Contacts of the helix formed by residues 766 - 790 (chain D) in PDB entry 6VVT
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 HIS 766 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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759D TYR* 3.8 19.6 + - - -
764D LEU* 3.2 6.4 - - - +
765D ASN* 1.3 76.7 - - - +
767D THR* 1.3 66.9 + - + +
768D GLU 3.0 6.2 + - - -
769D ARG* 3.5 11.6 + - - +
770D ASN* 4.5 1.6 + - - +
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Residues in contact with THR 767 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765D ASN* 3.0 6.0 + - - +
766D HIS* 1.3 82.0 - - + +
768D GLU* 1.3 66.5 + - - +
769D ARG 3.2 0.9 - - - -
770D ASN* 3.4 14.5 + - - +
771D GLU* 3.1 26.2 + - - +
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Residues in contact with GLU 768 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763D ALA 5.2 1.8 - - - +
764D LEU 3.4 15.9 - - - +
765D ASN* 3.2 23.7 + - + +
766D HIS 3.0 1.6 + - - -
767D THR* 1.3 79.0 - - - +
769D ARG* 1.3 57.6 + - - +
771D GLU* 3.8 3.7 - - - +
772D SER* 2.8 33.2 + - - -
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Residues in contact with ARG 769 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755D ILE* 5.0 8.5 - - + -
756D GLU* 2.7 40.6 + - - +
759D TYR* 3.1 48.4 - - + -
764D LEU 3.8 2.0 + - - +
766D HIS 3.5 3.4 + - - +
767D THR 3.2 0.6 - - - -
768D GLU* 1.3 76.0 - - - +
770D ASN* 1.3 80.5 + - - +
772D SER* 3.0 4.9 + - - -
773D LEU* 2.7 58.5 + - + +
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Residues in contact with ASN 770 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766D HIS 5.2 1.3 - - - -
767D THR* 3.4 18.4 + - - +
769D ARG* 1.3 113.9 + - - +
771D GLU* 1.3 59.4 + - - +
773D LEU* 4.1 4.4 - - - +
774D VAL* 3.0 33.5 + - + +
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Residues in contact with GLU 771 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767D THR* 3.1 21.4 + - - +
768D GLU* 4.0 3.1 - - - +
770D ASN* 1.3 74.8 - - - +
772D SER* 1.3 60.3 + - - +
774D VAL* 3.2 7.7 + - - +
775D LYS* 2.8 28.1 + - - +
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Residues in contact with SER 772 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755D ILE* 3.0 27.4 - - - +
768D GLU* 2.8 25.1 + - - -
769D ARG* 3.6 4.0 - - - -
771D GLU* 1.3 73.0 - - - +
773D LEU* 1.3 64.5 + - - +
775D LYS* 2.9 17.9 + - - +
776D ILE* 2.9 21.2 + - - +
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Residues in contact with LEU 773 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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752D ALA* 3.6 46.3 - - + +
755D ILE* 3.8 18.8 - - + -
756D GLU* 4.8 6.7 - - - +
769D ARG* 2.7 58.5 + - + +
770D ASN* 4.1 4.7 - - - +
772D SER* 1.3 73.0 - - - +
774D VAL* 1.3 57.3 + - + +
776D ILE* 3.9 4.8 - - + +
777D TRP* 2.9 31.1 + - - +
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Residues in contact with VAL 774 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770D ASN* 3.0 26.6 + - + +
771D GLU* 3.5 7.2 - - - +
772D SER 3.1 0.6 - - - -
773D LEU* 1.3 77.2 - - + +
775D LYS* 1.3 60.4 + - - +
777D TRP* 3.9 4.6 - - - +
778D GLN* 2.8 36.9 + - + +
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Residues in contact with LYS 775 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771D GLU 2.8 14.0 + - - +
772D SER* 2.9 11.9 + - - +
774D VAL* 1.3 76.6 - - - +
776D ILE* 1.3 59.0 + - + +
778D GLN* 4.2 3.0 - - - +
779D ASP* 2.7 33.1 + - - +
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Residues in contact with ILE 776 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748D HIS* 3.6 30.5 + - + +
751D GLU* 3.2 45.5 - - + +
752D ALA* 4.3 8.3 - - + +
755D ILE* 3.3 33.2 - - + -
772D SER* 2.9 14.4 + - - +
773D LEU* 3.9 5.4 - - - +
775D LYS* 1.3 75.9 - - + +
777D TRP* 1.3 61.6 + - - +
779D ASP* 3.2 5.1 + - - +
780D ALA* 2.8 30.5 + - - +
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Residues in contact with TRP 777 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748D HIS* 6.1 0.2 - - - -
773D LEU 2.9 18.5 + - - +
774D VAL* 3.9 4.7 - - - +
776D ILE* 1.3 77.6 - - - +
778D GLN* 1.3 57.2 + - - +
780D ALA* 3.8 4.3 - - - +
781D THR* 2.8 34.7 + - - +
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Residues in contact with GLN 778 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774D VAL* 2.8 29.5 + - + +
775D LYS* 4.2 2.5 - - - +
777D TRP* 1.3 71.5 - - - +
779D ASP* 1.3 56.2 + - - +
781D THR* 3.8 7.1 - - - -
782D GLU* 2.7 37.0 + - - +
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Residues in contact with ASP 779 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748D HIS* 4.2 13.2 - - + -
775D LYS 2.7 26.1 + - - +
776D ILE* 3.2 6.3 + - - +
778D GLN* 1.3 74.1 - - - +
780D ALA* 1.3 56.8 + - - +
782D GLU* 3.7 4.6 - - - +
783D GLU* 2.8 30.0 + - - +
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Residues in contact with ALA 780 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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745D LEU* 5.0 15.4 - - + +
748D HIS* 3.2 45.2 - - + -
776D ILE 2.8 16.4 + - - +
777D TRP* 3.9 4.9 - - - +
779D ASP* 1.3 71.2 - - - +
781D THR* 1.3 59.2 + - - +
783D GLU* 3.6 3.1 - - - +
784D VAL* 2.8 32.1 + - - +
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Residues in contact with THR 781 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745D LEU* 6.3 0.4 - - - -
777D TRP* 2.8 27.5 + - - +
778D GLN* 3.8 8.1 - - - +
780D ALA* 1.3 73.5 - - - +
782D GLU* 1.3 61.2 + - - +
784D VAL* 2.9 29.0 - - + +
785D GLY* 3.4 4.7 + - - -
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Residues in contact with GLU 782 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778D GLN 2.7 22.6 + - - +
779D ASP* 4.0 5.2 - - - +
781D THR* 1.3 73.7 - - - +
783D GLU* 1.3 61.8 + - - +
785D GLY* 3.6 7.9 + - - +
786D LYS* 3.6 12.5 + - - +
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Residues in contact with GLU 783 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744D ILE* 6.2 1.3 - - + -
747D ARG* 5.0 7.9 - - - +
748D HIS* 4.8 9.0 - - + +
779D ASP 2.8 20.2 + - - +
780D ALA* 3.1 8.2 + - - +
782D GLU* 1.3 75.9 - - - +
784D VAL* 1.3 59.2 + - - +
786D LYS* 3.6 5.1 + - - +
787D ALA* 3.0 27.4 + - - +
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Residues in contact with VAL 784 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738D PRO* 5.4 1.3 - - + -
741D LYS* 3.8 31.9 - - + +
745D LEU* 4.9 15.3 - - + -
780D ALA 2.8 13.9 + - - +
781D THR* 2.9 29.2 - - + +
783D GLU* 1.3 76.9 - - - +
785D GLY* 1.3 61.1 + - - +
787D ALA* 4.1 5.4 - - + -
788D LEU* 2.8 38.4 + - + +
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Residues in contact with GLY 785 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781D THR 3.4 6.8 + - - -
782D GLU 3.6 4.2 + - - -
783D GLU 3.3 0.8 - - - -
784D VAL* 1.3 85.5 - - - +
786D LYS* 1.3 51.5 + - - +
788D LEU* 3.8 4.3 - - - +
789D GLU* 2.6 40.9 + - - +
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Residues in contact with LYS 786 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782D GLU 3.6 10.8 + - - +
783D GLU* 4.0 7.4 - - - +
784D VAL 3.3 0.4 - - - -
785D GLY* 1.3 69.7 - - - +
787D ALA* 1.3 57.8 + - - +
788D LEU 3.0 1.3 - - - -
789D GLU* 4.3 3.1 - - - +
790D GLU* 2.7 57.4 + - + +
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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
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738D PRO* 4.0 11.7 - - + +
740D GLN* 4.7 19.5 - - + +
741D LYS* 5.3 5.4 - - - +
783D GLU 3.0 19.2 + - - +
784D VAL* 3.3 11.9 + - + +
786D LYS* 1.3 74.7 - - - +
788D LEU* 1.3 56.0 + - - +
790D GLU* 3.6 9.2 + - - +
791D PHE* 3.0 23.0 - - - +
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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
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735D VAL 6.0 2.0 - - - +
738D PRO* 4.0 31.2 - - + -
784D VAL* 2.8 19.9 + - + +
785D GLY* 3.8 3.8 - - - +
787D ALA* 1.3 77.5 - - - +
789D GLU* 1.3 66.6 + - + +
790D GLU 3.4 1.3 - - - -
791D PHE* 4.3 2.9 - - + -
792D TYR* 3.0 35.5 + - + +
799D ILE* 5.6 6.7 - - + -
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Residues in contact with GLU 789 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785D GLY 2.6 23.9 + - - +
786D LYS* 4.3 2.5 - - - +
788D LEU* 1.3 80.8 - - + +
790D GLU* 1.3 56.9 + - - +
792D TYR* 3.1 25.0 + - - +
799D ILE* 6.0 2.9 - - - +
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Residues in contact with GLU 790 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786D LYS* 2.7 47.8 + - - +
787D ALA* 3.6 8.6 + - - +
789D GLU* 1.3 75.7 - - - +
791D PHE* 1.3 65.0 + - + +
792D TYR 4.0 3.8 - - - +
793D PRO* 5.7 0.2 - - - +
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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
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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