Contacts of the helix formed by residues 443 - 466 (chain A) in PDB entry 5HLB
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 443 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A ARG* 2.6 39.9 + - - +
127A LEU* 5.9 0.7 - - - +
441A THR 3.6 0.4 + - - -
442A PHE* 1.3 76.0 - - - +
444A SER* 1.4 58.8 + - - +
445A VAL* 3.2 24.9 + - - +
446A ALA* 3.3 16.6 + - + +
447A GLN* 3.1 28.4 + - - +
485A ARG* 2.8 34.6 + - + +
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Residues in contact with SER 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ARG* 5.5 1.2 - - - +
130A ALA* 3.4 25.6 + - - -
131A THR* 5.6 1.8 - - - -
200A ARG* 3.1 37.8 + - - +
442A PHE* 3.8 16.3 + - - -
443A ASP* 1.4 68.9 + - - +
445A VAL* 1.3 60.8 + - - +
447A GLN* 3.9 0.5 - - - +
448A ASP* 3.0 41.1 + - - +
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Residues in contact with VAL 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLU* 5.7 3.4 - - + +
126A LYS* 3.7 35.8 + - + +
127A LEU* 4.1 38.1 - - + +
130A ALA* 4.1 11.2 - - + -
443A ASP* 3.2 10.4 + - - +
444A SER* 1.3 73.6 - - - +
446A ALA* 1.3 63.9 + - - +
448A ASP* 3.5 5.4 + - - +
449A ALA* 3.2 24.8 + - - +
750A GLN* 4.7 12.1 - - + +
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Residues in contact with ALA 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ASP* 3.3 26.3 + - + +
445A VAL* 1.3 76.9 - - - +
447A GLN* 1.3 58.1 + - - +
449A ALA* 4.5 1.3 - - - -
450A ALA* 3.0 25.5 + - - +
476A VAL* 4.6 1.8 - - + -
485A ARG* 4.4 7.2 - - + +
486A ALA* 3.9 13.0 - - + -
746A TYR* 3.4 31.9 - - - +
750A GLN* 5.4 5.4 + - - +
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Residues in contact with GLN 447 (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 GLN* 3.0 31.2 + - - +
414A PHE* 5.3 1.0 - - - +
442A PHE* 3.6 22.4 - - + -
443A ASP 3.1 21.0 + - - +
444A SER 3.9 2.5 - - - +
446A ALA* 1.3 72.8 - - - +
448A ASP* 1.4 57.2 + - - +
450A ALA* 3.0 3.7 + - - +
451A GLU* 2.7 62.8 + - - +
486A ALA* 3.4 8.8 - - + +
487A MET 3.0 44.4 + - - -
488A VAL* 3.9 7.3 - - - +
493A PRO* 5.3 2.0 - - - +
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Residues in contact with ASP 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ALA* 4.5 12.6 - - - +
200A ARG* 5.8 2.4 + - - -
411A GLN* 5.6 2.6 + - - -
444A SER* 3.0 30.8 + - - +
445A VAL* 3.9 4.7 - - - +
447A GLN* 1.4 75.9 - - - +
449A ALA* 1.4 55.6 + - - +
451A GLU* 3.7 13.4 - - - +
452A LYS* 3.0 32.8 + - - +
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Residues in contact with ALA 449 (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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126A LYS* 5.9 0.2 - - - +
445A VAL 3.2 17.6 + - - +
446A ALA 3.7 4.5 - - - +
448A ASP* 1.4 72.6 - - - +
450A ALA* 1.4 60.4 + - - +
452A LYS* 4.5 1.1 - - - -
453A ALA* 3.1 26.5 + - - +
746A TYR* 3.8 9.8 - - + -
749A ASN* 3.2 33.5 + - + +
750A GLN* 3.8 28.3 - - + -
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Residues in contact with ALA 450 (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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446A ALA 3.0 18.8 + - - +
447A GLN* 3.5 6.3 - - - +
449A ALA* 1.4 73.5 - - - +
451A GLU* 1.4 63.8 + - - +
453A ALA* 3.4 2.5 + - - +
454A ALA* 3.1 19.6 + - - +
474A ILE* 3.4 27.1 - - + +
486A ALA* 4.6 8.3 - - + -
488A VAL* 3.7 18.6 - - + -
746A TYR* 3.5 18.3 - - + -
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Residues in contact with GLU 451 (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 GLN* 2.9 36.5 + - - +
447A GLN* 2.7 39.0 + - - +
448A ASP* 3.7 12.5 - - - +
450A ALA* 1.4 73.0 - - - +
452A LYS* 1.4 50.2 + - - +
454A ALA* 3.2 3.9 + - - +
455A VAL* 2.9 41.2 + - + +
488A VAL* 4.3 3.8 - - + -
493A PRO* 3.9 30.3 - - + +
494A GLN* 3.0 25.4 - - - +
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Residues in contact with LYS 452 (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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448A ASP 3.0 19.1 + - - +
449A ALA* 4.4 0.7 - - - +
451A GLU* 1.4 72.9 - - - +
453A ALA* 1.4 55.2 - - - +
455A VAL* 3.4 5.3 + - - -
456A GLU* 2.9 71.3 + - + +
749A ASN* 2.9 41.0 + - - +
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Residues in contact with ALA 453 (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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449A ALA 3.1 19.0 + - - +
450A ALA* 3.5 6.7 - - - +
452A LYS* 1.4 74.5 - - - +
454A ALA* 1.3 56.5 + - - +
456A GLU* 5.2 0.4 - - - -
457A GLY* 2.9 27.4 + - - -
474A ILE* 4.6 0.4 - - + -
742A ILE* 3.6 35.4 - - + +
745A ARG* 3.8 13.3 - - + +
746A TYR* 3.7 18.2 - - + +
749A ASN* 3.5 5.3 - - - +
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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 ALA 3.1 13.5 + - - +
451A GLU* 3.4 8.1 - - - +
452A LYS 3.2 0.2 - - - -
453A ALA* 1.3 73.1 - - - +
455A VAL* 1.4 63.8 + - - +
458A ILE* 3.1 31.9 + - - +
472A THR* 3.8 27.6 - - + -
474A ILE* 4.4 2.5 - - + -
488A VAL* 4.0 17.5 - - + -
490A GLY 4.2 6.5 - - - +
491A SER 4.1 6.6 - - - +
493A PRO* 4.8 1.6 - - + -
742A ILE* 4.6 4.2 - - - +
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Residues in contact with VAL 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A GLU* 2.9 26.3 + - + +
452A LYS* 4.0 5.6 - - - +
454A ALA* 1.4 70.3 - - - +
456A GLU* 1.3 61.9 + - + +
459A PRO* 3.1 23.3 - - - +
491A SER 3.8 9.0 - - - +
492A GLU* 5.2 0.7 - - - -
493A PRO* 3.7 25.8 - - + -
494A GLN* 5.8 5.8 - - + -
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Residues in contact with GLU 456 (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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452A LYS* 2.9 56.1 + - + +
455A VAL* 1.3 83.9 - - + +
457A GLY* 1.3 62.1 + - - +
458A ILE 3.5 0.4 - - - -
459A PRO* 3.5 4.0 - - - +
460A ALA* 3.4 21.8 + - - +
745A ARG* 3.6 23.6 + - - +
749A ASN* 4.9 1.9 + - - +
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Residues in contact with GLY 457 (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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453A ALA 2.9 24.5 + - - -
456A GLU* 1.3 72.6 - - - +
458A ILE* 1.3 57.5 + - - +
460A ALA* 3.4 2.6 - - - +
461A LEU* 2.9 34.0 + - - +
742A ILE* 3.7 12.1 - - - -
745A ARG* 3.3 23.2 - - - +
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Residues in contact with ILE 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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454A ALA 3.1 21.2 + - - +
457A GLY* 1.3 71.2 - - - +
459A PRO* 1.4 70.7 - - + +
461A LEU* 3.1 6.3 + - + +
462A LYS* 2.9 40.4 + - + +
470A LEU* 3.4 40.1 - - + +
471A GLU 3.9 12.6 - - - +
472A THR* 3.6 38.4 - - + -
491A SER* 3.7 17.9 - - - -
723A VAL* 4.4 5.4 - - + -
742A ILE* 4.2 12.8 - - + -
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Residues in contact with PRO 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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455A VAL* 3.1 28.5 - - - +
456A GLU* 3.5 6.7 - - - +
458A ILE* 1.4 93.5 - - + +
460A ALA* 1.4 59.2 + - - +
462A LYS* 3.4 15.2 + - + +
463A LYS* 3.1 31.6 + - + +
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Residues in contact with ALA 460 (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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456A GLU 3.4 17.7 + - - +
457A GLY* 3.4 6.5 - - - +
458A ILE 3.2 0.2 - - - -
459A PRO* 1.4 79.1 - - - +
461A LEU* 1.4 55.9 + - + +
463A LYS* 3.4 5.9 + - - +
464A GLN* 3.1 42.8 + - - +
745A ARG* 3.6 20.0 - - - +
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Residues in contact with LEU 461 (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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457A GLY* 2.9 21.4 + - - +
458A ILE* 3.1 7.2 + - + +
460A ALA* 1.4 72.4 - - - +
462A LYS* 1.4 64.8 + - - +
464A GLN* 3.8 19.3 - - - +
465A ARG* 3.1 32.8 + - + +
467A LEU* 4.4 1.0 - - - +
470A LEU* 4.0 23.1 - - + -
723A VAL* 4.8 1.3 - - + -
733A LEU* 3.8 29.4 - - + -
737A SER 4.6 0.9 - - - +
738A GLY* 3.9 20.0 - - - +
741A SER* 4.0 15.5 - - - +
742A ILE* 3.7 23.1 - - + -
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Residues in contact with LYS 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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458A ILE* 2.9 32.1 + - + +
459A PRO* 3.5 16.9 - - + +
461A LEU* 1.4 74.6 - - - +
463A LYS* 1.3 52.6 + - + +
466A LYS* 2.8 14.2 + - - -
467A LEU* 2.8 50.8 + - + +
468A SER 3.9 18.4 + - - -
469A ASP* 3.9 1.4 - - - +
470A LEU* 3.6 40.0 + - + +
471A GLU* 5.8 0.4 + - - -
491A SER* 5.3 3.8 + - - -
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Residues in contact with LYS 463 (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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459A PRO* 3.1 21.2 + - + +
460A ALA* 3.5 7.0 - - - +
462A LYS* 1.3 74.5 - - + +
464A GLN* 1.4 64.6 + - + +
466A LYS* 3.3 26.8 + - - +
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Residues in contact with GLN 464 (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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460A ALA* 3.1 33.4 + - + +
461A LEU* 3.7 20.7 + - - +
463A LYS* 1.4 79.3 - - + +
465A ARG* 1.3 78.5 + - + +
466A LYS* 3.8 6.9 - - - +
745A ARG* 5.7 0.2 + - - -
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Residues in contact with ARG 465 (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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461A LEU* 3.1 17.6 + - + +
464A GLN* 1.3 87.9 - - + +
466A LYS* 1.3 79.6 + - - +
467A LEU* 4.1 14.9 - - + +
731A THR 4.4 3.1 - - - +
732A LYS* 3.3 40.6 + - + +
733A LEU* 3.6 46.4 - - + +
734A TYR 4.6 3.0 + - - +
737A SER* 4.7 11.5 + - - -
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Residues in contact with LYS 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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462A LYS 2.8 14.2 + - - -
463A LYS* 3.3 19.6 + - - +
464A GLN 3.8 6.7 - - - +
465A ARG* 1.3 90.0 - - - +
467A LEU* 1.3 67.8 + - - +
732A LYS* 4.9 3.1 - - - -
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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