Contacts of the helix formed by residues 764 - 781 (chain A) in PDB entry 2VUW
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 THR 764 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A CYS 3.9 0.2 - - - -
763A ASN* 1.3 98.0 - - - +
765A PRO* 1.3 81.2 - - - +
766A ALA* 3.7 6.7 + - - +
767A MSE 3.0 25.5 + - + +
768A LYS* 3.0 23.6 + - - +
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Residues in contact with PRO 765 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764A THR* 1.3 90.0 - - - +
766A ALA* 1.3 62.6 + - - +
767A MSE 3.1 0.5 + - - -
768A LYS* 3.4 5.4 + - + +
769A GLN* 3.2 22.8 + - - +
772A ARG* 4.9 2.1 + - - -
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Residues in contact with ALA 766 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764A THR* 3.1 8.8 + - - +
765A PRO* 1.3 79.9 - - + +
767A MSE 1.3 58.4 + - + +
769A GLN* 3.6 13.3 - - - +
770A ILE* 3.2 28.5 + - - +
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Residues in contact with MSE 767 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A SER* 3.7 34.8 - - - +
623A ALA* 4.3 18.4 - - - -
760A THR* 4.5 7.6 - - + -
761A LYS 4.0 11.4 - - - +
762A CYS* 3.2 29.3 - - + -
763A ASN* 4.0 16.8 - - - +
764A THR* 3.0 27.3 + - + +
766A ALA* 1.3 78.7 - - + +
768A LYS* 1.3 61.6 + - - +
769A GLN 2.9 5.2 - - - -
770A ILE* 3.4 11.2 + - + +
771A LYS 3.2 16.5 + - - -
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Residues in contact with LYS 768 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A CYS* 3.4 36.9 + - + +
763A ASN* 4.7 2.7 - - - +
764A THR 3.0 16.0 + - - +
765A PRO* 4.0 4.7 - - + +
767A MSE 1.3 76.9 - - - +
769A GLN* 1.3 57.2 + - - +
771A LYS* 3.5 9.4 - - + +
772A ARG* 3.2 40.3 + - + +
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Residues in contact with GLN 769 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765A PRO 3.2 18.0 + - - +
766A ALA* 3.6 11.4 - - - +
768A LYS* 1.3 75.9 - - - +
770A ILE* 1.3 66.6 + - + +
771A LYS 3.1 1.1 - - - -
772A ARG* 3.3 33.0 + - + +
773A LYS* 3.0 41.3 + - + +
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Residues in contact with ILE 770 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A LEU* 4.1 15.7 - - + +
623A ALA* 4.4 17.5 - - + +
626A LYS* 4.5 28.9 - - + +
766A ALA 3.2 18.1 + - - +
767A MSE 3.4 16.1 + - + +
769A GLN* 1.3 80.7 - - + +
771A LYS* 1.3 61.9 + - - +
773A LYS* 3.1 13.6 + - + +
774A ILE* 3.0 41.3 + - + +
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Residues in contact with LYS 771 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A LEU* 3.6 32.9 - - + +
753A LEU* 4.8 7.1 - - + +
762A CYS* 4.0 14.4 - - + -
767A MSE 3.2 10.3 + - - +
768A LYS* 3.5 15.0 - - + +
769A GLN 3.1 0.6 - - - -
770A ILE* 1.3 80.0 - - - +
772A ARG* 1.3 63.0 + - + +
774A ILE* 3.3 4.0 + - - +
775A GLN* 3.0 55.4 + - + +
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Residues in contact with ARG 772 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765A PRO 4.9 1.8 + - - -
768A LYS* 3.2 25.9 + - + +
769A GLN* 3.4 53.5 + - - +
770A ILE 3.3 0.4 - - - -
771A LYS* 1.3 80.2 - - + +
773A LYS* 1.3 58.5 + - + +
775A GLN* 3.3 17.0 + - - +
776A GLU* 2.9 28.8 + - - +
779A ARG* 5.1 1.6 + - - -
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Residues in contact with LYS 773 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A LYS* 5.2 6.7 - - - +
769A GLN* 3.0 38.3 + - + +
770A ILE* 3.5 18.8 - - + +
772A ARG* 1.3 74.6 - - + +
774A ILE* 1.3 59.7 + - - +
776A GLU* 3.3 10.5 + - - +
777A PHE* 3.0 26.3 + - - +
795A SER 6.0 0.9 - - - +
796A LEU* 3.9 30.1 - - + +
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Residues in contact with ILE 774 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A LEU* 3.8 39.5 - - + +
625A ALA* 4.0 11.0 - - + -
626A LYS* 4.1 10.1 - - + +
629A LEU* 4.2 13.2 - - + -
749A THR* 4.0 15.0 - - + +
752A MSE 5.2 3.4 - - + -
753A LEU* 3.9 25.6 - - + -
770A ILE* 3.0 23.1 + - + +
771A LYS 3.8 4.5 - - - +
773A LYS* 1.3 74.8 - - - +
775A GLN* 1.3 62.5 + - - +
777A PHE* 3.2 7.4 + - + +
778A HIS* 3.0 21.8 + - - +
796A LEU* 4.7 11.9 - - + -
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Residues in contact with GLN 775 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753A LEU* 4.0 24.8 - - + +
771A LYS* 3.0 49.6 + - - +
772A ARG* 3.6 19.2 + - - +
774A ILE* 1.3 75.5 - - - +
776A GLU* 1.3 62.1 + - - +
778A HIS* 3.2 4.9 + - - +
779A ARG* 3.2 31.6 + - - +
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Residues in contact with GLU 776 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772A ARG 2.9 16.9 + - - +
773A LYS* 3.5 10.0 - - - +
775A GLN* 1.3 74.0 - - - +
777A PHE* 1.3 57.4 + - - +
779A ARG* 3.2 41.6 + - - +
780A THR* 2.7 49.0 + - + +
794A HIS* 3.2 25.8 + - - -
795A SER* 3.7 13.4 + - - -
796A LEU* 5.6 0.5 - - - +
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Residues in contact with PHE 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A LEU* 4.4 15.9 - - + -
633A THR* 4.4 5.2 - - - -
745A LEU* 5.5 1.1 - - + -
749A THR* 3.4 31.9 - - + -
773A LYS 3.0 12.9 + - - +
774A ILE* 3.2 9.6 - - + +
776A GLU* 1.3 75.0 + - - +
778A HIS* 1.3 64.4 + - - +
780A THR* 3.7 4.3 - - - -
781A MSE 2.9 53.7 + - + +
790A LEU* 4.0 17.9 - - + -
794A HIS* 3.6 32.8 - + + -
796A LEU* 3.7 20.9 - - + -
797A PHE* 3.8 34.8 - + - -
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Residues in contact with HIS 778 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746A HIS* 3.1 51.0 + + - -
749A THR* 3.8 12.8 - - + +
750A ASP* 3.1 52.4 + - + +
753A LEU* 3.7 17.0 - - + +
754A LYS* 4.3 14.1 - - - -
774A ILE 3.0 13.3 + - - +
775A GLN* 3.4 10.7 + - - +
777A PHE* 1.3 77.7 - - - +
779A ARG* 1.3 64.1 + - - +
780A THR 3.6 0.3 + - - -
781A MSE 4.0 5.8 + - - +
782A LEU* 5.1 1.2 + - - +
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Residues in contact with ARG 779 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772A ARG 5.1 1.2 + - - -
775A GLN* 3.2 14.2 + - - +
776A GLU* 3.3 49.8 - - - +
778A HIS* 1.3 83.0 - - - +
780A THR* 1.3 65.1 + - + +
781A MSE 3.9 0.2 - - - -
782A LEU* 5.4 0.9 - - - -
783A ASN* 4.8 5.7 + - - -
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Residues in contact with THR 780 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776A GLU* 2.7 38.0 + - + +
777A PHE 3.4 0.2 + - - -
779A ARG* 1.3 90.5 - - + +
781A MSE 1.3 67.4 + - - +
782A LEU 3.2 2.7 - - - -
783A ASN* 3.0 30.2 + - - +
784A PHE* 3.6 9.9 - - - -
794A HIS* 2.8 30.5 + - - -
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Residues in contact with MSE 781 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742A VAL* 3.3 16.8 - - + +
745A LEU* 3.4 40.6 - - + -
746A HIS* 3.4 33.9 - - + +
749A THR* 3.6 17.5 - - - -
777A PHE* 2.9 54.4 + - + +
778A HIS* 4.0 0.4 - - - -
780A THR* 1.3 79.0 + - - +
782A LEU* 1.3 60.5 + - + +
783A ASN 3.0 4.8 + - - -
784A PHE* 3.1 24.7 + - - +
790A LEU* 3.7 19.5 - - + +
794A HIS* 4.6 0.7 - - - -
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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) + - + + + + + -
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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