Contacts of the helix formed by residues 450 - 477 (chain A) in PDB entry 1HKC
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 GLY 450 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ALA* 3.9 8.6 - - - +
84A ASP* 5.3 1.2 + - - -
93A LEU* 3.4 36.8 - - - -
95A VAL* 3.6 17.6 - - - +
447A SER* 3.6 9.3 + - - -
448A GLY 3.4 0.6 - - - -
449A SER* 1.3 82.3 - - - +
451A LYS* 1.3 60.9 + - - +
452A GLY 3.4 0.3 + - - -
453A ALA 3.8 0.3 + - - -
454A ALA* 3.7 10.2 + - - +
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Residues in contact with LYS 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A VAL* 4.2 15.0 - - + -
97A VAL* 5.1 3.6 - - + -
105A VAL* 4.9 17.7 - - + -
107A MET* 3.4 29.7 - - + +
216A THR* 3.4 30.3 + - + +
219A TYR* 3.7 25.8 - - + -
220A ASP* 3.6 30.5 + - - -
446A GLU* 5.8 3.4 + - - -
447A SER* 4.7 1.0 - - - -
448A GLY 4.7 0.6 - - - -
450A GLY* 1.3 73.5 - - - +
452A GLY* 1.3 63.6 + - - +
454A ALA* 3.3 7.7 - - - +
455A MET* 3.2 32.7 + - + +
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Residues in contact with GLY 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A VAL* 5.4 0.2 - - - -
212A GLY* 3.4 20.0 - - - -
215A MET* 3.9 15.3 - - - +
216A THR* 2.6 23.2 + - - -
449A SER 3.7 1.6 - - - -
450A GLY 3.2 1.0 - - - -
451A LYS* 1.3 71.7 - - - +
453A ALA* 1.3 66.4 + - - +
454A ALA 2.9 1.6 - - - -
455A MET* 2.9 15.6 + - - +
456A VAL* 3.2 11.5 + - - +
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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
----------------------------------------------------------
82A ALA* 4.5 13.5 - - + -
151A GLY* 4.5 2.2 - - - -
152A PHE 4.5 15.0 - - - +
153A THR* 3.4 24.9 - - - +
205A ALA* 5.4 0.5 - - - +
207A VAL* 4.1 16.4 - - + -
212A GLY* 4.5 3.6 - - - -
449A SER 3.3 10.3 + - - +
450A GLY 4.3 2.7 - - - +
451A LYS 3.6 0.2 - - - -
452A GLY* 1.3 74.2 - - - +
454A ALA* 1.3 55.9 + - - +
456A VAL* 3.5 4.4 + - - +
457A THR* 2.8 34.3 + - - -
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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
----------------------------------------------------------
80A PHE* 3.7 20.5 - - + -
81A ILE 5.6 3.6 - - - +
82A ALA* 5.2 3.3 - - + +
95A VAL* 3.8 34.3 - - + -
97A VAL* 4.9 2.5 - - + -
450A GLY 3.7 7.4 + - - +
451A LYS 3.3 11.4 - - - +
452A GLY 2.9 0.4 - - - -
453A ALA* 1.3 77.9 - - - +
455A MET* 1.3 61.6 + - - +
457A THR* 3.4 5.8 + - - -
458A ALA* 2.9 28.8 + - - +
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Residues in contact with MET 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PRO* 3.5 29.4 - - + -
76A GLU* 3.4 30.9 - - + +
97A VAL* 3.4 37.2 - - + -
215A MET* 4.6 10.4 - - + +
219A TYR* 3.2 35.2 - - + -
451A LYS* 3.2 22.9 - - + +
452A GLY* 2.9 9.0 + - - +
454A ALA* 1.3 75.0 - - - +
456A VAL* 1.3 65.1 + - - +
458A ALA* 3.4 6.0 - - + +
459A VAL* 3.2 26.9 + - - +
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Residues in contact with VAL 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A VAL* 3.8 19.3 - - + -
163A ILE* 3.7 16.4 - - + -
205A ALA* 3.7 15.7 - - + -
207A VAL* 3.6 29.6 - - + -
211A VAL* 4.7 1.3 - - + -
215A MET* 3.5 35.4 - - + -
452A GLY 3.2 5.6 + - - +
453A ALA 3.9 5.4 - - - +
455A MET* 1.3 75.2 - - - +
457A THR* 1.3 68.2 + - - +
459A VAL* 3.3 7.7 + - - +
460A ALA* 3.0 19.8 + - - +
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Residues in contact with THR 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE* 3.4 28.7 - - + -
81A ILE 5.5 0.2 - - - -
149A PRO* 3.6 13.7 - - + -
150A VAL 4.6 0.2 - - - -
151A GLY* 3.1 24.8 - - - -
204A VAL* 3.2 29.1 - - + +
205A ALA* 4.2 3.6 - - - +
453A ALA 2.8 22.2 + - - -
454A ALA* 3.6 7.0 - - - -
456A VAL* 1.3 78.6 - - - +
458A ALA* 1.3 64.8 + - - +
460A ALA* 2.9 6.4 + - - +
461A TYR* 2.8 21.9 + - + +
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Residues in contact with ALA 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU* 4.3 19.5 - - + -
77A LYS 4.9 7.0 - - - +
80A PHE* 3.5 26.5 - - + -
454A ALA 2.9 18.3 + - - +
455A MET* 3.4 12.1 - - + +
457A THR* 1.3 76.9 - - - +
459A VAL* 1.3 62.3 + - - +
461A TYR* 3.3 4.3 + - - +
462A ARG* 3.0 22.5 + - - +
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Residues in contact with VAL 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU* 4.4 18.4 - - + +
215A MET* 5.9 4.5 - - + -
455A MET 3.2 17.0 - - - +
456A VAL* 3.3 8.6 + - - +
458A ALA* 1.3 70.6 - - - +
460A ALA* 1.3 65.2 - - - +
462A ARG* 3.0 47.5 + - - +
463A LEU* 3.1 21.8 + - + +
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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
----------------------------------------------------------
163A ILE* 4.2 16.4 - - + -
204A VAL* 3.9 28.9 - - + +
205A ALA* 4.5 1.8 - - + -
456A VAL 3.0 12.2 + - - +
457A THR* 2.9 12.6 + - - +
459A VAL* 1.3 75.1 - - - +
461A TYR* 1.3 64.9 + - - +
463A LEU* 3.5 9.0 + - - +
464A ALA* 3.1 21.6 + - - +
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Residues in contact with TYR 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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80A PHE* 5.5 2.9 - + + -
147A LYS 5.0 6.7 + - - -
149A PRO* 4.1 33.2 - - + -
202A ASN* 3.7 19.4 + - - -
204A VAL* 4.2 15.6 - - + +
457A THR 2.8 11.0 + - - +
458A ALA* 3.6 9.9 - - - +
460A ALA* 1.3 73.5 - - - +
462A ARG* 1.3 70.0 + - - +
464A ALA* 2.7 26.3 + - + +
465A GLU* 3.0 34.4 + - + +
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Residues in contact with ARG 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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75A SER* 5.7 5.6 + - - -
458A ALA 3.0 11.5 + - - +
459A VAL* 3.0 40.8 + - - +
461A TYR* 1.3 81.5 - - - +
463A LEU* 1.3 96.7 + - - +
464A ALA 3.0 0.3 + - - -
465A GLU* 3.0 15.7 + - - +
466A GLN* 3.2 26.8 + - + +
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Residues in contact with LEU 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 VAL* 3.1 19.1 + - + +
460A ALA* 4.0 6.5 - - - +
462A ARG* 1.3 118.2 - - - +
464A ALA* 1.3 61.1 + - - +
466A GLN* 3.8 23.2 - - - +
467A HIS* 3.3 21.5 + - - +
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Residues in contact with ALA 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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204A VAL* 6.1 2.2 - - + -
460A ALA 3.1 12.8 + - - +
461A TYR* 2.7 30.4 + - + +
463A LEU* 1.3 72.5 - - - +
465A GLU* 1.3 61.7 + - - +
467A HIS* 3.5 6.4 + - - +
468A ARG* 3.0 24.9 + - - +
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Residues in contact with GLU 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 TYR* 3.0 40.9 + - + +
462A ARG* 3.0 10.1 + - - +
464A ALA* 1.3 83.1 - - - +
466A GLN* 1.3 55.9 + - + +
467A HIS 3.2 0.2 - - - -
468A ARG* 3.1 37.9 + - - +
469A GLN* 2.7 46.2 + - - +
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Residues in contact with GLN 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 ARG* 3.2 26.2 + - + +
463A LEU* 3.8 27.5 - - - +
465A GLU* 1.3 78.1 - - + +
467A HIS* 1.3 58.2 + - - +
469A GLN* 3.5 8.9 - - - +
470A ILE* 2.8 40.8 + - + +
765A GLY 3.7 13.5 - - - +
766A PHE* 3.8 46.6 + - + +
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Residues in contact with HIS 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 LEU 3.3 14.8 + - - +
464A ALA* 3.8 6.0 + - - +
465A GLU 3.2 0.2 - - - -
466A GLN* 1.3 78.1 - - - +
468A ARG* 1.3 65.1 + - - +
470A ILE* 4.4 11.4 - - + -
471A GLU* 3.0 63.4 + - + +
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Residues in contact with ARG 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 ALA 3.0 16.0 + - - +
465A GLU* 3.1 39.5 + - - +
467A HIS* 1.3 79.6 + - - +
469A GLN* 1.3 91.8 + - - +
471A GLU* 3.6 5.5 - - - +
472A GLU* 2.9 57.7 + - - +
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Residues in contact with GLN 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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465A GLU* 2.7 32.8 + - - +
466A GLN* 3.5 5.7 + - - +
468A ARG* 1.3 101.0 + - - +
470A ILE* 1.3 59.1 + - - +
472A GLU* 2.7 31.2 + - - +
473A THR* 3.0 14.8 + - - -
764A LYS* 4.8 9.7 - - - +
766A PHE* 4.1 28.0 - - + -
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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
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466A GLN* 2.8 36.9 + - + +
467A HIS* 4.0 11.7 - - + +
469A GLN* 1.3 72.2 - - - +
471A GLU* 1.3 66.0 + - + +
473A THR* 3.4 2.1 + - - -
474A LEU* 3.1 36.7 + - + +
761A PHE* 3.5 30.3 - - + -
766A PHE* 3.5 32.1 - - + -
818A LEU* 4.1 34.3 - - + -
821A THR* 6.2 0.7 - - + -
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Residues in contact with GLU 471 (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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467A HIS* 3.0 58.0 + - + +
468A ARG* 3.6 7.2 - - - +
469A GLN 2.9 0.2 + - - -
470A ILE* 1.3 80.5 - - + +
472A GLU* 1.3 61.7 + - + +
474A LEU* 3.7 11.6 + - - +
475A ALA* 3.2 21.0 + - - +
821A THR* 5.8 2.8 - - - +
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Residues in contact with GLU 472 (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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468A ARG* 2.9 58.3 + - - +
469A GLN* 2.7 15.5 + - - +
471A GLU* 1.3 72.2 - - + +
473A THR* 1.3 65.4 + - - +
475A ALA* 3.0 20.6 + - - +
476A HIS* 3.9 13.9 + - + -
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Residues in contact with THR 473 (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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469A GLN 3.0 11.5 + - - -
470A ILE 3.6 7.9 - - - -
472A GLU* 1.3 76.7 - - - +
474A LEU* 1.3 67.6 + - + +
475A ALA 3.3 0.9 + - - -
476A HIS* 3.4 28.3 + - + +
477A PHE* 4.0 6.1 - - + -
725A TYR* 3.4 35.6 + - + +
757A ILE* 4.9 0.7 - - + -
761A PHE* 3.9 26.2 - - + -
764A LYS* 4.4 9.0 + - - -
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Residues in contact with LEU 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A ILE* 3.1 32.5 + - + +
471A GLU* 4.0 12.3 - - - +
473A THR* 1.3 85.1 - - + +
475A ALA* 1.3 64.3 + - - +
476A HIS 3.2 1.3 - - - -
477A PHE* 3.1 28.0 + - + +
478A HIS* 3.8 3.1 + - - +
757A ILE* 4.4 21.3 - - + -
761A PHE* 4.3 9.6 - - + -
821A THR* 4.3 16.2 - - + -
822A VAL* 4.6 13.0 - - + -
825A VAL* 3.7 35.9 - - + +
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Residues in contact with ALA 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A GLU 3.2 12.8 + - - +
472A GLU* 3.0 18.7 + - - +
474A LEU* 1.3 78.3 - - - +
476A HIS* 1.3 58.9 + - + +
478A HIS* 2.9 32.9 + - + +
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Residues in contact with HIS 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A GLU 4.0 12.3 + - - -
473A THR* 3.4 25.9 - - + +
474A LEU 3.2 0.6 - - - -
475A ALA* 1.3 81.0 - - + +
477A PHE* 1.3 60.2 + - + +
478A HIS 3.2 4.6 + - - +
479A LEU* 4.5 5.9 - - - +
483A MET* 5.9 2.1 - - - +
721A ILE 4.9 4.7 - - - +
723A THR* 4.0 28.2 - - + +
725A TYR* 5.7 4.9 - + - -
829A ARG* 5.2 0.2 + - - -
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Residues in contact with PHE 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A THR 4.0 14.1 - - - -
474A LEU* 3.1 15.7 + - + +
475A ALA 3.0 0.8 - - - -
476A HIS* 1.3 78.6 - - + +
478A HIS* 1.3 61.1 + - - +
479A LEU* 3.4 13.4 + - - +
723A THR* 3.8 20.4 - - + -
725A TYR* 3.9 14.8 - + - -
753A ILE* 3.8 17.0 - - + -
757A ILE* 3.5 31.6 - - + -
825A VAL* 3.3 31.7 - - + +
826A VAL* 4.2 13.0 - - + -
828A ARG* 6.0 1.7 - - - -
829A ARG* 3.4 57.9 - - - +
832A GLN* 5.4 0.7 - - - +
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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