Contacts of the helix formed by residues 672 - 699 (chain M) in PDB entry 3HOU
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 ASP 672 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670M ILE 3.9 2.0 + - - -
671M ALA* 1.3 73.3 - - - +
673M GLY* 1.3 73.5 + - - +
674M PRO* 2.8 33.0 - - - +
675M THR* 3.0 5.9 + - - -
676M MET* 2.9 19.6 + - - +
736M ASN* 2.9 39.0 + - - +
738M LYS* 5.6 7.5 - - - +
195O GLN* 3.4 25.8 + - - +
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Residues in contact with GLY 673 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671M ALA 3.6 2.7 + - - -
672M ASP* 1.3 76.2 + - - +
674M PRO* 1.3 66.6 - - - +
676M MET* 3.1 20.5 + - - +
677M ARG* 3.2 6.9 + - - +
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Residues in contact with PRO 674 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672M ASP* 2.8 35.0 - - - +
673M GLY* 1.3 75.9 - - - +
675M THR* 1.3 52.0 + - - +
676M MET 2.7 15.7 + - - -
677M ARG* 2.9 25.8 + - + +
678M GLU* 2.7 30.8 + - - +
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Residues in contact with THR 675 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671M ALA* 4.7 3.8 - - + -
672M ASP* 3.0 10.9 + - - -
674M PRO* 1.3 79.9 - - - +
676M MET* 1.3 57.4 + - - +
678M GLU* 4.0 17.8 + - - +
679M ILE* 2.9 23.4 + - - +
732M LEU* 3.9 21.5 - - + +
733M ALA* 4.1 5.6 - - - -
736M ASN* 2.3 56.0 + - + +
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Residues in contact with MET 676 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670M ILE* 4.9 7.0 - - + -
671M ALA* 3.5 44.0 - - + +
672M ASP 2.9 3.6 + - - +
673M GLY* 3.1 12.3 - - - +
674M PRO 2.7 2.0 + - - -
675M THR* 1.3 76.4 - - - +
677M ARG* 1.3 58.1 + - - +
678M GLU 3.0 1.1 - - - -
679M ILE* 2.6 37.7 + - - +
680M THR* 3.0 12.1 + - - -
762M SER* 2.9 31.0 - - - +
763M ALA 5.6 1.6 - - - +
803M SER* 5.0 5.2 - - - +
805M LEU* 5.6 4.3 - - + -
806M ARG* 4.5 28.9 - - + +
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Residues in contact with ARG 677 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673M GLY 3.2 7.4 + - - +
674M PRO* 2.9 27.4 + - + +
676M MET* 1.3 76.9 - - - +
678M GLU* 1.3 73.0 + - - +
680M THR* 2.8 23.8 + - - +
681M GLU* 3.2 46.8 + - - +
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Residues in contact with GLU 678 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674M PRO 2.7 19.1 + - - +
675M THR* 4.0 19.4 + - - +
677M ARG* 1.3 85.5 + - - +
679M ILE* 1.3 57.0 + - - +
681M GLU* 3.0 29.9 - - - +
682M THR* 2.9 19.6 + - - +
732M LEU* 3.6 32.3 - - + +
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Residues in contact with ILE 679 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671M ALA* 4.7 1.6 - - + -
675M THR 2.9 24.2 - - - +
676M MET* 2.6 34.7 + - - +
678M GLU* 1.3 69.5 - - - +
680M THR* 1.3 58.1 + - - +
682M THR* 2.6 26.9 + - - -
683M ILE* 3.0 21.6 + - + +
729M ALA* 3.5 44.6 - - + +
732M LEU* 3.9 14.4 - - + -
733M ALA* 4.3 13.7 - - + +
762M SER 4.5 0.2 - - - +
763M ALA* 4.2 23.1 - - + +
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Residues in contact with THR 680 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676M MET 3.0 9.2 + - - -
677M ARG* 2.8 21.5 + - - +
679M ILE* 1.3 78.0 - - - +
681M GLU* 1.3 57.6 + - - +
683M ILE* 3.2 10.6 + - + +
684M ALA* 2.7 27.0 + - - +
801M GLU* 4.5 5.0 - - - +
806M ARG* 4.5 11.1 + - - +
729N ILE* 3.4 33.9 - - + -
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Residues in contact with GLU 681 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677M ARG* 3.2 45.0 + - - +
678M GLU* 3.0 25.9 - - - +
680M THR* 1.3 74.4 - - - +
682M THR* 1.3 59.5 + - - +
683M ILE 3.0 1.8 - - - -
684M ALA* 3.7 8.7 - - + -
685M GLU* 2.7 37.4 + - + +
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Residues in contact with THR 682 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678M GLU* 2.9 17.3 + - - +
679M ILE* 2.6 19.6 + - - -
681M GLU* 1.3 73.6 - - - +
683M ILE* 1.3 57.2 + - - -
685M GLU* 3.3 19.6 - - - +
686M ALA* 3.5 11.8 - - - +
725M ALA* 4.1 11.8 - - - +
728M LYS* 3.4 47.4 - - + +
729M ALA* 4.3 6.7 - - + +
732M LEU* 3.7 13.1 - - - +
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Residues in contact with ILE 683 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679M ILE* 3.0 28.6 + - + +
680M THR* 3.4 11.7 - - + +
682M THR* 1.3 78.0 - - - +
684M ALA* 1.3 54.0 + - - +
686M ALA* 3.1 7.2 + - - +
687M LYS* 2.8 39.6 + - + +
725M ALA* 4.9 6.7 - - + +
726M ARG 5.9 0.2 - - - +
729M ALA* 4.6 8.5 - - + -
763M ALA 4.8 1.3 - - - +
764M CYS* 4.0 18.4 - - + -
799M PHE* 4.0 20.0 - - + -
801M GLU* 3.3 56.5 - - + +
729N ILE* 5.9 0.4 - - + -
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Residues in contact with ALA 684 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680M THR 2.7 16.8 + - - +
681M GLU* 3.5 11.4 - - + +
683M ILE* 1.3 76.3 - - - +
685M GLU* 1.3 54.8 + - - +
687M LYS* 2.7 37.2 + - - +
688M LYS* 3.0 7.6 + - - +
801M GLU* 4.9 1.8 + - - +
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Residues in contact with GLU 685 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681M GLU* 2.7 29.6 + - + +
682M THR* 3.3 21.1 - - - +
684M ALA* 1.3 71.8 - - - +
686M ALA* 1.3 68.6 + - - +
688M LYS* 3.2 7.5 + - - +
689M LYS* 2.9 32.3 + - - +
725M ALA* 5.6 1.2 - - - +
728M LYS* 4.4 18.6 + - - -
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Residues in contact with ALA 686 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682M THR 3.5 8.7 - - - +
683M ILE 3.1 5.0 + - - +
685M GLU* 1.3 89.4 - - - +
687M LYS* 1.3 61.7 + - - +
689M LYS* 3.7 12.3 - - + +
690M VAL* 3.3 20.8 + - - +
721M PHE* 4.2 15.0 - - + +
722M LEU* 5.3 3.5 - - - +
725M ALA* 3.3 33.7 - - + -
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Residues in contact with LYS 687 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683M ILE* 2.8 18.8 + - + +
684M ALA* 2.7 21.1 + - - +
686M ALA* 1.3 78.9 - - - +
688M LYS* 1.3 54.7 + - - +
690M VAL* 2.7 29.9 - - - +
691M LEU* 3.0 7.0 + - - +
794M PRO* 4.3 10.1 - - + -
795M GLU* 2.8 47.3 + - - +
799M PHE* 5.2 6.3 - - + -
801M GLU* 3.1 32.7 + - - -
729N ILE* 5.8 1.4 - - - +
731N VAL* 5.2 2.6 - - - +
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Residues in contact with LYS 688 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684M ALA 3.0 9.3 + - - +
685M GLU* 3.8 8.1 - - - +
687M LYS* 1.3 74.5 - - - +
689M LYS* 1.3 54.1 + - - +
690M VAL 2.7 7.9 + - - -
691M LEU* 2.7 46.8 + - + -
692M ASP* 2.8 37.4 + - - +
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Residues in contact with LYS 689 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685M GLU* 2.9 21.7 + - - +
686M ALA* 3.7 12.1 - - + +
687M LYS 3.4 0.2 - - - -
688M LYS* 1.3 75.0 - - - +
690M VAL* 1.3 56.1 + - - +
692M ASP* 4.1 9.2 - - - +
693M VAL* 2.9 28.5 + - + +
721M PHE* 3.3 39.8 - - + -
724M GLU* 4.0 20.4 + - - +
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Residues in contact with VAL 690 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686M ALA 3.3 11.0 + - - +
687M LYS* 2.7 27.1 - - - +
688M LYS 2.7 0.8 + - - -
689M LYS* 1.3 77.3 - - - +
691M LEU* 1.3 59.5 + - - +
692M ASP 3.2 1.8 - - - -
693M VAL* 3.3 3.8 + - + +
694M THR* 2.8 35.8 + - - +
718M VAL* 3.4 48.5 - - + +
721M PHE* 4.0 9.9 - - + -
722M LEU* 4.6 6.5 - - + -
794M PRO* 3.8 29.2 - - + -
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Residues in contact with LEU 691 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687M LYS 3.6 8.5 - - - +
688M LYS* 2.7 43.7 + - + +
690M VAL* 1.3 78.6 - - - +
692M ASP* 1.3 67.6 + - - +
694M THR* 3.2 11.2 - - - -
695M LYS* 3.1 46.8 + - + +
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Residues in contact with ASP 692 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688M LYS* 2.8 48.0 + - - +
689M LYS* 4.1 8.5 - - - +
691M LEU* 1.3 75.8 - - - +
693M VAL* 1.3 56.5 + - + +
694M THR 2.6 15.7 + - - -
695M LYS* 2.8 18.7 + - - +
696M GLU* 2.8 17.2 + - + +
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Residues in contact with VAL 693 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689M LYS 2.9 24.2 + - - +
690M VAL* 3.3 9.7 + - + +
692M ASP* 1.3 78.6 - - + +
694M THR* 1.3 59.5 + - - +
696M GLU* 4.0 15.6 - - - +
697M ALA* 3.3 21.3 + - - +
702M LEU* 4.3 9.5 - - + +
714M PHE* 3.8 21.2 - - + +
717M ASN* 4.5 20.9 - - + +
718M VAL* 4.8 2.2 - - + -
721M PHE* 3.3 23.1 - - + -
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Residues in contact with THR 694 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690M VAL* 2.8 23.1 + - - +
691M LEU* 3.2 13.0 - - + -
692M ASP 2.6 5.3 + - - -
693M VAL* 1.3 72.1 - - - +
695M LYS* 1.3 62.4 + - + +
697M ALA* 2.9 17.7 + - - +
698M GLN* 3.0 38.2 + - + +
714M PHE* 3.7 25.7 - - + -
792M TYR* 5.3 12.3 + - + +
793M SER* 5.9 2.7 - - - +
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Residues in contact with LYS 695 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691M LEU* 3.1 33.9 + - + +
692M ASP* 2.8 11.5 + - - +
694M THR* 1.3 72.2 - - + +
696M GLU* 1.3 56.4 + - - +
697M ALA 2.9 4.7 - - - -
698M GLN* 2.8 41.2 + - - +
699M ALA* 3.2 13.9 + - - +
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Residues in contact with GLU 696 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692M ASP* 2.8 18.1 + - + +
693M VAL* 4.0 13.6 + - - +
695M LYS* 1.3 75.8 - - - +
697M ALA* 1.3 56.7 + - - +
699M ALA* 4.2 2.5 - - - +
701M LEU* 3.3 51.7 + - + +
702M LEU* 3.1 24.7 - - + +
----------------------------------------------------------
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Residues in contact with ALA 697 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693M VAL 3.3 13.9 + - - +
694M THR* 2.9 8.9 + - - +
695M LYS 2.9 0.8 - - - -
696M GLU* 1.3 76.4 - - - +
698M GLN* 1.3 61.9 + - - +
699M ALA 3.3 2.2 + - - -
700M ASN* 3.8 9.0 + - - +
702M LEU* 3.2 34.3 - - + +
710M LEU* 6.0 0.9 - - - +
714M PHE* 4.3 4.5 - - + -
96U SER* 5.7 0.2 - - - -
97U MET* 3.2 39.3 + - + +
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Residues in contact with GLN 698 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694M THR* 3.0 29.0 + - + +
695M LYS* 2.8 32.0 + - - +
697M ALA* 1.3 77.4 - - - +
699M ALA* 1.3 56.7 + - - +
700M ASN 3.3 3.4 - - - -
790M ASP 5.7 3.0 + - - -
85U PHE* 5.3 1.8 - - - -
87U GLN* 4.8 4.0 - - - +
97U MET* 2.9 20.2 - - + +
98U VAL* 3.2 15.3 - - - +
99U LEU* 3.2 46.0 - - + +
112U SER* 2.9 25.5 + - - +
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Residues in contact with ALA 699 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695M LYS 3.2 11.8 + - - +
696M GLU 4.2 0.4 + - - -
697M ALA 3.3 0.2 - - - -
698M GLN* 1.3 76.9 - - - +
700M ASN* 1.3 66.6 + - - +
701M LEU* 2.9 44.8 - - + +
112U SER 3.4 17.5 - - - +
113U ASP* 4.3 1.3 - - - -
114U GLN* 3.1 27.4 + - - +
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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