Contacts of the helix formed by residues 767 - 782 (chain A) in PDB entry 5LUQ
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 GLU 767 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763A THR 4.1 4.0 - - - -
764A PRO 3.7 6.0 + - - -
766A ALA* 1.3 69.4 - - - +
768A VAL* 1.3 58.3 + - - +
769A GLY 3.9 0.2 - - - -
770A LEU* 4.3 7.9 - - + -
771A ASN* 3.1 31.9 + - + +
846A ILE* 2.8 55.3 - - + +
847A SER* 3.7 2.6 - - - -
848A LEU* 3.7 15.4 + - - +
851A ILE* 3.3 22.0 - - + -
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Residues in contact with VAL 768 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A SER 5.4 1.1 - - - +
505A SER* 4.0 14.8 - - - +
506A GLU* 4.9 20.6 - - + +
509A ARG* 5.7 2.9 - - - +
732A PHE* 3.3 31.5 - - + -
763A THR* 4.0 0.4 + - + -
766A ALA* 2.2 49.2 + - + +
767A GLU 1.3 69.9 - - - +
769A GLY* 1.3 66.9 + - - +
770A LEU 3.4 0.3 + - - -
771A ASN* 3.6 5.8 + - - +
772A ALA* 3.8 10.2 + - - +
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Residues in contact with GLY 769 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732A PHE* 3.4 20.8 - - - -
759A GLY* 4.3 1.8 - - - -
763A THR* 3.6 24.8 - - - +
768A VAL* 1.3 79.9 - - - +
770A LEU* 1.3 63.0 + - - +
772A ALA* 3.7 4.9 + - - +
773A LEU* 2.9 24.9 - - - +
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Residues in contact with LEU 770 (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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759A GLY 3.3 14.1 - - - +
760A LEU* 3.3 22.7 - - - +
763A THR* 3.0 36.0 + - - +
764A PRO* 3.4 26.2 - - + -
767A GLU* 4.5 7.2 - - - -
768A VAL 3.2 0.4 - - - -
769A GLY* 1.3 75.9 - - - +
771A ASN* 1.3 67.1 + - - +
773A LEU* 3.1 24.4 + - - +
774A GLU* 4.0 5.2 + - - +
803A SER* 5.9 3.6 - - - -
807A ASP* 4.8 6.1 - - - +
851A ILE* 3.5 40.3 - - + +
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Residues in contact with ASN 771 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767A GLU* 3.1 19.5 + - - +
768A VAL* 3.9 3.8 - - - +
769A GLY 3.5 0.2 - - - -
770A LEU* 1.3 78.7 - - - +
772A ALA* 1.3 54.5 + - - +
773A LEU 2.3 17.3 + - - -
774A GLU* 3.0 26.3 + - - +
775A GLU* 4.1 10.0 + - - +
846A ILE* 3.2 37.5 - - - +
851A ILE* 5.2 3.2 - - - +
854A ARG* 3.7 17.4 + - - +
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Residues in contact with ALA 772 (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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732A PHE* 5.2 9.4 - - + +
735A SER* 4.1 19.6 + - - +
736A LEU* 4.7 13.5 - - + -
739A ASN* 3.4 23.2 + - - -
768A VAL 3.8 7.5 + - - +
769A GLY* 3.7 10.7 + - - +
770A LEU 3.4 1.0 + - - -
771A ASN* 1.3 74.2 - - - +
773A LEU* 1.3 63.2 + - + +
775A GLU* 4.6 11.4 - - - +
776A TRP* 3.7 5.9 + - - +
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Residues in contact with LEU 773 (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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735A SER* 4.8 8.5 - - - -
755A ALA* 4.2 13.9 - - + +
756A PHE* 3.3 49.4 - - + +
759A GLY* 3.3 38.1 - - - +
769A GLY 2.9 23.3 - - - +
770A LEU 3.1 12.1 - - - +
771A ASN 2.3 15.6 + - - -
772A ALA* 1.3 76.1 - - + +
774A GLU* 1.3 65.8 + - + +
775A GLU 3.3 1.1 - - - -
776A TRP* 2.8 16.7 + - + +
777A SER 2.9 11.8 + - - -
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Residues in contact with GLU 774 (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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756A PHE* 5.3 0.2 - - - -
770A LEU 4.7 4.7 - - - +
771A ASN* 3.0 17.7 + - - +
773A LEU* 1.3 75.7 - - - +
775A GLU* 1.3 60.6 + - + +
777A SER* 2.9 11.3 + - - -
778A ILE* 2.8 43.6 + - + +
851A ILE* 3.0 30.5 - - + +
854A ARG* 3.0 58.0 + - - +
855A VAL* 4.6 6.2 - - + +
858A MSE 5.1 5.8 - - + -
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Residues in contact with GLU 775 (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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736A LEU* 4.9 6.8 - - - +
739A ASN* 3.9 12.0 + - - +
771A ASN* 4.1 11.8 + - - +
772A ALA* 4.7 10.9 - - - +
773A LEU 3.3 0.4 - - - -
774A GLU* 1.3 78.2 - - + +
776A TRP* 1.3 63.9 + - - +
778A ILE* 4.3 10.0 - - + +
779A TYR* 2.9 56.0 + - + +
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Residues in contact with TRP 776 (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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735A SER* 4.0 22.3 + - - +
738A HIS* 4.3 10.7 - - - +
739A ASN* 3.1 29.3 + - - +
745A VAL* 3.3 24.9 - - + -
751A ALA* 6.2 1.9 - - + +
752A LEU* 3.2 39.6 - - + +
756A PHE* 3.6 23.3 - + + -
772A ALA 3.7 13.0 + - - +
773A LEU* 2.8 14.7 + - + +
775A GLU* 1.3 80.8 - - - +
777A SER* 1.3 77.0 + - - +
780A ILE* 3.1 44.0 + - + +
785A MSE 3.7 24.5 - - + -
796A LEU* 5.6 3.1 - - + -
799A TYR* 5.3 2.0 - - - -
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Residues in contact with SER 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756A PHE* 4.0 14.8 - - - -
773A LEU 2.9 10.4 + - - -
774A GLU* 2.9 15.9 + - - -
776A TRP* 1.3 85.4 - - - +
778A ILE* 1.3 53.4 + - - -
780A ILE 2.8 3.6 + - - -
781A ASP* 2.5 39.8 + - - +
796A LEU* 6.3 2.0 - - - -
799A TYR* 4.9 5.6 - - - -
800A LEU* 5.9 1.7 - - - +
858A MSE 3.0 30.0 - - - -
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Residues in contact with ILE 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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774A GLU* 2.8 38.4 + - + +
775A GLU* 4.1 8.5 - - + +
777A SER* 1.3 74.3 + - - +
779A TYR* 1.3 69.3 + - + +
781A ASP* 3.2 18.7 + - - +
782A ARG* 4.0 7.0 + - - +
854A ARG* 5.8 1.3 - - + +
858A MSE 3.6 28.7 - - + -
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Residues in contact with TYR 779 (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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670A LEU* 4.1 18.2 - - + -
739A ASN* 4.4 11.0 - - - +
742A GLU* 3.4 24.2 - - - +
775A GLU* 2.9 59.7 + - + +
776A TRP 4.1 1.1 - - - +
778A ILE* 1.3 78.8 - - + +
780A ILE* 1.3 65.7 + - + +
781A ASP 3.7 0.2 + - - -
782A ARG* 3.8 7.4 - - - +
783A HIS* 3.4 18.6 - - - +
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Residues in contact with ILE 780 (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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739A ASN* 4.5 7.6 - - - +
742A GLU* 4.3 19.3 - - + +
745A VAL* 4.1 22.4 - - + +
776A TRP* 3.1 54.7 - - + +
777A SER 2.8 2.4 + - - +
779A TYR* 1.3 81.7 - - + +
781A ASP* 1.3 57.1 + - - +
782A ARG 2.9 6.6 + - - -
783A HIS* 2.9 30.7 + - + +
785A MSE 3.4 44.1 - - + +
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Residues in contact with ASP 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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777A SER* 2.5 22.2 + - - +
778A ILE* 3.2 11.6 + - - +
780A ILE* 1.3 70.6 - - - +
782A ARG* 1.3 73.2 + - + +
785A MSE 5.3 7.7 - - - +
786A GLN* 3.9 11.3 + - - +
793A LEU* 5.0 9.9 - - - +
796A LEU* 6.1 0.3 - - - +
858A MSE 3.0 28.1 - - - +
861A SER* 4.3 2.1 + - - -
862A LEU* 3.1 34.8 - - - +
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Residues in contact with ARG 782 (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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778A ILE* 4.0 8.7 + - - +
779A TYR 3.8 5.6 - - - +
780A ILE 2.9 0.2 - - - -
781A ASP* 1.3 90.3 + - - +
783A HIS* 1.3 63.4 + - - +
784A VAL 3.8 2.0 - - - +
785A MSE 5.5 0.2 - - - +
786A GLN* 3.9 23.6 - - + +
861A SER* 5.5 12.5 + - - -
862A LEU* 5.7 3.6 - - - +
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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
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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