Contacts of the helix formed by residues 814 - 834 (chain B) in PDB entry 3E0D
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 ASN 814 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B GLY 3.2 5.7 - - - +
426B SER* 3.2 24.8 + - - +
452B ARG* 3.5 16.3 - - - +
744B GLN* 2.9 29.0 - - - +
745B GLU* 2.2 39.1 + - - -
813B PHE* 1.3 84.5 - - + +
815B LYS* 1.3 62.7 + - - +
816B SER* 2.9 24.0 + - - -
817B HIS* 3.4 7.2 + - + +
818B ALA 3.2 15.6 + - - -
1222B DTP 3.8 6.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 815 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B PHE* 3.2 27.6 - - - +
447B GLY* 2.4 47.2 - - - +
448B LEU* 3.0 12.6 - - + -
688B GLU* 5.7 4.0 - - - +
691B ILE* 4.4 12.3 - - + -
736B GLU* 3.9 24.1 + - - -
743B TYR* 4.0 42.6 - - + -
745B GLU* 2.8 18.3 + - + +
813B PHE 3.2 1.4 + - - -
814B ASN* 1.3 69.4 - - - +
816B SER* 1.3 57.3 + - - +
818B ALA* 3.1 3.1 + - - -
819B ALA* 2.7 34.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 816 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B GLY 3.3 5.4 + - - -
426B SER 3.7 6.6 + - - -
428B ALA* 3.4 20.0 - - - +
429B GLY* 3.5 11.2 - - - -
448B LEU* 2.8 38.0 - - - +
449B LEU 5.6 0.2 - - - -
745B GLU* 3.7 0.8 + - - -
814B ASN* 2.9 26.1 + - - +
815B LYS* 1.3 73.0 - - - +
817B HIS* 1.3 65.2 + - - +
819B ALA* 3.9 0.7 - - - +
820B ALA* 3.0 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 817 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B ARG* 3.4 10.3 - - + -
425B GLY* 2.9 23.8 + - - +
669B GLN* 5.4 3.8 - - - -
813B PHE* 4.1 17.4 - + + -
814B ASN* 3.4 18.0 + - + +
815B LYS 3.2 0.2 - - - -
816B SER* 1.3 82.9 + - - +
818B ALA* 1.3 63.5 + - - +
820B ALA* 3.9 2.6 - - - +
821B TYR* 3.1 53.7 + + + +
1222B DTP 1.4 81.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 818 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669B GLN* 4.8 0.9 - - - +
691B ILE* 3.7 13.9 - - + +
694B VAL* 5.5 7.5 - - + +
695B SER* 3.4 26.2 - - - +
813B PHE* 3.6 17.7 - - + -
814B ASN 3.2 5.5 + - - +
815B LYS* 3.1 9.3 + - - +
817B HIS* 1.3 80.3 + - - +
819B ALA* 1.3 53.9 + - - +
821B TYR* 3.8 3.4 - - - +
822B SER* 2.6 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 819 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B ILE* 3.1 29.2 - - + +
446B PHE* 4.3 14.8 - - + -
448B LEU* 4.6 3.8 - - + -
687B LEU* 5.2 1.0 - - - +
691B ILE* 3.7 28.9 - - + +
815B LYS* 2.7 21.7 + - + +
816B SER 3.9 2.5 - - - +
818B ALA* 1.3 71.8 - - - +
820B ALA* 1.3 64.2 + - - +
822B SER* 3.2 12.2 + - - -
823B LEU 3.2 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 820 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B PRO* 2.8 37.4 - - + +
423B GLY* 3.4 31.9 - - - +
428B ALA* 4.7 1.6 - - + -
441B ILE* 3.3 16.7 - - + +
816B SER 3.0 17.3 + - - +
817B HIS 3.9 1.8 - - - +
819B ALA* 1.3 77.8 - - - +
821B TYR* 1.3 63.4 + - - +
823B LEU* 3.3 9.4 + - - +
824B LEU 3.8 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 821 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B PRO* 4.9 1.8 - - + -
423B GLY 3.2 24.7 - - - -
424B ARG* 2.9 30.5 + - + -
467B ASP* 2.7 30.8 + - - -
620B LEU* 4.6 0.3 - - - +
622B LEU* 4.4 7.5 - - + +
668B PHE* 3.4 32.3 - + - -
669B GLN* 3.4 27.4 - - - +
817B HIS* 3.1 44.3 + + + +
818B ALA* 4.0 2.5 - - - +
820B ALA* 1.3 78.7 - - - +
822B SER* 1.3 64.5 + - - +
824B LEU* 2.8 24.2 + - + +
825B SER* 3.3 9.0 + - - -
1222B DTP 6.0 1.1 - - - -
7E G 5.3 4.6 + - - -
8E T 5.9 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 822 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669B GLN* 3.7 5.7 + - - -
687B LEU* 4.0 9.1 - - - +
690B ILE* 3.8 15.9 + - - +
691B ILE* 3.3 37.1 + - - +
694B VAL* 4.8 2.6 - - - +
818B ALA* 2.6 25.3 + - - +
819B ALA 3.3 6.5 - - - -
821B TYR* 1.3 74.0 - - - +
823B LEU* 1.3 58.2 + - - +
825B SER* 3.0 13.9 + - - -
826B TYR* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 823 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B PRO* 4.0 23.3 - - + -
440B ASN* 4.0 14.4 - - - +
441B ILE* 4.4 14.8 - - + -
645B TYR 5.3 1.1 - - - +
650B LEU* 3.9 29.2 - - + -
687B LEU* 4.4 8.9 - - + +
819B ALA 3.2 6.0 + - - +
820B ALA 3.3 10.8 - - - +
821B TYR 3.0 0.2 + - - -
822B SER* 1.3 79.5 - - - +
824B LEU* 1.3 56.2 + - + +
826B TYR* 3.4 9.0 + - + +
827B GLN* 2.9 66.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 824 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B GLY* 4.9 1.1 - - - -
422B PRO* 4.0 29.4 - - + -
467B ASP* 5.4 0.7 - - - +
622B LEU* 3.9 27.1 - - + -
624B THR* 4.1 8.4 - - + +
625B LEU* 3.6 26.9 - - + -
628B LEU* 3.9 7.6 - - + +
668B PHE* 3.6 23.1 - - + -
821B TYR* 2.8 16.1 + - + +
823B LEU* 1.3 75.0 - - + +
825B SER* 1.3 59.9 + - - +
827B GLN* 3.3 22.7 + - - +
828B THR* 2.9 34.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 825 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659B LEU* 6.1 1.3 - - - -
667B VAL* 3.5 11.2 - - - +
668B PHE* 2.9 33.5 + - - -
669B GLN* 3.3 24.6 + - - +
670B LEU* 4.7 5.7 - - - +
690B ILE* 4.4 14.6 - - - +
821B TYR 3.3 1.8 + - - -
822B SER* 3.0 12.5 + - - -
824B LEU* 1.3 78.2 - - - +
826B TYR* 1.3 63.7 + - - +
828B THR* 3.2 2.3 + - - -
829B ALA* 2.9 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 826 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B LEU* 4.9 6.5 - - + -
649B PRO 2.5 31.2 + - - -
650B LEU* 3.3 25.1 - - + -
652B ASP* 3.1 28.3 + - + +
655B THR* 3.7 22.4 - - + +
656B PHE* 3.5 37.0 - + - -
659B LEU* 5.6 0.2 - - - -
687B LEU* 3.8 18.8 - - + -
690B ILE* 4.7 8.2 - - + +
822B SER 2.9 12.2 + - - +
823B LEU* 3.5 9.2 - - - +
825B SER* 1.3 74.8 - - - +
827B GLN* 1.3 61.9 + - + +
829B ALA* 3.1 7.5 + - - +
830B TYR* 2.6 49.7 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 827 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628B LEU* 3.7 20.5 - - + +
645B TYR* 3.3 48.8 + - + +
646B ASP* 4.4 6.5 + - - +
648B LEU* 4.5 10.1 - - + -
823B LEU* 2.9 44.8 + - + +
824B LEU* 3.6 24.1 - - - +
826B TYR* 1.3 79.3 - - + +
828B THR* 1.3 62.9 + - - +
830B TYR* 3.5 7.3 - - - +
831B VAL* 3.0 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 828 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624B THR* 3.9 12.3 + - - +
627B PHE* 4.6 10.5 - - + -
628B LEU* 4.0 13.4 - - - +
666B GLY 3.0 29.6 - - - +
667B VAL* 3.3 15.3 - - + -
668B PHE* 3.6 15.8 - - - +
824B LEU 2.9 16.5 + - - -
825B SER 3.4 8.1 - - - -
827B GLN* 1.3 75.2 - - - +
829B ALA* 1.3 56.6 + - - +
839B PHE* 2.5 44.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 829 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655B THR* 4.0 14.6 - - + -
658B LEU* 4.2 9.3 - - + +
659B LEU* 3.7 31.9 - - + -
667B VAL* 3.8 13.0 - - + +
825B SER 2.9 15.7 + - - +
826B TYR 3.5 7.0 - - - +
828B THR* 1.3 74.0 - - - +
830B TYR* 1.3 52.6 + - - +
832B LYS* 3.2 5.0 + - - +
833B ALA* 2.8 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 830 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643B LEU* 4.1 15.8 - - + +
648B LEU* 3.6 42.6 - - + +
649B PRO* 4.9 11.0 - - + +
652B ASP* 3.6 19.1 - - + -
655B THR* 3.2 29.9 - - + +
826B TYR* 2.6 33.1 + + + +
827B GLN* 3.5 7.6 - - - +
829B ALA* 1.3 71.5 - - - +
831B VAL* 1.3 68.3 - - + +
833B ALA* 3.2 2.8 + - - +
834B HIS* 3.0 47.8 + + + +
835B TYR* 5.2 6.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 831 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628B LEU* 4.5 4.3 - - + -
631B ALA* 4.3 14.4 - - + -
635B VAL* 5.3 2.9 - - + -
643B LEU* 4.2 15.3 - - + -
645B TYR* 3.8 31.6 - - + +
827B GLN 3.0 18.9 + - - +
828B THR 3.5 0.2 - - - +
830B TYR* 1.3 83.2 - - + +
832B LYS* 1.3 59.4 + - - +
834B HIS* 5.3 0.9 - - - -
835B TYR* 3.1 32.7 + - + +
839B PHE* 1.9 61.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 832 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658B LEU* 3.9 14.9 - - + +
663B GLU 2.9 27.6 + - - +
665B LYS* 3.1 58.3 - - - +
666B GLY 3.5 4.4 - - - +
667B VAL* 4.2 9.4 - - + -
828B THR 3.2 0.6 + - - +
829B ALA* 3.5 8.1 - - - +
831B VAL* 1.3 73.2 - - - +
833B ALA* 1.3 62.7 + - - +
836B PRO* 4.3 14.4 - - - +
839B PHE* 2.1 57.3 - - + -
840B MET* 3.6 20.4 - - + +
843B LEU* 4.9 0.7 - - + -
864B LEU* 5.1 6.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 833 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654B LYS* 3.5 38.9 - - + +
655B THR* 4.0 8.5 - - - +
658B LEU* 3.7 13.7 - - + -
829B ALA 2.8 19.3 + - - +
830B TYR 3.5 5.6 - - - +
831B VAL 3.2 0.2 - - - -
832B LYS* 1.3 76.5 - - - +
834B HIS* 1.3 67.8 + - + +
836B PRO* 4.9 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 834 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652B ASP* 2.8 39.9 + - - -
654B LYS* 4.0 26.9 - - + +
830B TYR* 3.0 45.7 + + + +
833B ALA* 1.3 84.4 + - + +
835B TYR* 1.0 88.6 + - + +
836B PRO* 3.1 10.0 - - - +
----------------------------------------------------------
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