Contacts of the helix formed by residues 769 - 791 (chain D) in PDB entry 3IYD
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 VAL 769 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555C TYR* 3.9 14.2 - - + +
618C GLN* 4.3 9.2 - - - +
619C ALA* 6.2 0.9 - - + -
620C ASN* 3.3 28.3 - - - +
657C THR* 3.1 29.8 - - - +
660C VAL* 3.7 30.3 - - + +
1187C PHE* 3.5 29.4 - - + -
768D ASN* 1.3 82.4 + - - +
770D LEU* 1.3 62.0 + - - +
772D TYR* 3.5 3.6 + - - +
773D PHE* 3.3 19.2 + - - +
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Residues in contact with LEU 770 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555C TYR* 5.2 4.7 - - + -
618C GLN* 3.5 36.1 - - + +
635C THR* 4.5 20.6 - - + +
637C ARG* 3.3 28.0 - - - +
768D ASN* 3.3 11.3 - - - +
769D VAL* 1.3 78.5 - - - +
771D GLN* 1.3 67.4 + - + +
772D TYR 3.1 2.0 - - - -
773D PHE* 3.1 19.0 + - + +
774D ILE* 3.2 34.1 - - + +
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Residues in contact with GLN 771 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757D THR* 6.0 0.2 + - - -
758D PRO 5.2 4.9 + - - +
759D ILE* 3.6 39.4 - - + +
760D THR 5.9 0.2 - - - +
761D ALA* 3.2 31.6 - - - +
767D LEU* 4.6 6.6 - - + +
768D ASN* 3.3 34.3 + - + +
770D LEU* 1.3 79.4 - - + +
772D TYR* 1.3 59.4 + - - +
773D PHE 3.3 0.2 - - - -
774D ILE* 3.9 3.7 + - - +
775D SER* 3.7 16.3 + - - -
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Residues in contact with TYR 772 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561C ILE* 3.7 31.2 - - + +
660C VAL* 5.6 3.1 - - + -
671C LEU* 3.9 25.7 - - + +
672C GLU* 5.5 1.6 - - - -
674C ASP 3.3 22.4 - - - -
675C ASP* 3.9 1.6 - - - -
676C ALA* 3.3 35.0 + - + +
679C ALA* 3.6 16.6 - - - +
1187C PHE* 3.9 22.9 - + + -
763D PHE* 6.3 0.7 - + - -
767D LEU* 4.7 20.0 - - + -
768D ASN 2.9 17.5 + - - +
769D VAL 3.8 4.7 - - - +
770D LEU 3.1 0.2 - - - -
771D GLN* 1.3 75.5 - - - +
773D PHE* 1.3 63.6 + - - +
774D ILE 3.2 1.2 + - - -
775D SER* 3.5 13.5 + - - -
776D THR* 3.3 15.2 + - + +
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Residues in contact with PHE 773 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550C VAL* 4.7 0.7 - - + -
551C HIS 4.0 5.2 - - - -
552C PRO* 3.7 38.8 - - + -
555C TYR* 3.5 44.9 - + + -
560C PRO* 3.5 31.0 - - + -
561C ILE* 6.3 0.4 - - - -
637C ARG* 5.5 4.3 - - - -
660C VAL* 4.1 9.4 - - + -
749D LYS* 6.2 0.7 - - - -
769D VAL 3.3 11.9 + - - +
770D LEU* 3.1 18.8 + - + +
772D TYR* 1.3 80.4 - - - +
774D ILE* 1.3 67.6 + - + +
775D SER 3.4 0.2 - - - -
776D THR* 2.7 23.3 + - - -
777D HIS* 2.9 32.3 + + - -
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Residues in contact with ILE 774 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747D MET* 3.6 27.4 - - + +
748D ALA 5.5 0.9 - - - +
749D LYS* 4.3 11.7 - - + +
755D ILE* 3.7 44.6 - - + -
757D THR* 6.4 1.1 - - + -
759D ILE* 5.0 9.0 - - + -
770D LEU* 3.2 31.1 + - + +
771D GLN* 4.3 7.0 - - - +
772D TYR 3.2 0.4 - - - -
773D PHE* 1.3 89.7 - - + +
775D SER* 1.3 56.1 + - - +
776D THR 3.0 5.4 - - - -
777D HIS* 2.9 31.6 + - + +
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Residues in contact with SER 775 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675C ASP* 4.2 6.1 + - - -
676C ALA* 4.4 5.3 + - - +
744D ARG* 3.3 29.5 + - - -
747D MET* 3.6 21.6 - - - +
759D ILE* 4.4 8.0 - - - +
767D LEU* 4.9 7.1 - - - +
771D GLN 3.7 12.3 + - - -
772D TYR* 3.5 18.9 + - - -
773D PHE 3.4 0.6 - - - -
774D ILE* 1.3 77.9 - - - +
776D THR* 1.3 59.7 + - - +
777D HIS 3.3 0.4 + - - -
779D ALA* 3.5 16.5 - - - +
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Residues in contact with THR 776 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550C VAL* 4.8 2.9 - - - +
560C PRO* 3.6 34.9 - - - +
561C ILE* 4.0 19.7 - - + -
676C ALA* 3.7 22.9 - - + -
772D TYR* 3.3 18.2 - - + +
773D PHE* 2.7 22.4 + - - -
775D SER* 1.3 76.6 - - - +
777D HIS* 1.3 64.8 + - - +
779D ALA* 3.8 9.6 + - - +
780D ARG* 3.4 26.0 + - - +
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Residues in contact with HIS 777 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549C ASP* 5.6 1.5 - - - +
550C VAL* 3.0 48.3 + - + +
552C PRO* 4.1 14.4 - - + -
748D ALA 3.3 17.7 - - - +
749D LYS* 4.8 10.6 + - + -
750D PRO* 3.6 14.3 - - + +
773D PHE* 2.9 50.8 + + - -
774D ILE* 2.9 24.1 + - + +
776D THR* 1.3 77.9 + - - +
778D GLY* 1.3 60.3 + - - +
779D ALA 3.1 6.1 + - - -
780D ARG* 3.3 13.3 + - - +
781D LYS* 3.3 19.2 - - - +
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Residues in contact with GLY 778 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747D MET* 4.1 18.3 - - - +
748D ALA* 3.6 18.7 + - - -
774D ILE 3.8 5.5 + - - -
775D SER 4.1 1.2 + - - -
777D HIS* 1.3 77.0 - - - +
779D ALA* 1.3 57.7 + - - +
780D ARG 3.2 4.6 + - - -
781D LYS* 3.7 23.6 + - - +
782D GLY 4.5 1.9 + - - -
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Residues in contact with ALA 779 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675C ASP* 5.9 0.2 - - - +
676C ALA* 4.6 6.1 - - + -
677C ASN* 3.4 30.3 + - - +
744D ARG* 5.6 4.5 - - - +
775D SER 3.5 18.6 + - - +
776D THR* 4.0 9.9 - - - +
777D HIS 3.1 1.2 - - - -
778D GLY* 1.3 77.2 - - - +
780D ARG* 1.3 66.2 + - - +
781D LYS 3.4 0.9 - - - -
782D GLY* 4.1 4.7 + - - +
783D LEU* 4.1 17.2 - - - +
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Residues in contact with ARG 780 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545C PHE* 5.9 0.7 - - - -
548C ARG 4.4 4.0 + - - -
549C ASP* 3.8 29.9 - - + +
550C VAL* 3.5 26.5 - - + +
560C PRO 2.9 26.9 + - - -
561C ILE 4.7 0.2 + - - -
563C THR* 3.2 35.5 + - - +
569C ILE* 3.7 31.3 - - + +
570C GLY* 4.2 13.9 - - - -
776D THR* 3.4 19.3 + - - +
777D HIS* 3.6 10.8 - - - +
778D GLY 3.2 1.2 - - - -
779D ALA* 1.3 83.4 - - - +
781D LYS* 1.3 62.1 + - + +
782D GLY 3.3 3.0 + - - -
783D LEU* 3.9 11.6 - - - +
784D ALA* 3.5 17.8 - - - +
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Residues in contact with LYS 781 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545C PHE* 3.3 32.3 - - + -
549C ASP* 3.1 27.5 + - - -
748D ALA* 3.8 18.2 - - + -
749D LYS 3.7 22.9 + - - -
750D PRO* 3.8 1.5 - - - +
777D HIS 3.3 24.7 - - - +
778D GLY* 3.7 15.5 + - - +
779D ALA 3.4 0.4 - - - -
780D ARG* 1.3 79.3 + - - +
782D GLY* 1.3 64.6 + - - +
784D ALA* 3.9 7.0 + - - -
785D ASP* 3.5 29.3 - - - +
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Residues in contact with GLY 782 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778D GLY 4.5 2.0 + - - -
779D ALA 4.1 6.8 + - - -
780D ARG 3.3 1.6 - - - -
781D LYS* 1.3 79.6 - - - +
783D LEU* 1.3 62.2 + - - +
784D ALA 3.1 5.6 + - - -
785D ASP* 3.8 6.4 + - - +
786D THR* 4.0 11.6 + - - +
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Residues in contact with LEU 783 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565C GLU* 4.8 26.2 - - + +
566C GLY* 5.0 10.7 - - - +
567C PRO* 6.1 0.5 - - - +
569C ILE* 4.1 36.5 - - + +
677C ASN* 6.1 2.0 - - - +
779D ALA 4.1 14.8 - - - +
780D ARG* 3.9 18.8 - - - +
782D GLY* 1.3 73.2 - - - +
784D ALA* 1.3 56.0 + - + +
785D ASP 3.9 0.2 - - - -
786D THR* 4.4 13.2 - - + -
787D ALA* 4.8 8.1 - - - +
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Residues in contact with ALA 784 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545C PHE* 5.0 12.6 - - + -
548C ARG* 5.9 4.9 - - - +
549C ASP* 6.1 0.2 - - - +
569C ILE* 5.9 3.6 - - + -
780D ARG 3.5 20.2 - - - +
781D LYS* 4.3 4.5 - - - +
782D GLY 3.1 1.0 + - - -
783D LEU* 1.3 80.3 - - + +
785D ASP* 1.3 73.7 + - - +
786D THR 3.5 2.0 - - - +
787D ALA* 4.4 13.1 + - - +
935D PHE* 4.9 6.4 - - - -
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Residues in contact with ASP 785 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545C PHE* 4.8 7.6 - - - -
781D LYS* 3.5 24.3 - - - +
782D GLY 3.8 3.6 + - - +
784D ALA* 1.3 87.0 - - - +
786D THR* 1.3 58.9 + - - +
787D ALA 3.5 1.6 - - - -
788D LEU* 4.9 5.5 + - - +
789D LYS* 4.4 11.4 + - - +
931D THR 5.7 1.0 - - - +
935D PHE* 4.0 27.2 - - + -
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Residues in contact with THR 786 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782D GLY 4.0 15.9 - - - +
783D LEU* 4.4 11.0 - - + -
785D ASP* 1.3 78.8 - - - +
787D ALA* 1.3 57.3 + - - +
788D LEU 3.1 7.8 + - - +
789D LYS* 4.1 22.2 + - - +
790D THR* 3.0 36.1 + - + +
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Residues in contact with ALA 787 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567C PRO* 6.4 1.6 - - + -
783D LEU 4.8 9.0 - - - +
784D ALA* 4.4 14.5 + - - +
785D ASP 3.5 2.0 - - - +
786D THR* 1.3 77.9 - - - +
788D LEU* 1.3 57.8 + - - +
790D THR* 4.0 8.9 + - - -
791D ALA* 4.4 8.5 - - - +
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Residues in contact with LEU 788 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785D ASP 5.3 4.7 - - - +
786D THR 3.1 1.0 - - - -
787D ALA* 1.3 80.4 - - - +
789D LYS* 1.3 72.4 + - + +
790D THR 3.3 1.1 - - - -
791D ALA* 3.3 20.6 + - + +
792D ASN 4.0 5.2 + - - -
793D SER* 5.2 0.3 + - - -
931D THR* 5.0 19.1 - - + +
1138D LEU* 6.1 5.4 - - + -
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Residues in contact with LYS 789 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785D ASP 4.4 7.2 + - - +
786D THR* 3.9 28.4 + - - +
788D LEU* 1.3 82.4 - - + +
790D THR* 1.3 62.0 + - + +
791D ALA 3.2 0.6 + - - -
793D SER* 4.1 20.7 + - - -
927D GLY 5.0 4.7 - - - +
928D THR* 4.0 45.6 + - + +
929D GLN* 5.2 4.0 - - - +
930D LEU 3.7 11.7 + - - +
931D THR* 3.3 30.2 + - + +
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Residues in contact with THR 790 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427D PRO* 5.8 3.1 - - - +
786D THR* 3.0 34.8 + - + +
787D ALA* 4.0 8.3 - - - -
789D LYS* 1.3 75.9 - - + +
791D ALA* 1.3 68.2 + - - +
928D THR* 5.7 2.0 - - + -
19J T 4.7 9.2 + - - +
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Residues in contact with ALA 791 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787D ALA 4.4 9.4 + - - +
788D LEU* 3.3 16.0 + - - +
789D LYS 3.2 0.6 - - - -
790D THR* 1.3 86.2 + - - +
792D ASN* 1.3 67.6 + - + +
19J T 3.5 36.2 + - + -
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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