Contacts of the helix formed by residues 680 - 714 (chain D) in PDB entry 5EP6
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 680 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679D SER* 1.3 74.5 - - - +
681D ASN* 1.3 56.6 + - - +
683D LEU* 3.5 12.8 + - - +
684D VAL* 3.0 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 681 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679D SER* 3.7 12.3 - - - -
680D SER* 1.3 76.8 - - - +
682D THR* 1.3 67.5 + - - +
684D VAL* 3.3 8.2 + - - +
685D GLU* 2.9 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 682 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A SER* 5.2 6.7 - - - +
219A MET* 5.8 2.2 - - + -
220A GLN* 3.8 20.0 - - + +
679D SER* 3.4 21.6 + - - -
681D ASN* 1.3 85.2 + - - +
683D LEU* 1.3 59.8 + - + +
685D GLU* 3.2 9.6 + - - +
686D MET* 2.9 58.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 683 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A MET* 4.6 7.6 - - - -
679B SER* 5.8 3.6 - - - +
683B LEU* 3.7 28.9 - - + -
215C SER 3.9 21.8 - - - +
216C SER* 5.5 1.8 - - - -
219C MET* 3.7 29.2 - - + +
679D SER 3.2 17.7 + - - +
680D SER* 3.7 15.0 - - - +
682D THR* 1.3 79.1 - - + +
684D VAL* 1.3 60.3 + - + +
686D MET* 3.4 3.8 + - - +
687D THR* 2.9 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 684 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680D SER* 3.0 26.5 + - - +
681D ASN* 3.3 6.5 + - - +
683D LEU* 1.3 73.5 - - + +
685D GLU* 1.3 66.6 + - - +
687D THR* 3.1 6.8 + - - -
688D LEU* 2.9 45.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 685 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A GLN* 3.8 22.4 + - - +
223A TYR* 3.8 19.4 + - + +
227A LYS* 5.0 5.0 + - - -
681D ASN* 2.9 23.2 + - - +
682D THR* 3.6 13.8 + - - +
684D VAL* 1.3 77.1 - - - +
686D MET* 1.3 58.8 + - + +
688D LEU* 3.5 7.7 + - - +
689D GLY* 2.8 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 686 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A MET* 3.5 32.1 - - + +
220A GLN* 3.3 59.5 - - + +
223A TYR* 3.8 34.2 - - + -
690B MET* 4.4 2.7 - - - +
219C MET* 4.1 14.6 - - + -
682D THR* 2.9 28.5 + - + +
683D LEU* 4.0 3.6 - - - +
685D GLU* 1.3 75.8 - - + +
687D THR* 1.3 61.7 + - - +
689D GLY 3.6 0.7 - - - +
690D MET* 2.9 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 687 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C ASN* 3.9 36.6 - - + +
219C MET* 3.6 20.8 + - - +
222C ALA* 4.0 10.2 - - + +
683D LEU 2.9 19.2 + - - -
684D VAL* 3.6 7.2 - - - -
686D MET* 1.3 75.7 - - - +
688D LEU* 1.3 65.3 + - + +
690D MET* 3.3 5.8 + - - +
691D LYS* 3.0 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 688 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684D VAL* 2.9 37.7 + - + +
685D GLU* 3.7 6.7 - - - +
687D THR* 1.3 79.2 - - + +
689D GLY* 1.3 56.9 + - - +
691D LYS* 3.3 18.1 + - + +
692D LYS* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 689 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A TYR* 3.1 32.3 + - - -
227A LYS* 5.8 0.2 - - - +
685D GLU 2.8 15.2 + - - -
686D MET 3.4 1.3 + - - -
687D THR 3.2 0.2 - - - -
688D LEU* 1.3 74.0 - - - +
690D MET* 1.3 55.9 + - - +
692D LYS* 3.3 9.1 + - - +
693D LEU* 2.9 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 690 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A TYR* 5.1 2.7 - - + -
226A LEU* 5.1 0.4 - - + -
686B MET* 4.7 1.3 - - - +
690B MET* 4.5 26.7 - - - +
219C MET* 3.5 53.8 - - + +
222C ALA* 3.9 14.9 - - + +
223C TYR* 3.9 27.4 - - + +
226C LEU* 4.1 23.5 - - + +
686D MET 2.9 20.9 + - - +
687D THR 3.9 2.7 - - - +
689D GLY* 1.3 72.8 - - - +
691D LYS* 1.3 65.0 - - - +
693D LEU* 3.4 12.7 + - + +
694D LYS* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 691 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C ASN 5.9 0.9 - - - -
222C ALA* 4.1 15.7 - - + +
225C GLU* 6.0 2.9 - - - +
687D THR* 3.0 33.6 + - + +
688D LEU* 3.3 20.3 + - + +
690D MET* 1.3 75.6 - - - +
692D LYS* 1.3 62.0 + - - +
694D LYS* 3.3 9.3 + - - +
695D GLU* 3.1 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 692 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LYS* 6.5 0.9 - - - -
688D LEU 2.9 16.6 + - - +
689D GLY* 3.6 8.5 - - - +
690D MET 3.3 0.2 - - - -
691D LYS* 1.3 74.9 - - - +
693D LEU* 1.3 60.8 + - + +
695D GLU* 3.1 12.8 + - - +
696D GLU* 2.9 51.6 + - + +
801D GOL 4.6 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 693 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A TYR* 4.6 5.4 - - + -
226A LEU* 3.8 34.8 - - + +
227A LYS* 4.3 26.0 - - + -
230A MET* 3.6 39.7 - - + +
697B MET* 6.2 0.4 - - - -
226C LEU* 3.9 18.5 - - + +
689D GLY 2.9 21.9 + - - +
690D MET* 3.7 9.2 - - + +
691D LYS 3.3 0.2 - - - -
692D LYS* 1.3 75.8 - - - +
694D LYS* 1.3 58.3 + - - +
696D GLU* 3.3 12.9 + - - +
697D MET* 2.8 30.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 694 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C ALA 5.5 0.4 - - - +
225C GLU* 3.7 43.4 + - + +
226C LEU* 3.7 18.7 - - + +
228C ARG* 4.4 14.2 - - - +
229C GLU* 4.0 16.7 - - + +
690D MET 3.0 17.8 + - - +
691D LYS* 3.6 8.7 - - - +
692D LYS 3.2 0.2 - - - -
693D LEU* 1.3 75.1 - - - +
695D GLU* 1.3 65.2 + - + +
697D MET* 3.3 3.7 + - - +
698D GLU* 2.9 57.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 695 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691D LYS* 3.1 19.1 + - - +
692D LYS* 3.1 13.1 + - - +
694D LYS* 1.3 82.6 - - + +
696D GLU* 1.3 63.2 + - - +
698D GLU* 3.3 18.7 - - - +
699D GLY* 3.1 18.0 + - - -
801D GOL 2.7 45.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 696 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A MET* 3.9 12.2 - - + +
234A HIS* 2.9 35.3 + - - +
692D LYS* 2.9 42.7 + - - +
693D LEU* 3.6 26.5 - - - +
695D GLU* 1.3 77.6 - - - +
697D MET* 1.3 62.9 + - - +
699D GLY* 3.1 3.9 + - - -
700D VAL* 3.0 24.8 + - - +
801D GOL 3.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 697 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A MET* 4.0 15.7 - - - +
233A LEU* 4.8 2.2 - - + -
693B LEU* 6.0 0.7 - - + -
697B MET* 4.2 22.4 - - + -
226C LEU* 4.4 15.7 - - + +
229C GLU* 3.6 17.9 - - + +
230C MET* 3.5 57.0 - - + -
233C LEU* 4.0 21.8 - - + -
693D LEU* 2.8 16.5 + - + +
694D LYS* 3.3 5.4 + - - +
696D GLU* 1.3 73.1 - - - +
698D GLU* 1.3 59.5 + - - +
700D VAL* 3.2 3.0 + - - +
701D VAL* 2.9 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 698 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C GLU* 3.5 31.1 - - - +
694D LYS* 2.9 37.9 + - - +
695D GLU* 3.3 21.5 - - - +
697D MET* 1.3 76.7 - - - +
699D GLY* 1.3 57.6 + - - +
701D VAL* 3.4 3.0 + - - +
702D LYS* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 699 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695D GLU 3.1 10.0 + - - -
696D GLU 3.1 4.6 + - - -
698D GLU* 1.3 81.0 - - - +
700D VAL* 1.3 55.5 + - - +
702D LYS* 3.4 10.0 + - - +
703D GLU* 3.0 29.2 + - - +
801D GOL 5.9 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 700 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A MET* 3.7 20.4 - - + -
233A LEU* 4.0 18.4 - - + -
234A HIS* 3.7 18.6 - - + +
237A THR* 3.5 28.5 - - + +
233C LEU* 4.1 7.4 - - + -
696D GLU 3.0 17.4 + - - +
697D MET* 3.2 9.2 + - - +
699D GLY* 1.3 73.0 - - - +
701D VAL* 1.3 59.7 + - - +
703D GLU* 3.1 6.9 + - - +
704D LEU* 2.8 43.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 701 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C GLU* 3.8 19.3 - - - +
232C ASN* 4.1 8.5 - - + +
233C LEU* 3.7 38.8 - - + +
236C VAL* 3.5 29.8 - - + +
697D MET* 2.9 21.9 + - + +
698D GLU 3.7 4.7 - - - +
700D VAL* 1.3 75.6 - - - +
702D LYS* 1.3 57.6 + - - +
704D LEU* 3.3 1.6 + - - +
705D ALA* 2.9 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 702 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698D GLU 3.0 18.3 + - - +
699D GLY* 3.6 9.2 - - - +
701D VAL* 1.3 77.7 - - - +
703D GLU* 1.3 57.3 + - - +
705D ALA* 3.4 7.2 + - - +
706D GLU* 3.0 47.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 703 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A THR* 3.9 17.6 - - + +
238A GLN* 2.8 32.1 + - - +
241A ALA* 3.7 16.8 - - - +
699D GLY 3.0 17.2 + - - +
700D VAL* 3.1 4.8 + - - +
702D LYS* 1.3 75.1 - - - +
704D LEU* 1.3 64.4 + - - +
706D GLU* 3.2 20.6 + - - +
707D ASN* 3.0 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 704 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A THR* 4.1 21.5 - - + +
240A GLN* 3.5 25.1 - - - +
704B LEU* 3.9 33.2 - - + -
233C LEU* 3.8 19.3 - - + -
236C VAL* 4.0 17.5 - - + +
237C THR* 4.4 1.1 - - - +
240C GLN* 4.3 3.5 + - - +
700D VAL* 2.8 37.1 + - + +
701D VAL 3.8 3.8 - - - +
703D GLU* 1.3 76.5 - - - +
705D ALA* 1.3 57.6 + - - +
707D ASN* 3.2 7.6 + - - +
708D ASN* 2.9 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 705 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C VAL* 4.7 2.2 - - + +
301C GOL 3.4 43.0 + - - +
701D VAL* 2.9 19.0 + - + +
702D LYS* 3.7 7.9 - - - +
704D LEU* 1.3 72.1 - - - +
706D GLU* 1.3 64.9 + - + +
708D ASN* 3.3 3.2 + - - +
709D HIS* 3.0 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 706 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702D LYS* 3.0 41.1 + - + +
703D GLU* 3.2 21.9 + - - +
705D ALA* 1.3 78.3 - - - +
707D ASN* 1.3 58.5 + - - +
709D HIS* 3.2 9.1 + - - +
710D ILE* 3.0 34.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 707 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A THR* 4.8 1.8 + - - +
240A GLN* 2.9 41.1 + - - +
241A ALA* 4.5 8.7 - - - +
244A LEU* 3.5 26.2 - - + +
240C GLN* 4.4 1.8 - - - +
703D GLU* 3.0 30.4 + - - +
704D LEU* 3.4 15.2 - - - +
706D GLU* 1.3 79.0 - - - +
708D ASN* 1.3 56.3 + - - +
710D ILE* 3.2 10.3 + - - +
711D LEU* 2.9 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 708 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C VAL* 3.2 23.6 + - - +
239C VAL* 3.7 8.4 - - + +
240C GLN* 3.0 42.2 + - - +
243C LEU* 3.2 20.0 - - + +
301C GOL 3.1 30.5 - - - +
704D LEU* 2.9 17.3 + - - +
705D ALA* 3.5 8.4 - - - +
706D GLU 3.3 0.2 - - - -
707D ASN* 1.3 75.2 - - - +
709D HIS* 1.3 57.7 + - - +
711D LEU* 3.3 1.9 + - - +
712D GLU* 2.8 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 709 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C GOL 4.9 2.1 + - - +
705D ALA 3.0 13.3 + - - +
706D GLU* 3.2 12.3 + - - +
708D ASN* 1.3 76.4 - - - +
710D ILE* 1.3 66.7 + - + +
712D GLU* 3.4 10.4 + - - +
713D ARG* 3.1 53.8 + - + +
714D PHE* 6.3 1.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 710 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU* 4.5 18.4 - - + -
717B LEU* 3.9 30.1 - - + -
706D GLU* 3.0 21.4 + - + +
707D ASN* 3.5 20.6 - - - +
709D HIS* 1.3 79.3 - - + +
711D LEU* 1.3 59.8 + - - +
714D PHE* 2.8 46.9 + - + +
715D GLY 3.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 711 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A GLN* 5.5 0.7 - - - +
244A LEU* 4.0 20.4 - - + -
247A LEU* 5.3 0.9 - - + -
711B LEU* 3.8 33.7 - - + -
716B SER 5.7 0.2 - - - +
717B LEU* 4.7 6.1 - - + -
722B GLY* 3.9 3.3 - - - -
240C GLN* 4.4 21.3 - - + +
243C LEU* 3.9 12.1 - - + -
244C LEU* 4.5 18.4 - - + -
247C LEU* 4.2 11.6 - - + +
707D ASN* 2.9 25.8 + - + +
708D ASN* 3.7 7.0 - - - +
710D ILE* 1.3 77.2 - - - +
712D GLU* 1.3 59.7 - - - +
715D GLY* 2.8 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 712 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722B GLY* 3.0 0.9 - - - -
723B LEU* 2.9 67.9 + - + +
243C LEU* 3.9 19.9 - - + +
708D ASN 2.8 21.4 + - - +
709D HIS* 3.9 11.4 + - - +
710D ILE 3.4 0.2 - - - -
711D LEU* 1.3 73.4 - - - +
713D ARG* 1.3 71.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 713 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719B MET* 4.7 9.1 + - - +
721B GLY 3.2 18.0 + - - +
722B GLY* 3.5 2.0 - - - -
709D HIS* 3.1 43.5 + - + +
712D GLU* 1.3 92.0 - - - +
714D PHE* 1.3 108.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 714 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716B SER 3.5 0.2 - - - +
717B LEU* 3.2 16.8 - - + -
718B THR* 2.8 50.7 + - - +
719B MET* 3.9 30.7 - - + -
721B GLY* 3.9 2.1 - - - -
722B GLY 3.6 3.6 - - - +
709D HIS* 6.3 1.8 - + - -
710D ILE* 2.8 33.3 + - + +
713D ARG* 1.3 119.8 - - + +
715D GLY* 1.3 66.7 + - - +
----------------------------------------------------------
Back to top of page
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