Contacts of the helix formed by residues 449 - 471 (chain A) in PDB entry 5ID6
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 ASN 449 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442A LEU* 3.4 24.9 - - + +
443A GLU* 4.3 9.5 + - - +
444A LYS* 3.5 29.5 - - - +
445A SER 2.8 13.8 + - - +
446A LEU* 2.9 12.1 + - - +
448A LYS* 1.3 77.2 - - - +
450A ASP* 1.3 66.1 + - - +
451A ALA* 3.2 9.6 + - - +
452A VAL* 3.2 33.1 + - + +
453A VAL* 3.2 22.7 + - - +
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Residues in contact with ASP 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A LYS 4.4 12.0 - - - +
448A LYS 3.6 4.4 + - - -
449A ASN* 1.3 73.1 + - - +
451A ALA* 1.3 64.7 + - - +
453A VAL* 3.3 6.0 + - - +
454A ALA* 2.9 25.8 + - - +
889A ASN* 4.6 14.2 + - - +
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Residues in contact with ALA 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A ASN* 3.2 8.2 - - - +
450A ASP* 1.3 80.1 - - - +
452A VAL* 1.3 64.0 + - + +
454A ALA* 3.4 6.2 + - - +
455A ILE* 3.1 27.2 + - + +
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Residues in contact with VAL 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LEU* 4.8 12.1 - - + -
435A LEU* 4.1 25.8 - - + -
440A PHE* 4.8 13.9 - - + -
442A LEU* 4.6 5.6 - - + -
446A LEU* 4.5 15.5 - - + -
449A ASN* 3.2 35.4 + - + +
451A ALA* 1.3 76.1 - - + +
453A VAL* 1.3 64.6 + - - +
455A ILE* 2.9 20.1 + - - +
456A MSE 3.0 18.2 + - + +
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Residues in contact with VAL 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A LEU* 3.4 44.6 - - + +
449A ASN 3.2 9.0 + - - +
450A ASP* 3.7 6.1 - - - +
452A VAL* 1.3 77.7 - - - +
454A ALA* 1.3 57.1 + - - +
456A MSE 3.4 11.1 + - - +
457A LYS* 3.0 28.1 + - + +
511A VAL* 4.0 39.0 - - + -
889A ASN* 6.0 6.3 - - + -
890A TRP* 4.5 10.4 - - + +
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Residues in contact with ALA 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A ASP 2.9 17.3 + - - +
451A ALA* 3.7 6.3 - - - +
453A VAL* 1.3 74.2 - - - +
455A ILE* 1.3 66.1 + - + +
457A LYS* 4.1 8.1 - - - +
458A ASP* 3.1 31.6 + - - +
887A ARG* 6.5 0.9 - - + -
889A ASN* 6.1 6.1 - - + -
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Residues in contact with ILE 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PHE* 5.5 0.2 - - + -
431A SER* 3.9 17.5 - - - +
432A SER* 3.5 34.2 + - - +
435A LEU* 3.5 27.4 - - + -
451A ALA* 3.1 18.8 + - + +
452A VAL* 2.9 10.4 + - - +
454A ALA* 1.3 78.8 - - + +
456A MSE 1.3 62.7 + - - +
458A ASP* 3.7 6.6 - - - +
459A LEU* 3.3 20.8 + - - +
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Residues in contact with MSE 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A VAL* 4.3 15.9 - - + +
301A LEU* 3.6 40.2 - - + +
304A PHE* 3.6 60.0 - - + -
435A LEU* 4.1 7.0 - - + -
446A LEU* 5.1 7.6 - - - -
452A VAL* 3.0 21.9 + - + +
453A VAL* 3.6 13.2 - - - +
455A ILE* 1.3 79.3 - - - +
457A LYS* 1.3 62.4 + - - +
459A LEU* 3.4 1.7 + - - +
460A LEU* 3.0 33.2 + - + +
507A ILE* 4.7 11.7 - - + -
890A TRP* 5.5 1.6 - - + -
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Residues in contact with LYS 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A VAL* 3.0 19.5 + - + +
454A ALA* 4.1 7.9 - - - +
456A MSE 1.3 74.1 - - - +
458A ASP* 1.3 63.9 + - - +
460A LEU* 3.8 0.8 - - - +
461A ASP* 2.6 57.6 + - - +
504A TYR* 4.8 0.6 + - - -
887A ARG 4.9 5.4 + - - +
888A GLN* 3.4 27.6 + - - +
889A ASN* 4.1 15.3 - - + +
890A TRP* 3.4 60.7 - - + +
893A ILE* 5.6 2.1 - - - +
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Residues in contact with ASP 458 (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 VAL* 3.9 16.9 - - + +
454A ALA* 3.1 24.3 + - - +
455A ILE* 3.7 7.6 - - - +
456A MSE 3.3 0.2 - - - -
457A LYS* 1.3 82.0 + - - +
459A LEU* 1.3 57.5 + - - +
461A ASP* 3.5 6.5 + - - +
462A SER* 3.0 27.9 + - - -
887A ARG* 5.7 2.9 + - - +
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Residues in contact with LEU 459 (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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304A PHE* 4.2 9.0 - - + -
308A LEU* 3.9 37.2 - - + -
428A VAL* 3.6 15.4 - - + +
429A TYR* 4.0 33.2 - - + +
432A SER* 3.9 18.8 - - - +
436A PHE* 3.9 27.6 - - + -
455A ILE 3.3 9.5 + - - +
456A MSE 3.4 5.4 + - - +
458A ASP* 1.3 74.4 - - - +
460A LEU* 1.3 68.8 + - - +
462A SER* 2.9 20.5 + - - +
463A VAL* 3.1 15.7 + - + +
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Residues in contact with LEU 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PHE* 4.4 7.6 - - + -
308A LEU* 3.5 26.9 - - + -
456A MSE 3.0 22.9 + - - +
457A LYS* 3.8 2.9 - - - +
459A LEU* 1.3 76.5 - - - +
461A ASP* 1.3 58.1 + - - +
463A VAL* 3.2 5.5 + - + +
464A LYS* 2.8 31.2 + - - +
500A VAL* 5.1 8.0 - - + +
503A ILE* 4.3 15.7 - - + -
504A TYR* 3.7 32.0 - - + +
507A ILE* 4.1 26.9 - - + -
890A TRP* 3.9 24.0 - - + -
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Residues in contact with ASP 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A LYS* 2.6 57.0 + - - +
458A ASP* 3.6 6.7 - - - +
460A LEU* 1.3 72.2 - - - +
462A SER* 1.3 57.6 + - - +
464A LYS* 3.9 2.9 - - - +
465A SER* 2.9 33.3 + - - -
504A TYR* 2.6 34.6 + - - -
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Residues in contact with SER 462 (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 LYS* 4.8 1.2 - - - +
424A GLU* 4.3 24.6 - - - +
425A ILE* 3.3 37.9 - - - +
428A VAL* 4.2 8.0 - - - +
458A ASP 3.0 13.7 + - - -
459A LEU* 2.9 19.4 + - - +
461A ASP* 1.3 76.3 - - - +
463A VAL* 1.3 62.6 + - - +
465A SER* 4.1 5.7 + - - -
466A PHE* 3.5 12.5 + - - +
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Residues in contact with VAL 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LEU* 5.1 4.9 - - + -
314A ILE* 4.6 2.2 - - + -
318A ILE* 4.1 12.6 - - + -
425A ILE* 3.7 33.0 - - + -
429A TYR* 4.8 4.0 - - + +
459A LEU* 3.1 28.0 + - + +
460A LEU* 3.8 4.3 - - + +
461A ASP 3.1 0.2 - - - -
462A SER* 1.3 76.1 - - - +
464A LYS* 1.3 58.7 + - - +
466A PHE* 3.2 3.7 + - + +
467A GLU* 2.7 33.5 + - - +
497A LEU* 4.0 15.9 - - + -
500A VAL* 3.8 28.9 - - + -
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Residues in contact with LYS 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A LEU 2.8 17.6 + - - +
461A ASP* 3.9 4.5 - - - +
463A VAL* 1.3 77.7 - - - +
465A SER* 1.3 57.2 + - - +
467A GLU* 2.4 35.0 + - - +
468A ASN* 2.8 41.0 + - + +
471A LYS* 5.3 3.0 - - - +
500A VAL* 4.3 11.6 - - + +
501A ASP* 3.0 36.8 + - - +
504A TYR* 3.8 32.8 - - + -
505A ASP* 6.1 0.9 - - - -
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Residues in contact with SER 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A LYS* 3.7 19.3 - - - +
461A ASP 2.9 19.5 + - - -
462A SER* 4.1 5.9 + - - -
464A LYS* 1.3 72.2 - - - +
466A PHE* 1.3 62.7 + - - +
468A ASN* 3.8 5.6 + - - +
469A TYR* 2.9 32.2 + - - +
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Residues in contact with PHE 466 (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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318A ILE* 4.5 18.2 - - + -
321A LEU* 4.2 27.4 - - + -
325A PHE* 5.3 0.2 - + - -
418A ILE* 4.3 8.1 - - + -
421A LYS* 4.0 28.7 - - + -
422A VAL* 3.5 29.6 - - + -
425A ILE* 3.7 16.8 - - + -
462A SER 3.5 13.9 + - - +
463A VAL 3.2 8.2 + - - +
465A SER* 1.3 82.7 + - - +
467A GLU* 1.3 62.4 + - - +
469A TYR* 3.8 1.2 - - - +
470A ILE* 3.0 50.7 + - + +
497A LEU* 3.8 23.6 - - + -
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Residues in contact with GLU 467 (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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463A VAL 2.7 19.5 + - - +
464A LYS* 2.4 41.4 + - - +
466A PHE* 1.3 73.2 - - - +
468A ASN* 1.3 67.6 + - - +
470A ILE* 3.2 4.4 + - - +
471A LYS* 3.1 30.1 + - - +
494A TYR* 2.4 35.3 + - + +
497A LEU* 3.6 42.8 - - + +
498A LEU* 4.5 9.3 - - - +
500A VAL* 4.4 7.2 - - + +
501A ASP* 5.7 1.8 - - - -
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Residues in contact with ASN 468 (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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464A LYS* 2.8 32.8 + - + +
465A SER* 3.9 5.4 + - - +
467A GLU* 1.3 83.5 + - - +
469A TYR* 1.3 63.6 + - - +
471A LYS* 3.3 37.9 + - - +
472A ALA* 4.6 1.7 + - - +
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Residues in contact with TYR 469 (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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346A THR* 3.8 18.4 - - + -
347A ILE* 4.0 18.9 - - + +
350A ASP* 3.0 31.5 + - - +
414A LEU* 4.2 9.9 - - + +
417A ILE* 3.4 26.6 - - + +
418A ILE* 4.2 17.0 - - + -
421A LYS* 3.9 29.2 - - + -
465A SER 2.9 18.0 + - - +
466A PHE 3.8 3.1 - - - +
468A ASN* 1.3 79.4 - - - +
470A ILE* 1.3 75.9 + - + +
471A LYS 3.5 0.2 + - - -
472A ALA* 3.5 19.4 + - - +
473A PHE* 4.2 10.1 - + - -
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Residues in contact with ILE 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU* 4.8 6.3 - - + -
325A PHE* 3.4 29.4 - - + -
418A ILE* 3.6 33.0 - - + -
466A PHE* 3.0 39.4 + - + +
467A GLU 3.2 4.5 + - - +
469A TYR* 1.3 83.1 - - + +
471A LYS* 1.3 66.5 + - - +
472A ALA 3.0 3.9 + - - -
473A PHE* 3.2 20.3 + - + -
490A PHE* 3.5 17.6 - - + -
494A TYR* 3.7 25.8 - - + -
497A LEU* 4.7 7.6 - - + -
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Residues in contact with LYS 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LYS* 5.2 3.5 - - - +
464A LYS* 5.3 2.8 - - - +
467A GLU* 3.1 14.1 + - - +
468A ASN* 3.3 37.2 + - - +
470A ILE* 1.3 76.2 - - - +
472A ALA* 1.3 61.4 + - - +
473A PHE 3.1 1.7 + - - -
474A PHE* 3.5 30.5 - - + +
490A PHE* 5.0 0.4 - - - -
494A TYR* 3.2 33.9 - - + +
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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