Contacts of the helix formed by residues 661 - 684 (chain A) in PDB entry 5IYB
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 661 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656A SER 3.4 1.4 + - - -
657A TYR 3.4 17.7 + - - -
658A LEU 5.3 0.7 - - - -
659A GLU 3.5 1.2 - - - -
660A MET* 1.3 79.5 - - - +
662A HIS* 1.3 67.3 + - - -
663A ASP 3.3 2.2 - - - -
664A ILE 3.0 15.0 + - - -
665A THR* 3.1 13.2 + - - -
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Residues in contact with HIS 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A PRO* 3.2 43.2 - - + +
523A ARG* 3.5 42.6 + - - -
525A ILE* 4.3 2.6 - - - +
657A TYR* 3.5 28.0 + - + +
661A GLY* 1.3 71.9 - - - -
663A ASP* 1.3 77.1 + - + +
665A THR* 3.3 2.9 + - - -
666A ARG* 2.8 30.0 + - - +
127F ASP* 5.5 2.7 - - - -
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Residues in contact with ASP 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A PRO* 5.3 0.2 - - - -
661A GLY 3.1 1.2 + - - -
662A HIS* 1.3 96.4 + - + +
664A ILE* 1.3 63.9 + - + +
666A ARG* 3.1 22.2 - - - +
667A LEU* 3.1 21.0 + - - +
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Residues in contact with ILE 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A PRO* 3.7 24.0 - - + -
660A MET* 3.4 57.4 - - + +
661A GLY 3.0 4.2 + - - +
663A ASP* 1.3 74.7 - - + +
665A THR* 1.3 61.4 + - - +
667A LEU* 3.3 9.5 + - + +
668A PHE* 2.9 26.6 + - + +
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Residues in contact with THR 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A ILE* 3.8 18.8 - - + -
653A VAL 4.2 14.8 - - - +
656A SER* 3.6 7.1 + - - -
657A TYR* 3.2 30.6 + - + -
661A GLY 3.1 10.4 + - - -
662A HIS* 3.7 7.9 - - - -
664A ILE* 1.3 75.4 - - - +
666A ARG* 1.3 57.2 - - - +
668A PHE* 3.3 15.1 + - + +
669A TYR* 2.9 53.1 + - + -
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Residues in contact with ARG 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A SER* 4.8 5.3 + - - +
375A ILE* 3.0 47.9 - - - +
376A ASP* 4.5 9.4 - - - +
473A ARG* 6.0 0.4 - - - +
521A VAL* 2.5 44.1 + - - +
522A PRO* 2.9 37.2 - - + +
525A ILE* 3.2 20.7 - - - +
535A MET* 3.6 12.5 - - - +
662A HIS 2.8 10.8 + - - +
663A ASP* 3.1 20.0 - - - +
665A THR* 1.3 77.3 - - - +
667A LEU* 1.3 64.5 + - + +
669A TYR* 3.3 18.7 + - - +
670A SER* 3.4 15.4 + - - -
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Residues in contact with LEU 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A SER* 5.9 3.1 - - - +
568A SER* 4.2 15.5 - - - +
569A THR* 3.7 25.1 - - + +
663A ASP* 3.1 22.5 + - - +
664A ILE* 3.3 10.1 + - + +
666A ARG* 1.3 79.5 - - + +
668A PHE* 1.3 55.9 + - - +
670A SER* 3.5 6.9 + - - -
671A ASN* 2.6 46.2 + - - +
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Residues in contact with PHE 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A PHE* 5.4 0.2 - + - -
595A ILE* 3.4 42.8 - - + +
596A ILE* 3.7 17.5 - - + -
597A PRO* 4.1 15.3 - - + -
600A ILE* 5.4 0.4 - - + -
645A LEU* 5.0 0.9 - - + -
652A LEU* 4.2 26.9 - - + -
653A VAL* 4.0 25.4 - - + -
656A SER* 4.0 18.8 - - - -
664A ILE* 2.9 17.5 + - + +
665A THR* 3.6 11.4 - - + +
666A ARG 3.2 0.2 - - - -
667A LEU* 1.3 76.5 - - - +
669A TYR* 1.3 64.0 + + - +
671A ASN* 3.3 2.0 + - - +
672A ILE* 2.9 41.8 + - + +
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Residues in contact with TYR 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ILE* 3.5 23.8 - - + -
487A SER* 4.0 22.9 - - - -
525A ILE* 4.3 10.4 - - + +
535A MET* 2.2 55.8 + - + +
536A GLY* 4.7 0.9 - - - -
537A ILE* 4.3 18.6 - - + -
653A VAL* 3.4 38.1 - - + +
665A THR* 2.9 43.9 + - + -
666A ARG* 3.3 8.5 + - - +
668A PHE* 1.3 74.9 - + - +
670A SER* 1.3 64.0 + - - +
672A ILE* 3.2 21.2 - - + +
673A GLN* 3.5 14.0 + - - +
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Residues in contact with SER 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A PRO 5.7 0.6 - - - +
373A LEU 4.1 3.5 + - - -
374A SER* 3.1 35.9 + - - -
375A ILE* 3.5 12.7 + - - +
485A ASN* 5.1 1.8 - - - +
666A ARG 3.4 9.1 + - - -
667A LEU* 4.1 9.9 - - - -
669A TYR* 1.3 76.8 - - - +
671A ASN* 1.3 64.2 + - - +
673A GLN* 3.3 7.1 + - - +
674A THR* 3.1 28.8 + - - -
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Residues in contact with ASN 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A PHE 4.3 1.7 - - - +
567A LEU* 3.3 21.3 - - + -
568A SER* 2.6 52.8 + - - -
569A THR* 4.2 6.9 + - - -
595A ILE* 4.7 11.2 - - + +
667A LEU* 2.6 37.7 + - - +
668A PHE* 3.8 4.4 - - - +
670A SER* 1.3 74.3 - - - +
672A ILE* 1.3 65.9 + - - +
674A THR* 3.3 4.7 + - - +
675A VAL* 3.0 30.5 + - - +
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Residues in contact with ILE 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A ILE* 3.9 25.8 - - + -
541A THR* 5.3 2.9 - - + -
545A VAL* 5.1 1.1 - - + -
592A PHE* 3.9 25.6 - - + -
595A ILE* 4.1 6.2 - - + +
645A LEU* 3.7 38.4 - - + -
653A VAL* 6.3 0.2 - - + -
668A PHE* 2.9 35.1 + - + +
669A TYR* 3.2 17.7 - - - +
671A ASN* 1.3 75.4 - - - +
673A GLN* 1.3 66.7 + - - +
675A VAL* 3.4 5.7 - - - +
676A ILE* 3.1 36.6 + - + +
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Residues in contact with GLN 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A PRO* 4.2 19.5 - - + +
375A ILE* 4.0 2.2 - - - +
485A ASN* 3.2 40.0 + - - +
486A LEU* 4.7 6.2 + - - +
487A SER* 3.5 21.4 + - - -
537A ILE* 4.5 8.5 - - + +
541A THR* 3.8 26.2 + - + +
669A TYR* 3.6 14.5 + - - +
670A SER* 3.3 7.1 + - - +
671A ASN 3.3 0.6 - - - -
672A ILE* 1.3 80.7 - - + +
674A THR* 1.3 54.3 + - - +
677A ASN* 2.5 49.8 + - - +
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Residues in contact with THR 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A PRO* 4.8 10.0 + - - -
372A ASN* 5.1 13.3 + - - +
566A PHE* 3.5 43.7 - - + +
670A SER* 3.1 18.7 + - - -
671A ASN* 3.3 5.8 + - - -
673A GLN* 1.3 75.0 - - - +
675A VAL* 1.3 65.4 + - - +
677A ASN* 4.8 2.9 - - - -
678A ASN* 2.7 34.9 + - - +
62K LYS* 6.0 0.2 - - - +
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Residues in contact with VAL 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A PHE* 6.0 2.5 - - + -
563A LEU* 3.7 36.4 - - + +
566A PHE* 4.9 4.0 - - + -
567A LEU* 4.3 20.6 - - + +
591A ILE* 6.0 4.3 - - + -
592A PHE* 5.8 1.1 - - + -
595A ILE* 3.4 34.5 - - + -
671A ASN* 3.0 19.3 + - - +
672A ILE* 3.4 7.6 - - - +
674A THR* 1.3 76.6 - - - +
676A ILE* 1.3 81.0 + - + +
679A TRP* 3.1 28.1 + - - +
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Residues in contact with ILE 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A THR* 3.8 19.1 - - + +
544A ALA* 3.6 12.6 - - + +
545A VAL* 3.6 42.0 - - + +
548A PHE* 3.4 43.3 - - + -
592A PHE* 4.5 6.5 - - + -
672A ILE* 3.1 28.1 + - + +
673A GLN 3.9 0.9 - - - +
675A VAL* 1.3 89.5 - - + +
677A ASN* 1.3 63.9 + - - +
679A TRP* 4.1 3.2 - - + +
680A LEU* 3.2 20.4 + - - +
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Residues in contact with ASN 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A PRO* 4.6 16.0 - - + +
541A THR* 3.2 27.3 + - - +
673A GLN* 2.5 51.5 + - - +
674A THR* 4.4 3.8 - - - +
676A ILE* 1.3 68.2 - - - +
678A ASN* 1.3 60.0 + - - +
680A LEU* 3.3 15.9 + - - +
681A LEU* 3.0 24.3 + - - +
785B TYR 4.6 4.5 - - - +
786B THR* 3.9 11.8 - - - +
787B GLY* 3.8 26.3 - - - +
790B GLN* 4.4 7.4 + - - +
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Residues in contact with ASN 678 (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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562A ASN* 5.5 5.9 + - - +
563A LEU* 4.0 13.0 - - + -
566A PHE* 3.2 54.1 - - + -
674A THR* 2.7 30.4 + - - +
675A VAL 3.9 2.5 - - - +
677A ASN* 1.3 74.9 - - - +
679A TRP* 1.3 67.3 + - - +
681A LEU* 3.0 37.3 - - + +
682A ILE* 3.5 7.3 + - - +
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Residues in contact with TRP 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A ALA 4.1 7.2 - - - -
547A LYS* 4.5 11.7 - - + -
548A PHE* 3.1 65.2 - + + -
553A VAL* 4.0 18.4 - - + +
555A LEU* 4.0 22.4 - - + +
563A LEU* 3.8 13.1 - - + +
675A VAL 3.1 17.7 + - - +
676A ILE* 4.2 6.3 - - + +
678A ASN* 1.3 75.2 - - - +
680A LEU* 1.3 70.6 + - + +
682A ILE* 3.0 40.4 + - + +
683A GLU* 3.1 54.9 + - + -
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Residues in contact with LEU 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A ASP* 3.8 17.9 - - + +
544A ALA* 3.6 30.5 - - + +
547A LYS* 5.3 2.7 - - + +
676A ILE 3.2 14.9 + - - +
677A ASN* 3.3 17.5 - - - +
678A ASN 3.2 0.4 - - - -
679A TRP* 1.3 83.1 - - + +
681A LEU* 1.3 56.2 - - - +
683A GLU* 2.9 10.0 + - + -
684A GLY* 2.7 56.2 + - - +
685A HIS* 4.0 10.5 - - + -
784B SER* 3.7 27.1 - - - +
785B TYR 4.8 6.5 - - - +
787B GLY* 6.1 0.9 - - - +
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Residues in contact with LEU 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A ASN* 6.0 4.5 - - - +
677A ASN 3.0 13.4 + - - +
678A ASN* 3.0 30.1 - - - +
680A LEU* 1.3 77.0 - - - +
682A ILE* 1.3 60.8 + - + +
684A GLY* 5.3 0.2 - - - -
785B TYR* 4.2 22.4 - - + +
786B THR* 3.8 26.2 - - + -
1030B ASN* 3.6 29.1 + - - +
1032B PHE* 3.9 23.3 - - + -
1033B THR* 6.1 1.8 - - + -
1037B ILE* 3.2 18.5 - - - +
40K HIS* 6.3 1.3 - - + -
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Residues in contact with ILE 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A LEU* 5.4 2.2 - - + -
559A GLU* 3.9 38.1 - - + +
562A ASN* 5.4 7.0 - - - +
678A ASN 3.5 4.4 + - - +
679A TRP* 3.0 49.8 + - + +
681A LEU* 1.3 80.2 - - + +
683A GLU* 1.3 63.3 + - - +
1030B ASN* 4.9 11.2 - - - +
1033B THR* 5.1 6.5 - - + +
1035B ARG* 4.0 31.1 + - + +
1036B LYS 3.9 4.3 - - - +
1037B ILE* 3.8 9.2 - - - +
1038B THR* 3.5 20.1 + - - -
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Residues in contact with GLU 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A LYS* 3.4 35.4 + - + +
553A VAL* 5.7 0.7 - - - +
679A TRP* 3.1 54.7 + - + +
680A LEU* 2.9 10.5 + - + +
682A ILE* 1.3 78.9 - - - +
684A GLY* 1.3 59.7 + - - +
1037B ILE* 3.3 4.0 - - - +
1038B THR* 3.3 30.7 + - - +
1039B SER* 3.1 30.1 + - - -
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Residues in contact with GLY 684 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A LYS* 2.7 26.2 + - - -
680A LEU* 2.7 24.9 + - - +
681A LEU 4.6 0.4 + - - -
682A ILE 3.7 1.0 - - - -
683A GLU* 1.3 75.5 - - - +
685A HIS* 1.3 62.0 + - - +
783B ALA* 6.3 0.4 - - - -
784B SER* 5.5 2.0 - - - -
785B TYR 6.0 1.8 - - - -
1037B ILE* 3.5 18.8 - - - +
1039B SER* 4.2 5.4 - - - -
1041B ILE* 5.1 1.8 - - - -
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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