.3 64.3 + - - +
418A LEU* 3.6 1.8 + - - +
419A GLN* 2.9 28.5 + - - +
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Residues in contact with ASP 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 ARG* 2.9 22.1 + - - +
413A LYS* 4.1 9.0 - - - +
415A ARG* 1.3 88.7 + - - +
417A VAL* 1.3 57.9 + - - +
419A GLN* 3.3 16.7 + - - +
420A GLN* 2.9 27.5 + - - +
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Residues in contact with VAL 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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331A TYR* 4.2 18.6 - - + +
336A PRO* 5.2 15.3 - - + -
337A LEU* 5.8 4.3 - - + -
339A ILE* 3.8 25.4 - - + -
413A LYS 3.4 13.8 + - - +
414A LEU* 3.2 12.8 + - - +
416A ASP* 1.3 76.7 - - - +
418A LEU* 1.3 64.2 + - - +
420A GLN* 4.2 17.3 - - + +
421A ARG* 2.9 29.6 + - + +
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Residues in contact with LEU 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A TYR* 4.3 18.2 - - + -
339A ILE* 4.4 12.6 - - + -
341A SER* 4.3 3.4 - - - +
343A PHE* 3.6 29.2 - - + -
379A ILE* 3.7 27.8 - - + +
380A LEU* 3.9 14.8 - - + -
391A VAL* 3.8 24.2 - - + -
414A LEU* 2.9 30.4 + - + +
415A ARG 3.8 4.7 - - - +
417A VAL* 1.3 79.7 - - + +
419A GLN* 1.3 55.2 + - - +
421A ARG* 3.9 3.7 - - + +
422A LEU* 2.9 37.0 + - - +
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Residues in contact with GLN 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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380A LEU* 4.9 0.4 - - - +
381A PRO* 3.3 23.1 - - + +
383A TRP* 3.2 21.4 + - - +
384A LEU* 4.3 15.0 - - + -
415A ARG* 2.9 19.4 + - - +
416A ASP* 3.4 16.5 + - - +
418A LEU* 1.3 74.1 - - - +
420A GLN* 1.3 65.2 + - - +
422A LEU* 3.4 0.7 + - - +
423A ILE* 2.9 48.2 + - + +
460A VAL* 4.4 20.7 - - - +
463A ASP* 6.4 0.2 - - - +
464A ILE* 4.3 6.8 - - - +
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Residues in contact with GLN 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 ASP 2.9 15.3 + - - +
417A VAL* 3.9 18.3 - - + +
419A GLN* 1.3 78.4 - - - +
421A ARG* 1.3 64.4 + - - +
423A ILE* 3.6 6.5 - - - +
424A LYS* 2.9 54.1 + - + +
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Residues in contact with ARG 421 (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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329A LEU* 3.8 36.2 - - + +
331A TYR* 3.5 54.0 - - + +
343A PHE* 6.0 0.4 - - + -
417A VAL* 2.9 19.7 + - + +
418A LEU* 3.9 4.0 - - + +
420A GLN* 1.3 79.1 - - - +
422A LEU* 1.3 58.3 + - + +
424A LYS* 3.3 12.1 + - - +
425A PHE* 2.9 39.7 + - - +
428A ASP* 4.2 16.3 + - - -
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Residues in contact with LEU 422 (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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329A LEU* 3.9 18.6 - - + -
343A PHE* 4.2 32.5 - - + -
380A LEU* 3.8 25.6 - - + -
384A LEU* 4.0 26.2 - - + -
387A ILE* 4.4 12.8 - - + -
418A LEU 2.9 21.0 + - - +
419A GLN 3.8 2.9 - - - +
421A ARG* 1.3 73.1 - - + +
423A ILE* 1.3 67.9 + - - +
425A PHE* 3.0 12.7 + - + +
426A PHE* 2.9 42.2 + - + -
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Residues in contact with ILE 423 (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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383A TRP* 3.9 20.6 - - + -
419A GLN* 2.9 41.4 + - + +
420A GLN* 3.6 6.7 - - - +
422A LEU* 1.3 74.0 - - - +
424A LYS* 1.3 74.9 + - + +
426A PHE 3.1 2.1 + - - -
427A ILE* 3.0 36.1 + - + +
463A ASP* 3.5 43.3 - - + +
464A ILE* 4.2 16.2 - - + +
466A LYS* 5.4 0.2 - - + -
467A LEU* 3.5 21.0 - - + +
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Residues in contact with LYS 424 (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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420A GLN* 2.9 47.4 + - + +
421A ARG* 3.5 15.9 - - - +
423A ILE* 1.3 86.9 - - + +
425A PHE* 1.3 57.5 + - - +
427A ILE* 3.2 13.6 + - + +
428A ASP* 2.8 41.3 + - - +
463A ASP* 3.4 28.1 + - - -
466A LYS* 4.5 8.3 - - - +
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Residues in contact with PHE 425 (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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327A TYR* 4.1 18.2 - + + -
328A THR 3.7 28.9 - - - -
329A LEU* 3.8 37.7 - - + -
343A PHE 6.0 0.4 - - - -
345A VAL* 5.5 0.7 - - + -
421A ARG* 2.9 27.3 + - - +
422A LEU* 3.2 15.9 - - + +
424A LYS* 1.3 77.0 - - - +
426A PHE* 1.3 86.5 + + - +
428A ASP* 3.3 7.5 + - + +
429A GLN* 2.9 68.9 + - + +
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Residues in contact with PHE 426 (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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327A TYR* 4.1 10.1 - + - -
345A VAL* 3.8 24.2 - - + -
383A TRP* 5.2 0.9 - + - -
384A LEU* 4.2 23.8 - - + -
386A PHE* 4.3 2.7 - + - -
387A ILE* 3.8 12.1 - - + -
422A LEU* 2.9 30.8 + - + -
423A ILE* 3.1 0.9 + - - +
425A PHE* 1.3 96.7 - + - +
427A ILE* 1.3 52.9 + - - +
429A GLN* 3.6 2.6 + - + +
430A SER* 2.6 36.0 + - - -
437A TYR* 3.4 13.2 - + + -
440A PHE* 3.4 42.0 - + - -
467A LEU* 3.6 32.5 - - + -
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Residues in contact with ILE 427 (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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423A ILE* 3.0 27.6 + - + +
424A LYS* 3.5 17.7 - - + +
426A PHE* 1.3 74.8 - - - +
428A ASP* 1.3 70.3 + - - +
430A SER* 3.0 20.7 + - - -
431A LYS* 3.0 14.3 + - + +
466A LYS* 3.8 39.3 - - + +
467A LEU* 3.7 12.8 - - + -
469A ARG* 5.3 2.7 - - - +
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Residues in contact with ASP 428 (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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421A ARG* 4.2 16.5 + - - +
424A LYS* 2.8 20.9 + - - +
425A PHE* 3.5 9.9 - - + +
427A ILE* 1.3 77.8 - - - +
429A GLN* 1.3 62.0 + - + +
431A LYS* 3.1 9.7 + - - +
432A LYS* 3.0 29.1 + - - +
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Residues in contact with GLN 429 (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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327A TYR* 3.4 37.1 + - + +
328A THR 5.5 0.6 + - - -
425A PHE* 2.9 56.9 + - + +
426A PHE* 3.7 8.1 - - - +
428A ASP* 1.3 73.9 - - + +
430A SER* 1.3 64.0 + - - +
432A LYS* 4.5 19.0 - - - +
433A ASP* 2.8 34.6 + - - +
436A LYS* 5.3 2.4 + - - +
437A TYR* 4.3 2.9 - - + +
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Residues in contact with SER 430 (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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426A PHE 2.6 22.3 + - - -
427A ILE* 3.0 14.4 + - - -
429A GLN* 1.3 77.3 - - - +
431A LYS* 1.3 60.0 + - - +
433A ASP 3.3 13.2 - - - +
434A ALA* 3.9 9.8 - - - +
437A TYR* 3.2 30.9 - - - -
467A LEU* 5.5 0.2 - - - +
469A ARG* 3.1 32.8 + - - -
485A GLU* 5.6 0.4 - - - -
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Residues in contact with LYS 431 (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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427A ILE* 3.0 13.1 + - + +
428A ASP* 3.1 9.8 + - - +
430A SER* 1.3 78.5 - - - +
432A LYS* 1.3 60.7 + - + +
433A ASP* 4.9 0.2 - - - -
434A ALA* 6.0 0.5 - - - +
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Residues in contact with LYS 432 (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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428A ASP 3.0 14.5 + - - +
429A GLN* 4.5 21.3 - - - +
430A SER 3.3 0.2 - - - -
431A LYS* 1.3 81.5 - - + +
433A ASP* 1.3 67.3 + - + +
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Residues in contact with ASP 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A TYR* 4.9 1.1 + - - +
429A GLN* 2.8 26.7 + - - +
430A SER 3.3 4.7 - - - +
431A LYS 5.1 0.2 - - - -
432A LYS* 1.3 83.6 - - + +
434A ALA* 1.3 64.0 + - - +
435A GLU* 3.4 4.7 + - - +
436A LYS* 3.1 43.1 + - + +
437A TYR* 3.4 15.4 + - - +
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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