Contacts of the helix formed by residues 665 - 693 (chain A) in PDB entry 5A63
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 SER 665 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A PHE* 3.4 49.9 + - - -
664A ALA* 1.3 74.3 - - - +
666A LYS* 1.3 65.1 + - - +
667A GLU* 3.7 11.4 + - - +
668A LEU* 2.8 37.5 + - - +
669A GLU* 3.0 11.2 + - - +
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Residues in contact with LYS 666 (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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210A PHE* 4.7 9.9 - - + -
664A ALA 3.5 3.0 + - - +
665A SER* 1.3 70.3 - - - +
667A GLU* 1.3 57.9 + - + +
669A GLU* 3.2 22.2 + - - +
670A LEU* 2.9 29.7 + - - +
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Residues in contact with GLU 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A PHE* 6.1 1.4 - - - -
665A SER* 3.0 10.2 - - - +
666A LYS* 1.3 79.8 - - + +
668A LEU* 1.3 57.9 + - - +
670A LEU* 3.2 10.5 + - - +
671A ILE* 2.9 35.2 + - + +
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Residues in contact with LEU 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A ALA* 4.0 21.8 - - + -
665A SER* 2.8 24.6 + - - +
667A GLU* 1.3 75.9 - - - +
669A GLU* 1.3 58.0 + - + +
671A ILE* 3.2 15.0 + - + +
672A THR* 2.9 38.0 + - - +
146C VAL* 5.6 1.3 - - + -
154C PRO* 5.4 8.5 - - + +
155C TYR* 3.7 39.7 - - + +
158C LEU* 6.5 0.7 - - + -
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Residues in contact with GLU 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663A ILE* 5.1 3.8 - - - +
664A ALA* 4.1 24.4 + - + +
665A SER 3.0 12.3 + - - +
666A LYS* 3.2 22.3 + - - +
668A LEU* 1.3 76.5 - - - +
670A LEU* 1.3 56.8 + - - +
672A THR* 3.2 7.1 + - - +
673A LEU* 2.9 29.2 + - - +
2C GLY 3.1 23.8 + - - -
4C ALA* 4.8 12.7 - - + +
5C VAL* 3.4 30.5 - - + +
144C PRO 4.7 7.8 - - - +
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Residues in contact with LEU 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666A LYS 2.9 12.4 + - - +
667A GLU* 3.4 12.8 - - - +
669A GLU* 1.3 76.4 - - - +
671A ILE* 1.3 70.0 + - + +
673A LEU* 3.2 11.0 + - + +
674A THR* 2.9 41.3 + - - +
4C ALA* 5.9 1.1 - - - -
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Residues in contact with ILE 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A GLU* 2.9 19.6 + - + +
668A LEU* 3.4 18.8 - - + +
670A LEU* 1.3 87.7 - - + +
672A THR* 1.3 59.2 + - - +
674A THR* 3.2 10.0 + - + +
675A VAL* 2.9 39.2 + - + +
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Residues in contact with THR 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A LEU* 2.9 22.7 + - - +
669A GLU* 3.4 12.0 - - - -
671A ILE* 1.3 79.8 - - - +
673A LEU* 1.3 57.8 + - - +
675A VAL* 3.2 7.1 + - - +
676A GLY 2.9 24.4 + - - -
5C VAL* 3.8 32.9 - - + +
8C GLY* 3.7 9.3 - - - -
9C CYS* 4.2 5.8 - - - +
158C LEU* 3.4 38.4 - - + +
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Residues in contact with LEU 673 (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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669A GLU 2.9 12.9 + - - +
670A LEU* 3.2 13.2 + - + +
672A THR* 1.3 76.7 - - - +
674A THR* 1.3 61.5 + - - +
676A GLY* 3.2 1.7 + - - -
677A PHE* 2.9 56.8 + - + +
4C ALA* 3.5 39.0 - - + +
7C PHE* 4.4 12.3 - - + -
8C GLY* 4.0 11.1 - - - +
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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
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670A LEU* 2.9 27.2 + - - +
671A ILE* 3.3 14.0 - - + +
673A LEU* 1.3 81.4 - - - +
675A VAL* 1.3 55.1 + - + +
677A PHE* 3.4 4.0 + - - +
678A GLY* 2.6 36.4 + - - -
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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
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671A ILE* 2.9 27.8 + - + +
672A THR* 3.4 10.8 - - - +
674A THR* 1.3 78.9 - - + +
676A GLY* 1.3 54.0 + - - +
678A GLY* 4.8 0.9 - - - -
679A ILE* 2.6 42.6 + - + +
12C VAL* 3.7 9.9 - - + -
158C LEU* 4.9 6.5 - - + -
162C PHE* 3.5 35.0 - - + -
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Residues in contact with GLY 676 (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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672A THR 2.9 11.1 + - - -
673A LEU 3.6 3.6 - - - -
675A VAL* 1.3 76.0 - - - +
677A PHE* 1.3 57.0 - - - +
679A ILE* 3.3 1.4 - - - +
680A LEU* 2.9 25.6 + - - +
8C GLY* 3.3 26.9 - - - -
11C PHE* 3.2 21.3 - - - +
12C VAL* 3.9 6.3 - - - -
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Residues in contact with PHE 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A LEU* 2.9 49.2 + - + +
674A THR* 3.9 4.3 - - - +
676A GLY* 1.3 72.7 - - - +
678A GLY* 1.3 54.4 + - - +
680A LEU* 3.5 9.5 - - + +
681A ILE* 2.8 59.2 + - + +
7C PHE* 5.8 0.9 - - + -
11C PHE* 3.7 34.5 - + - -
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Residues in contact with GLY 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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674A THR* 2.6 23.7 + - - -
675A VAL* 3.6 1.1 - - - -
677A PHE* 1.3 72.6 - - - +
679A ILE* 1.3 56.9 + - - +
681A ILE* 3.2 8.5 + - - +
682A PHE* 2.9 30.4 + - - +
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Residues in contact with ILE 679 (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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675A VAL* 2.6 31.2 + - + +
676A GLY* 3.3 7.4 - - - +
678A GLY* 1.3 71.0 - - - +
680A LEU* 1.3 58.9 + - - +
682A PHE* 3.3 21.5 + - + +
683A SER* 2.9 29.3 + - - -
11C PHE 3.9 3.4 - - - +
12C VAL* 3.6 35.0 - - + +
16C PRO* 5.1 12.6 - - + -
162C PHE* 4.7 15.5 - - + -
165C ALA* 6.5 0.4 - - + -
218C TYR* 5.8 3.8 - - + +
1245C PC1 6.2 2.7 - - + -
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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
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676A GLY 2.9 17.7 + - - +
677A PHE* 3.5 12.3 - - + +
679A ILE* 1.3 78.5 - - - +
681A ILE* 1.3 60.8 + - + +
683A SER* 2.5 24.7 + - - -
684A LEU* 2.9 35.3 + - + +
11C PHE* 3.8 44.2 - - + -
15C GLY* 3.7 31.6 - - - +
18C PHE* 4.5 13.9 - - + -
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Residues in contact with ILE 681 (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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677A PHE* 2.8 49.3 + - + +
678A GLY* 3.6 7.0 - - - +
680A LEU* 1.3 79.8 - - + +
682A PHE* 1.3 58.8 - - - +
684A LEU* 3.2 12.4 + - + +
685A ILE* 2.9 40.7 + - + +
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Residues in contact with PHE 682 (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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678A GLY 2.9 16.0 + - - +
679A ILE* 3.5 23.8 - - + +
681A ILE* 1.3 79.3 - - - +
683A SER* 1.3 61.6 + - - +
685A ILE* 3.2 8.0 + - + +
686A VAL* 2.9 58.5 + - + +
1245C PC1 4.7 15.5 - - + -
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Residues in contact with SER 683 (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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679A ILE* 2.9 14.0 + - - -
680A LEU 2.5 20.6 + - - -
682A PHE* 1.3 83.5 - - - +
684A LEU* 1.3 58.0 + - - +
686A VAL* 4.8 1.1 - - - -
687A THR* 2.6 39.3 + - - -
15C GLY 3.5 8.7 + - - -
16C PRO* 3.5 24.6 - - - +
19C ALA* 3.3 14.8 - - - +
1245C PC1 3.8 17.0 - - - -
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Residues in contact with LEU 684 (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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680A LEU* 2.9 34.6 + - + +
681A ILE* 3.4 14.4 - - + +
683A SER* 1.3 79.6 + - - +
685A ILE* 1.3 59.9 + - + +
688A TYR* 3.0 33.1 + - - +
18C PHE* 5.1 4.5 - - + -
19C ALA* 3.6 30.3 - - + +
22C LEU* 4.8 16.2 - - + -
23C ILE* 3.3 15.9 - - + +
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Residues in contact with ILE 685 (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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681A ILE* 2.9 29.8 + - + +
682A PHE* 3.5 10.5 - - + +
684A LEU* 1.3 79.4 - - + +
686A VAL* 1.3 64.1 + - + +
688A TYR* 3.2 7.6 + - + +
689A CYS* 2.9 44.6 + - - -
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Residues in contact with VAL 686 (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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682A PHE* 2.9 55.0 + - + +
683A SER* 4.1 3.1 - - - +
685A ILE* 1.3 79.1 - - + +
687A THR* 1.3 58.8 + - - +
689A CYS* 3.2 8.1 + - - +
690A ILE* 2.9 52.8 + - + +
1245C PC1 4.8 16.8 - - + -
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Residues in contact with THR 687 (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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683A SER* 2.6 25.0 + - - -
686A VAL* 1.3 77.5 - - - +
688A TYR* 1.3 56.8 + - - +
690A ILE* 3.2 12.1 + - - +
691A ASN* 2.9 27.4 + - - +
19C ALA* 4.0 5.4 - - - +
20C LEU* 3.2 35.3 - - + +
23C ILE* 3.5 30.5 - - + -
24C THR* 4.1 10.1 - - - +
1245C PC1 4.0 16.2 - - + +
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Residues in contact with TYR 688 (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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684A LEU 3.0 20.8 + - - +
685A ILE* 3.4 7.9 - - + +
687A THR* 1.3 78.2 - - - +
689A CYS* 1.3 62.1 + - - +
691A ASN* 3.2 6.5 + - + +
692A ALA* 2.9 35.5 + - + +
23C ILE* 3.5 25.3 - - + +
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Residues in contact with CYS 689 (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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685A ILE* 2.9 33.5 + - - -
686A VAL* 3.4 11.2 - - - +
688A TYR* 1.3 81.5 - - - +
690A ILE* 1.3 58.8 + - + +
692A ALA* 3.2 8.9 + - - +
693A LYS* 2.9 34.7 + - + +
697A LEU* 5.4 0.7 - - - -
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Residues in contact with ILE 690 (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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686A VAL* 2.9 41.2 + - + +
687A THR 3.5 5.6 - - - +
689A CYS* 1.3 77.6 - - + +
691A ASN* 1.3 61.7 + - - +
693A LYS 3.0 4.3 - - - -
694A ALA* 3.0 22.9 + - - +
697A LEU* 4.0 24.5 - - + -
698A PHE* 4.2 13.9 - - + -
229C PHE* 6.2 2.0 - - + -
1245C PC1 3.6 66.9 - - + -
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Residues in contact with ASN 691 (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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687A THR 2.9 6.7 + - - +
688A TYR* 3.2 11.7 + - + +
690A ILE* 1.3 74.8 - - - +
692A ALA* 1.3 63.5 + - - +
694A ALA* 3.3 20.3 + - - +
23C ILE* 3.4 44.9 + - + +
24C THR* 4.3 6.6 - - - +
31C ARG* 5.1 2.4 + - - -
1245C PC1 3.9 25.2 - - + +
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Residues in contact with ALA 692 (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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688A TYR* 2.9 24.6 + - + +
689A CYS* 3.2 12.8 + - - +
691A ASN* 1.3 78.9 - - - +
693A LYS* 1.3 70.2 - - + +
694A ALA 3.5 2.1 + - - -
695A ASP 5.3 0.2 + - - -
696A VAL* 5.2 1.7 - - - +
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Residues in contact with LYS 693 (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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689A CYS* 2.9 17.1 + - + +
690A ILE 3.0 3.8 - - - -
692A ALA* 1.3 86.8 - - + +
694A ALA* 1.3 58.1 + - - +
695A ASP 3.6 2.2 - - - -
696A VAL* 3.8 26.7 - - + +
697A LEU* 3.0 37.0 + - + +
241C ARG 4.5 1.2 + - - -
242C SER* 2.4 57.5 + - - +
244C LEU* 2.9 19.8 + - - +
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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
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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) + - + + + + + -
------------------------------------------------------------
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