Contacts of the helix formed by residues 553 - 581 (chain A) in PDB entry 3H52
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 PRO 553 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A SER 5.2 0.9 - - - +
551A SER 3.2 9.9 - - - +
552A VAL* 1.3 89.5 - - + +
554A ASP* 1.3 65.9 + - - +
555A SER* 3.2 7.6 + - - +
556A THR* 3.2 27.3 + - + +
557A TRP 3.0 18.9 + - - -
558D ARG* 3.5 2.1 + - - -
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Residues in contact with ASP 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A TYR* 4.9 6.4 + - - -
553A PRO* 1.3 72.3 - - - +
555A SER* 1.3 56.5 + - - +
557A TRP* 3.4 2.6 + - - +
558A ARG* 3.0 29.5 + - - +
554D ASP* 3.7 23.6 - - + +
555D SER* 3.0 30.4 + - - +
558D ARG* 3.3 32.1 + - - +
559D ILE* 5.9 0.5 - - - +
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Residues in contact with SER 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A PRO* 3.2 5.2 - - - +
554A ASP* 1.3 77.3 - - - +
556A THR* 1.3 64.9 + - - +
558A ARG* 3.5 2.2 + - - +
559A ILE* 3.1 27.1 + - - +
633A ARG* 3.9 17.1 + - - -
554D ASP* 3.2 24.6 + - - -
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Residues in contact with THR 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A VAL* 3.7 15.9 - - + -
553A PRO* 3.2 28.7 + - + +
555A SER* 1.3 79.5 - - - +
557A TRP* 1.3 62.9 + - - +
559A ILE* 3.0 8.6 - - - +
560A MET* 3.0 35.0 + - + +
633A ARG* 5.1 2.5 + - - +
638A ASP* 3.9 37.6 + - + +
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Residues in contact with TRP 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A ALA 5.4 1.8 - - - -
547A GLY 3.6 25.4 - - - -
549A ASP* 5.7 0.9 - - + -
552A VAL* 3.7 14.7 - - + +
553A PRO 3.0 10.4 + - - +
554A ASP 3.8 3.1 - - - +
556A THR* 1.3 77.0 - - - +
558A ARG* 1.3 58.3 + - - +
560A MET* 4.2 2.2 - - - +
561A THR* 2.7 67.0 + - + +
748A GLU* 4.3 13.5 - - + -
557D TRP* 5.1 1.3 - + - -
558D ARG* 3.6 63.2 - - + +
561D THR* 4.6 9.4 - - + +
562D THR* 4.0 20.0 + - + -
565D MET* 5.3 13.7 - - - -
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Residues in contact with ARG 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A ASP 3.0 17.6 + - - +
555A SER 3.8 3.8 - - - +
556A THR 3.4 0.2 - - - -
557A TRP* 1.3 83.8 - - + +
559A ILE* 1.3 56.0 + - - +
561A THR* 3.8 1.8 - - - -
562A THR* 2.4 44.2 + - - +
548D TYR* 3.4 31.3 + - + +
549D ASP* 2.8 34.1 + - - +
550D SER* 4.9 1.2 - - - +
552D VAL* 2.6 39.0 + - - +
553D PRO 3.9 0.2 - - - -
554D ASP* 3.0 32.7 + - + +
557D TRP* 3.5 49.3 - - + -
558D ARG* 5.9 0.4 - - + +
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Residues in contact with ILE 559 (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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555A SER 3.1 13.6 + - - +
556A THR* 3.0 18.8 - - - +
558A ARG* 1.3 80.5 - - - +
560A MET* 1.3 72.6 + - + +
562A THR* 3.3 5.7 + - - -
563A LEU* 2.9 39.8 + - + +
627A LEU* 4.8 11.6 - - + +
629A ILE* 3.2 36.1 - - + -
633A ARG* 4.2 19.7 - - - +
638A ASP* 4.8 4.7 - - - +
639A MET* 3.8 19.5 - - + -
548D TYR* 6.2 1.6 - - - -
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Residues in contact with MET 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A 486 3.8 39.9 - - + +
556A THR* 3.0 30.4 + - + +
557A TRP* 4.2 2.2 - - - +
559A ILE* 1.3 78.7 - - + +
561A THR* 1.3 63.1 + - - +
563A LEU* 4.1 6.2 - - + +
564A ASN* 2.9 52.1 + - - +
638A ASP* 5.5 1.1 - - + +
639A MET* 3.8 26.5 - - + -
642A GLN* 4.5 1.3 - - - +
735A TYR* 4.6 10.5 - - - +
753A LEU* 5.1 9.6 - - + -
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Residues in contact with THR 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A TRP* 2.7 64.2 + - + +
558A ARG* 3.8 3.6 - - - -
560A MET* 1.3 73.6 - - - +
562A THR* 1.3 64.0 + - - +
564A ASN* 3.3 8.3 + - - +
565A MET* 3.2 38.3 + - - +
557D TRP* 4.9 5.8 - - - +
561D THR* 4.5 15.3 - - + -
565D MET* 6.0 3.8 - - - -
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Residues in contact with THR 562 (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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558A ARG* 2.4 40.0 + - - +
559A ILE* 3.8 6.2 - - - -
561A THR* 1.3 77.8 - - - +
563A LEU* 1.3 62.0 + - - +
565A MET* 3.7 10.1 - - + +
566A LEU* 3.1 21.8 + - - +
627A LEU* 4.2 7.9 - - + -
546D ALA* 3.5 40.7 - - + +
547D GLY 5.3 0.2 - - - -
548D TYR* 4.4 14.9 - - + -
557D TRP* 4.4 13.9 + - + -
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Residues in contact with LEU 563 (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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3A 486 3.8 57.9 - - + -
559A ILE* 2.9 35.4 + - + +
560A MET* 4.1 9.6 - - - +
561A THR 3.2 0.2 - - - -
562A THR* 1.3 75.2 - - - +
564A ASN* 1.3 55.9 + - - +
566A LEU* 3.1 6.3 + - + +
567A GLY* 2.5 36.4 + - - -
623A PHE* 3.5 44.2 - - + -
627A LEU* 3.8 19.3 - - + -
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Residues in contact with ASN 564 (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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3A 486 3.3 39.6 + - + +
560A MET* 2.9 34.5 + - - +
561A THR* 3.3 8.6 + - - +
563A LEU* 1.3 76.2 - - - +
565A MET* 1.3 57.4 + - - +
567A GLY* 3.3 0.9 + - - -
568A GLY* 2.9 24.8 + - - -
752A MET* 3.7 41.7 - - + +
753A LEU* 5.5 7.5 - - - +
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Residues in contact with MET 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A THR* 3.2 30.8 + - - +
562A THR* 3.7 13.2 - - + +
564A ASN* 1.3 77.6 - - - +
566A LEU* 1.3 59.2 + - - +
568A GLY* 3.3 4.1 + - - -
569A ARG* 3.1 35.3 + - - +
752A MET* 5.2 1.1 - - - -
528B LEU* 3.1 25.1 - - + +
529B THR* 3.0 40.4 - - - +
530B PRO 4.4 10.1 - - - +
531B THR* 4.8 2.5 - - - +
546D ALA 5.6 2.2 - - - +
557D TRP* 5.2 15.5 - - + -
561D THR* 5.9 2.5 - - - -
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Residues in contact with LEU 566 (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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3A 486 4.4 9.4 - - + -
562A THR 3.1 19.0 + - - +
563A LEU* 3.1 13.4 + - + +
565A MET* 1.3 73.1 - - - +
567A GLY* 1.3 60.0 + - - +
569A ARG* 3.1 31.4 + - - +
570A GLN* 2.8 41.5 + - + +
623A PHE* 3.9 23.6 - - + +
624A ALA* 4.2 4.7 - - + -
627A LEU* 4.7 0.2 - - + -
544D LEU* 3.9 22.2 - - + +
545D TYR 3.4 10.1 - - - +
546D ALA* 3.9 21.1 - - + -
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Residues in contact with GLY 567 (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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3A 486 3.3 45.0 - - - -
563A LEU 2.5 15.9 + - - -
564A ASN 3.6 0.4 - - - -
566A LEU* 1.3 72.4 - - - +
568A GLY* 1.3 62.4 + - - +
570A GLN* 2.9 15.7 + - - +
571A VAL* 3.0 16.5 + - - +
604A MET* 4.0 0.6 - - - +
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Residues in contact with GLY 568 (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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3A 486 3.9 15.7 - - - -
564A ASN 2.9 14.6 + - - -
565A MET* 3.3 5.8 + - - -
567A GLY* 1.3 74.3 - - - +
569A ARG* 1.3 61.3 + - - +
571A VAL* 3.3 4.4 + - - +
572A ILE* 3.2 27.7 + - - +
529B THR* 5.2 8.3 - - - -
2266N ILE* 4.5 14.0 - - - +
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Residues in contact with ARG 569 (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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565A MET* 3.1 17.3 + - - +
566A LEU* 3.1 25.6 + - - +
568A GLY* 1.3 76.3 - - - +
570A GLN* 1.3 61.7 + - - +
572A ILE* 3.4 10.3 + - + +
573A ALA* 3.1 22.0 + - - +
529B THR* 3.8 27.4 + - + -
534B SER* 3.6 31.1 + - - +
537B GLU* 3.2 36.6 + - - +
538B VAL* 4.8 5.4 - - + -
661C GLU* 5.8 1.2 + - - -
544D LEU* 3.6 20.8 - - + +
545D TYR* 2.4 33.3 + - - +
546D ALA* 3.6 15.8 + - - +
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Residues in contact with GLN 570 (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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3A 486 2.6 54.6 + - - +
566A LEU* 2.8 26.0 + - + +
567A GLY 2.9 7.8 + - - +
569A ARG* 1.3 73.9 - - - +
571A VAL* 1.3 56.6 + - - +
573A ALA* 3.3 4.2 + - - +
574A ALA* 2.7 34.8 + - - +
604A MET* 3.5 24.8 + - + +
611A ARG* 3.3 16.6 + - - +
623A PHE 3.9 6.8 - - - +
544D LEU* 4.3 19.0 + - + +
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Residues in contact with VAL 571 (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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3A 486 3.4 25.4 - - - -
567A GLY 3.0 13.2 + - - +
568A GLY* 3.5 7.0 - - - +
569A ARG 3.3 0.2 - - - -
570A GLN* 1.3 73.0 - - - +
572A ILE* 1.3 66.4 + - - +
573A ALA 3.1 0.2 + - - -
574A ALA* 3.2 2.9 + - + +
575A VAL* 3.0 26.4 + - + +
600A TRP* 4.1 11.2 - - + -
604A MET* 3.0 30.5 - - + -
2263N LEU* 4.4 8.1 - - + -
2266N ILE* 4.3 13.7 - - + -
2267N ILE* 4.0 28.3 - - + -
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Residues in contact with ILE 572 (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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568A GLY 3.2 15.3 + - - +
569A ARG* 3.6 11.4 - - - +
570A GLN 3.4 0.2 - - - -
571A VAL* 1.3 79.8 - - - +
573A ALA* 1.3 56.3 + - - +
575A VAL* 3.2 3.8 + - - +
576A LYS* 3.0 46.8 + - + +
529B THR* 5.2 8.3 - - + -
538B VAL* 3.5 41.1 - - + +
2266N ILE* 3.6 22.4 - - + -
2270N ALA* 4.3 19.7 - - + +
2274N SER* 4.9 8.3 - - - +
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Residues in contact with ALA 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A ARG 3.1 14.2 + - - +
570A GLN* 3.6 7.9 - - - +
571A VAL 3.1 0.6 - - - -
572A ILE* 1.3 75.2 - - - +
574A ALA* 1.3 65.3 + - - +
576A LYS* 3.4 16.5 + - - +
577A TRP* 2.9 24.3 + - - +
537B GLU* 6.4 0.9 - - + -
541D PRO* 4.1 17.7 - - + +
544D LEU* 4.2 22.9 - - + -
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Residues in contact with ALA 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A GLN 2.7 20.7 + - - +
571A VAL* 3.2 8.7 + - - +
573A ALA* 1.3 74.1 - - - +
575A VAL* 1.3 51.1 + - + +
577A TRP* 3.3 16.2 - - + +
578A ALA* 2.7 33.4 + - - +
596A LEU* 4.4 4.9 - - + -
600A TRP* 5.4 3.4 - - + -
603A LEU* 4.4 22.4 - - + -
604A MET* 4.6 13.7 - - + -
541D PRO* 5.7 0.4 - - - -
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Residues in contact with VAL 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A VAL* 3.0 19.1 + - + +
572A ILE 3.6 7.0 - - - +
574A ALA* 1.3 72.7 - - + +
576A LYS* 1.3 69.9 + - - +
578A ALA* 2.8 3.3 + - - +
579A LYS* 2.7 24.3 + - + +
596A LEU* 3.6 40.8 - - + -
600A TRP* 6.5 0.9 - - + -
2267N ILE* 4.1 24.0 - - + +
2270N ALA* 3.5 27.8 - - + +
2271N LEU* 3.6 21.3 - - + +
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Residues in contact with LYS 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A ILE* 3.0 34.7 + - + +
573A ALA* 3.6 16.2 - - - +
575A VAL* 1.3 77.2 - - - +
577A TRP* 1.3 63.2 + - - +
579A LYS* 3.1 6.4 + - - +
580A ALA* 3.1 18.4 + - - +
537B GLU* 2.8 30.3 + - - +
538B VAL* 3.1 21.1 + - - +
540B GLU* 3.9 13.3 + - - +
542B GLU* 3.8 45.6 - - + +
541D PRO* 6.2 0.2 - - + -
2270N ALA* 5.3 5.4 - - + +
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Residues in contact with TRP 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A ALA 2.9 14.1 + - - +
574A ALA* 3.3 19.5 - - + +
576A LYS* 1.3 72.4 - - - +
578A ALA* 1.3 72.9 + - + +
580A ALA* 2.7 30.3 + - - +
581A ILE* 3.2 38.3 + - + +
603A LEU* 3.6 43.7 - - + -
667A LYS* 3.0 41.5 - - + +
668A THR* 3.9 11.2 - - - -
671A LEU* 4.0 16.6 - - + -
536D LEU* 4.9 3.2 + - + +
539D ILE* 3.4 35.2 - - + +
540D GLU* 3.7 4.3 + - - -
541D PRO* 3.7 23.5 - - + +
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Residues in contact with ALA 578 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A ALA 2.7 18.0 + - - +
575A VAL 2.8 6.9 + - - +
577A TRP* 1.3 76.7 - - + +
579A LYS* 1.3 63.8 + - - +
581A ILE* 3.0 30.8 + - - +
584A PHE* 3.4 21.1 - - + -
585A ARG 4.6 0.2 + - - -
596A LEU* 3.6 25.8 - - + -
671A LEU* 3.7 18.6 - - + -
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Residues in contact with LYS 579 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A VAL* 2.7 21.6 + - + +
576A LYS* 3.4 8.7 - - - +
578A ALA* 1.3 72.8 - - + +
580A ALA* 1.3 57.1 + - - +
581A ILE 3.4 0.2 - - - -
585A ARG* 3.0 35.0 + - - +
589A LEU* 5.8 2.0 - - + -
592A GLN* 4.2 13.0 - - - +
542B GLU* 2.8 46.2 + - - +
2270N ALA 3.4 6.1 + - - -
2271N LEU* 2.7 60.7 + - + +
2272N MET* 4.0 7.3 + - - +
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Residues in contact with ALA 580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A LYS 3.1 9.4 + - - +
577A TRP* 2.7 19.6 + - - +
579A LYS* 1.3 72.1 - - - +
581A ILE* 1.3 60.3 + - - -
582A PRO* 3.3 1.2 - - - +
585A ARG* 4.1 9.2 - - - +
542B GLU* 6.4 0.2 - - + -
543B VAL* 4.0 21.5 - - + +
545B TYR* 2.8 30.4 + - - -
539D ILE* 3.3 31.4 - - + +
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Residues in contact with ILE 581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A TRP* 3.2 51.3 + - + +
578A ALA* 3.0 26.5 + - - +
580A ALA* 1.3 73.4 - - - +
582A PRO* 1.3 82.0 - - + +
584A PHE* 3.8 14.1 - - + -
585A ARG* 2.8 24.6 + - - +
668A THR* 3.8 20.2 - - + +
671A LEU* 4.4 5.2 - - + -
672A LEU* 6.0 0.2 - - + -
693A TYR* 3.4 18.8 - - + +
536D LEU* 4.1 9.0 - - + -
539D ILE* 4.0 2.7 - - + -
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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).
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