Contacts of the helix formed by residues 677 - 704 (chain A) in PDB entry 1H3N
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 THR 677 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A TRP* 4.0 15.9 - - + +
663A THR* 4.6 3.6 - - - +
675A VAL* 3.3 29.2 + - + +
676A TRP* 1.3 86.9 - - - +
678A GLU* 1.3 63.7 + - - +
679A GLU* 3.5 10.5 + - - +
680A GLY* 3.1 22.6 + - - -
681A VAL* 3.0 26.5 + - - +
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Residues in contact with GLU 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A THR* 1.3 71.2 - - - +
679A GLU* 1.3 64.5 + - + +
681A VAL* 3.1 16.0 + - - +
682A GLN* 2.8 64.7 + - - +
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Residues in contact with GLU 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A THR* 3.2 10.4 + - - +
678A GLU* 1.3 81.4 - - + +
680A GLY* 1.3 57.4 + - - +
682A GLN* 3.5 22.2 + - - +
683A GLY* 2.9 23.7 + - - -
686A ARG* 4.7 10.9 + - - -
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Residues in contact with GLY 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663A THR* 3.6 22.2 + - - +
677A THR* 3.1 19.0 + - - -
679A GLU* 1.3 75.5 - - - +
681A VAL* 1.3 64.8 + - - +
683A GLY* 3.1 2.8 + - - -
684A ALA* 3.0 18.5 + - - +
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Residues in contact with VAL 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651A PHE* 3.9 28.7 - - + -
655A GLN* 4.2 7.2 - - + +
659A ILE* 3.9 17.7 - - + -
663A THR* 3.4 12.3 - - + +
676A TRP* 4.0 20.6 - - + +
677A THR 3.0 15.4 + - - +
678A GLU* 3.1 19.3 + - - +
680A GLY* 1.3 75.8 - - - +
682A GLN* 1.3 62.4 + - - +
684A ALA* 3.1 4.9 + - - +
685A TRP* 3.1 33.1 + - + +
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Residues in contact with GLN 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678A GLU* 2.8 48.7 + - - +
679A GLU* 3.7 22.4 + - - +
681A VAL* 1.3 77.5 - - + +
683A GLY* 1.3 56.9 + - - +
685A TRP* 3.3 12.0 + - + +
686A ARG* 3.0 47.8 + - - +
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Residues in contact with GLY 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A ILE* 5.5 0.2 - - - -
666A PHE* 6.3 2.7 - - - -
679A GLU 2.9 13.4 + - - -
680A GLY* 3.1 4.9 + - - -
681A VAL 3.1 0.6 - - - -
682A GLN* 1.3 74.5 - - - +
684A ALA* 1.3 64.3 + - - +
686A ARG* 3.3 25.4 + - - +
687A PHE* 3.1 23.4 + - - +
749A MET* 5.2 4.3 - - - +
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Residues in contact with ALA 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A ILE* 3.4 33.4 - - + +
662A ILE* 3.9 26.7 - - + -
663A THR* 3.5 9.4 - - - +
680A GLY 3.0 6.9 + - - +
681A VAL 3.4 8.7 - - - +
683A GLY* 1.3 77.9 - - - +
685A TRP* 1.3 61.6 + - - +
687A PHE* 3.3 3.4 + - - +
688A LEU* 3.0 30.3 + - - +
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Residues in contact with TRP 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TYR* 3.8 29.4 - + - -
6A PRO* 3.8 18.8 - - + -
7A HIS* 5.9 2.2 - + - -
654A GLU 5.0 2.5 - - - -
655A GLN* 2.6 37.1 + - - -
659A ILE* 3.2 33.5 - - + +
681A VAL* 3.1 31.3 + - + -
682A GLN* 3.5 13.2 - - + +
683A GLY 3.3 0.2 - - - -
684A ALA* 1.3 77.9 - - - +
686A ARG* 1.3 59.0 + - + +
688A LEU* 3.8 3.0 - - - +
689A ASN* 2.8 60.9 + - - +
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Residues in contact with ARG 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A GLU* 4.7 10.5 + - - -
682A GLN* 3.0 43.6 + - + +
683A GLY* 3.5 23.8 - - - +
684A ALA 3.3 0.2 - - - -
685A TRP* 1.3 75.8 - - + +
687A PHE* 1.3 58.0 + - - +
689A ASN* 3.8 8.1 - - - +
690A ARG* 3.1 31.1 + - - +
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Residues in contact with PHE 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A ILE* 4.2 24.0 - - + -
683A GLY 3.1 13.4 + - - +
684A ALA* 3.7 7.6 - - - +
685A TRP 3.2 0.2 - - - -
686A ARG* 1.3 74.5 - - - +
688A LEU* 1.3 71.7 + - + +
690A ARG* 3.2 7.2 + - + +
691A ILE* 3.1 37.5 + - + +
745A ILE* 4.1 14.8 - - + -
748A LEU* 4.2 12.8 - - + -
749A MET* 3.6 50.3 - - + -
752A LEU* 4.0 11.0 - - + -
775A TYR* 3.4 26.7 - + - -
779A LEU* 4.5 9.2 - - + -
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Residues in contact with LEU 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TYR* 3.7 36.1 - - + +
658A ASP* 3.8 9.4 - - + +
659A ILE* 3.8 35.0 - - + +
662A ILE* 4.2 11.7 - - + -
684A ALA 3.0 18.6 + - - +
685A TRP 4.0 1.6 - - - +
687A PHE* 1.3 78.2 - - + +
689A ASN* 1.3 62.3 + - - +
691A ILE* 3.3 14.7 + - + +
692A TYR* 3.0 23.7 + - - +
783A ALA* 4.0 21.5 - - + -
786A LEU* 3.8 23.2 - - + +
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Residues in contact with ASN 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LYS* 5.3 8.8 - - + +
4A TYR* 3.4 36.4 + - - +
685A TRP* 2.8 46.2 + - - +
686A ARG* 3.8 6.9 - - - +
688A LEU* 1.3 72.7 - - - +
690A ARG* 1.3 57.6 + - - +
692A TYR* 3.5 2.1 + - - +
693A ARG* 2.9 31.6 + - - +
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Residues in contact with ARG 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A ARG 3.1 19.8 + - - +
687A PHE* 3.2 8.5 + - - +
689A ASN* 1.3 75.3 - - - +
691A ILE* 1.3 62.9 + - - +
693A ARG* 4.4 3.8 - - - +
694A ARG* 3.3 10.2 + - - +
752A LEU* 3.7 15.2 - - + +
753A ASN* 3.0 31.2 + - - +
756A TYR* 2.7 79.4 + - + +
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Residues in contact with ILE 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A PHE* 3.1 47.7 + - + +
688A LEU* 3.3 15.7 + - + +
690A ARG* 1.3 73.3 - - - +
692A TYR* 1.3 66.4 + - - +
694A ARG* 3.3 3.8 + - - +
695A VAL* 3.2 25.7 + - + +
752A LEU* 3.7 23.8 - - + -
775A TYR* 4.0 19.7 - - + +
776A LEU* 5.1 1.1 - - + -
779A LEU* 4.0 28.3 - - + -
786A LEU* 4.3 5.6 - - + -
790A LEU* 3.8 21.1 - - + -
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Residues in contact with TYR 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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2A GLU* 2.9 56.3 + - + +
3A LYS* 3.7 11.1 + - - -
4A TYR* 3.6 35.9 - + + -
5A ASN 5.1 1.3 - - - -
688A LEU 3.0 13.6 + - - +
689A ASN 3.7 4.0 - - - +
691A ILE* 1.3 82.4 - - - +
693A ARG* 1.3 60.4 + - - +
695A VAL* 3.2 3.5 + - - +
696A ALA* 2.8 33.9 + - + -
786A LEU* 4.1 13.0 - - + -
789A GLU* 5.7 4.0 - - + -
790A LEU* 4.0 20.4 - - + -
793A TRP* 3.7 26.2 - + - -
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Residues in contact with ARG 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.5 26.3 - - + +
689A ASN 2.9 18.6 + - - +
690A ARG* 4.4 2.2 - - - +
692A TYR* 1.3 81.2 - - + +
694A ARG* 1.3 59.4 + - - +
697A GLU* 3.0 47.8 + - - +
756A TYR* 3.7 31.7 - - - +
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Residues in contact with ARG 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A ARG 3.3 16.0 + - - +
691A ILE 3.6 4.9 - - - +
692A TYR 3.3 0.6 - - - -
693A ARG* 1.3 80.2 - - - +
695A VAL* 1.3 64.4 + - + +
697A GLU* 3.7 19.2 + - - +
698A ASP* 3.0 52.2 + - - +
752A LEU* 4.3 12.6 - - + -
755A LEU* 4.6 6.7 - - + -
756A TYR* 3.4 61.2 + - + +
759A ARG* 3.7 29.1 - - - +
768A TYR* 3.3 14.4 + - - +
772A ILE* 4.9 7.6 - - + -
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Residues in contact with VAL 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691A ILE* 3.5 17.0 - - + +
692A TYR 3.2 6.5 + - - +
694A ARG* 1.3 77.7 - - + +
696A ALA* 1.3 59.9 + - - +
698A ASP 3.2 2.9 + - - -
699A ARG* 2.8 27.0 + - - -
702A LEU* 4.2 7.8 - - + +
772A ILE* 4.4 24.7 - - + -
776A LEU* 5.1 4.0 - - + -
790A LEU* 3.9 26.7 - - + -
793A TRP* 3.8 12.1 - - + -
794A PHE* 3.5 33.4 - - + -
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Residues in contact with ALA 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.1 18.4 - - + +
2A GLU* 3.9 20.9 - - - +
692A TYR* 2.8 34.2 + - + +
693A ARG 4.1 2.9 - - - +
695A VAL* 1.3 72.2 - - - +
697A GLU* 1.3 63.9 + - - +
698A ASP 3.3 0.5 + - - -
699A ARG* 3.3 15.9 + - - +
700A GLU 5.0 0.2 + - - -
793A TRP* 3.8 14.5 - - + -
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Residues in contact with GLU 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.5 23.6 - - - +
693A ARG* 3.0 36.3 + - + +
694A ARG* 3.7 26.5 - - - +
695A VAL 3.3 0.2 - - - -
696A ALA* 1.3 77.9 - - - +
698A ASP* 1.3 62.5 + - - +
699A ARG 3.8 0.2 + - - -
700A GLU* 5.1 2.8 + - - +
759A ARG* 5.3 2.0 - - - +
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Residues in contact with ASP 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A ARG* 3.0 25.1 + - - +
695A VAL 3.2 4.3 + - - -
697A GLU* 1.3 79.6 - - - +
699A ARG* 1.3 58.8 + - - +
700A GLU 3.4 2.5 - - - -
701A ALA* 3.3 6.1 + - - +
702A LEU* 2.8 43.3 + - + +
759A ARG* 2.8 41.0 + - - -
764A VAL* 3.6 15.6 - - + +
768A TYR* 2.7 26.9 + - + -
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Residues in contact with ARG 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A GLU* 4.8 6.3 + - - -
695A VAL 2.8 13.3 + - - +
696A ALA* 3.3 17.5 + - - +
697A GLU 3.5 0.4 - - - -
698A ASP* 1.3 77.0 - - - +
700A GLU* 1.3 64.1 + - - +
702A LEU* 3.6 1.9 - - - +
703A LEU* 3.0 42.0 + - + +
793A TRP* 3.3 69.0 + - + +
794A PHE* 3.9 19.7 - - + -
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Residues in contact with GLU 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A ALA 5.0 0.4 + - - -
697A GLU 5.1 2.0 + - - +
698A ASP 3.4 1.0 - - - -
699A ARG* 1.3 79.4 - - - +
701A ALA* 1.3 64.0 + - - +
703A LEU* 3.3 18.5 + - + +
704A GLU* 3.4 23.3 + - - +
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Residues in contact with ALA 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697A GLU 5.7 0.2 + - - -
698A ASP* 3.3 6.3 + - - +
700A GLU* 1.3 78.6 - - - +
702A LEU* 1.3 62.1 + - - +
704A GLU* 3.0 25.9 + - - +
705A THR* 2.8 21.4 + - - +
759A ARG* 6.1 0.2 - - - +
764A VAL* 3.7 30.7 - - + -
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Residues in contact with LEU 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A VAL* 4.2 11.4 - - + +
698A ASP* 2.8 40.8 + - + +
700A GLU 3.3 0.2 - - - -
701A ALA* 1.3 71.2 - - - +
703A LEU* 1.3 62.0 + - - +
705A THR* 3.1 12.9 + - - +
764A VAL* 3.7 22.2 - - + +
768A TYR* 4.1 8.5 - - + -
769A ARG* 2.9 57.5 + - + +
772A ILE* 4.4 16.6 - - + -
794A PHE* 3.6 37.9 - - + -
795A TRP* 6.3 0.9 - - + -
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Residues in contact with LEU 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699A ARG* 3.0 36.3 + - + +
700A GLU* 3.5 11.9 - - - +
701A ALA 3.2 0.2 - - - -
702A LEU* 1.3 78.6 - - - +
704A GLU* 1.3 58.0 + - - +
705A THR 3.3 3.3 + - - +
769A ARG* 4.3 6.5 + - - +
793A TRP 3.6 22.2 - - - +
794A PHE* 3.9 14.1 - - + +
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Residues in contact with GLU 704 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700A GLU* 3.4 21.0 - - - +
701A ALA* 3.0 25.4 - - - +
703A LEU* 1.3 77.5 - - - +
705A THR* 1.3 60.0 + - - +
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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