Contacts of the helix formed by residues 738 - 762 (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 PRO 738 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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735D VAL 5.3 2.0 - - - +
736D LEU* 4.7 1.3 - - + +
737D VAL* 1.3 92.2 - - + +
739D PRO* 1.3 65.7 - - + +
740D GLN* 3.1 3.6 - - + +
741D LYS* 2.8 44.0 + - + +
742D GLN 3.9 0.5 + - - -
784D VAL* 5.4 2.0 - - + -
787D ALA* 4.0 21.5 - - + +
788D LEU* 4.0 32.5 - - + +
791D PHE* 5.0 7.2 - - + -
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Residues in contact with PRO 739 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737D VAL* 3.0 15.6 - - + +
738D PRO* 1.3 82.4 - - + +
740D GLN* 1.3 61.8 + - - +
741D LYS 3.3 0.3 + - - -
742D GLN* 3.6 7.2 + - + +
743D GLU* 3.4 19.4 + - - +
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Residues in contact with GLN 740 (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* 3.0 3.3 + - + -
739D PRO* 1.3 82.1 - - + +
741D LYS* 1.3 52.8 + - - +
743D GLU* 3.9 7.2 - - - +
744D ILE* 2.7 41.0 + - + +
787D ALA* 4.7 17.7 - - + +
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Residues in contact with LYS 741 (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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737D VAL* 5.1 3.1 - - + -
738D PRO* 2.8 33.3 + - + +
740D GLN* 1.3 74.6 - - - +
742D GLN* 1.3 56.8 + - - +
744D ILE* 4.0 3.3 - - - +
745D LEU* 2.7 48.5 + - + +
784D VAL* 3.8 26.2 - - + -
787D ALA* 5.3 4.4 - - + +
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Residues in contact with GLN 742 (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 3.9 1.4 + - - -
739D PRO* 3.6 8.8 + - + +
740D GLN 3.5 0.2 - - - -
741D LYS* 1.3 78.8 - - - +
743D GLU* 1.3 61.2 + - - +
745D LEU* 3.8 16.6 - - - +
746D GLU* 3.3 22.9 + - - +
841D GLU* 3.7 33.0 + - + +
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Residues in contact with GLU 743 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739D PRO 3.4 14.6 + - - +
740D GLN* 3.9 6.7 - - - +
741D LYS 3.2 0.4 - - - -
742D GLN* 1.3 79.4 - - - +
744D ILE* 1.3 64.9 + - + +
746D GLU* 3.2 9.2 + - - +
747D ARG* 3.1 27.4 + - - +
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Residues in contact with ILE 744 (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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740D GLN* 2.7 24.6 + - + +
741D LYS* 4.0 3.4 - - - +
743D GLU* 1.3 77.7 - - + +
745D LEU* 1.3 62.2 + - + +
747D ARG* 3.0 37.7 + - - +
748D HIS* 3.0 30.3 + - + -
783D GLU* 6.2 1.8 - - + -
787D ALA* 6.6 0.2 - - + -
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Residues in contact with LEU 745 (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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741D LYS* 2.7 40.3 + - + +
742D GLN* 3.8 17.9 - - - +
744D ILE* 1.3 75.2 - - + +
746D GLU* 1.3 57.3 + - - +
748D HIS* 3.5 4.4 + - - +
749D GLU* 3.0 29.7 + - - +
780D ALA* 5.0 15.5 - - + +
784D VAL* 4.9 19.5 - - + -
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Residues in contact with GLU 746 (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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742D GLN* 3.3 15.9 + - - +
743D GLU* 3.2 13.7 + - - +
745D LEU* 1.3 77.6 - - - +
747D ARG* 1.3 61.9 + - - +
749D GLU* 3.7 8.0 + - - +
750D ALA* 3.4 17.5 + - - +
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Residues in contact with ARG 747 (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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743D GLU* 3.1 18.7 + - - +
744D ILE* 3.0 36.1 + - - +
746D GLU* 1.3 73.8 - - - +
748D HIS* 1.3 91.7 + - + +
750D ALA* 3.2 20.4 + - - +
751D GLU* 3.6 15.1 + - - +
783D GLU* 5.0 9.3 - - - +
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Residues in contact with HIS 748 (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* 3.0 29.2 + - + +
745D LEU 4.2 2.9 - - - +
747D ARG* 1.3 104.9 + - + +
749D GLU* 1.3 65.1 + - - +
751D GLU* 3.0 30.5 + - - +
752D ALA* 3.3 10.0 + - - +
776D ILE* 3.6 27.7 + - + +
779D ASP* 4.2 12.9 + - + -
780D ALA* 3.2 46.7 - - + +
783D GLU* 4.8 4.1 - - + +
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Residues in contact with GLU 749 (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 3.0 20.3 + - - +
746D GLU* 3.8 9.9 - - - +
747D ARG 3.2 0.2 - - - -
748D HIS* 1.3 77.2 - - - +
750D ALA* 1.3 60.3 + - - +
752D ALA* 3.3 8.8 + - - +
753D ASP* 3.1 21.8 + - - +
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Residues in contact with ALA 750 (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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746D GLU 3.4 10.0 + - - +
747D ARG* 3.2 12.2 + - - +
748D HIS 3.1 0.8 - - - -
749D GLU* 1.3 79.1 - - - +
751D GLU* 1.3 58.3 + - + +
753D ASP* 3.9 6.1 - - - +
754D ALA* 3.0 33.1 + - - +
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Residues in contact with GLU 751 (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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747D ARG* 4.0 16.8 - - - +
748D HIS* 3.0 26.4 + - - +
750D ALA* 1.3 77.8 - - + +
752D ALA* 1.3 58.4 + - - +
754D ALA* 4.7 2.0 - - - +
755D ILE* 3.1 35.4 + - + +
776D ILE* 3.2 36.9 - - + +
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Residues in contact with ALA 752 (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 3.3 10.3 + - - +
749D GLU* 3.3 9.8 + - - +
750D ALA 3.2 0.6 - - - -
751D GLU* 1.3 74.6 - - - +
753D ASP* 1.3 63.8 + - - +
756D GLU* 3.4 19.4 + - - +
773D LEU* 3.6 32.6 - - + +
776D ILE* 4.3 6.0 - - + +
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Residues in contact with ASP 753 (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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749D GLU 3.1 15.1 + - - +
750D ALA* 3.3 7.1 + - - +
752D ALA* 1.3 75.8 - - - +
754D ALA* 1.3 65.1 + - - +
756D GLU* 3.1 17.3 + - - +
757D ARG* 3.1 11.0 + - - +
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Residues in contact with ALA 754 (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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750D ALA 3.0 15.7 + - - +
751D GLU* 4.7 2.7 - - - +
753D ASP* 1.3 74.6 - - - +
755D ILE* 1.3 59.9 + - - +
757D ARG* 3.0 23.6 + - + +
758D LYS* 2.8 28.1 + - - +
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Residues in contact with ILE 755 (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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751D GLU* 3.1 20.4 + - + +
752D ALA 3.9 3.4 - - - +
753D ASP 3.2 0.2 - - - -
754D ALA* 1.3 77.2 - - - +
756D GLU* 1.3 54.7 + - - +
758D LYS* 3.2 8.9 + - + +
759D TYR* 2.7 33.2 + - + +
769D ARG* 5.0 13.2 - - + -
772D SER* 3.0 30.7 - - - +
773D LEU* 3.8 24.9 - - + -
776D ILE* 3.3 24.9 - - + -
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Residues in contact with GLU 756 (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 3.4 9.9 + - - +
753D ASP* 3.1 12.6 + - - +
755D ILE* 1.3 77.0 - - - +
757D ARG* 1.3 65.8 + - - +
759D TYR* 3.2 19.7 + - - +
760D GLN* 3.0 24.3 + - - +
769D ARG* 2.7 36.7 + - - +
773D LEU* 4.8 8.1 - - - +
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Residues in contact with ARG 757 (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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753D ASP 3.1 7.5 + - - +
754D ALA* 3.0 27.6 + - - +
756D GLU* 1.3 75.5 - - - +
758D LYS* 1.3 72.5 + - - +
760D GLN* 3.2 15.6 + - - +
761D ARG* 3.5 12.1 + - - +
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Residues in contact with LYS 758 (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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754D ALA 2.8 15.6 + - - +
755D ILE* 3.6 11.2 - - + +
757D ARG* 1.3 87.7 - - - +
759D TYR* 1.3 62.2 + - - +
760D GLN 3.5 0.2 + - - -
761D ARG* 3.8 7.5 + - - +
762D GLY 3.8 0.5 + - - -
763D ALA* 3.1 39.2 + - + +
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Residues in contact with TYR 759 (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* 2.7 21.2 + - + +
756D GLU* 3.2 21.5 + - + +
758D LYS* 1.3 75.4 - - - +
760D GLN* 1.3 70.1 + - - +
761D ARG 3.5 0.2 + - - -
762D GLY* 3.8 3.5 + - - -
763D ALA 4.4 0.4 - - - -
764D LEU* 3.2 49.5 + - + +
766D HIS* 3.8 15.5 + - - -
769D ARG* 3.1 53.1 - - + -
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Residues in contact with GLN 760 (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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756D GLU* 3.0 15.3 + - - +
757D ARG* 3.2 8.4 + - - +
759D TYR* 1.3 85.3 - - - +
761D ARG* 1.3 66.9 + - - +
762D GLY* 4.4 0.3 - - - -
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Residues in contact with ARG 761 (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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757D ARG* 3.5 13.7 + - - +
758D LYS* 4.3 7.4 - - - +
759D TYR 3.4 0.4 - - - -
760D GLN* 1.3 82.6 - - - +
762D GLY* 1.3 59.0 + - - +
763D ALA* 4.9 0.9 - - + +
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Residues in contact with GLY 762 (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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759D TYR 3.8 3.3 + - - -
760D GLN 3.4 2.4 - - - -
761D ARG* 1.3 80.7 - - - +
763D ALA* 1.3 59.8 + - - +
764D LEU* 3.2 9.8 + - - -
765D ASN 4.6 3.1 + - - -
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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) + - + + + + + -
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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