Contacts of the helix formed by residues 758 - 780 (chain A) in PDB entry 5QSY
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 SER 758 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756A SER 3.9 1.2 + - - -
757A PRO* 1.3 77.1 - - - +
759A LYS* 1.3 66.8 + - - +
760A GLU* 4.0 11.2 + - - +
761A ASP* 2.9 34.5 + - - -
762A LEU* 3.2 24.0 + - - +
509B GLU* 5.1 11.2 - - - -
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Residues in contact with LYS 759 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758A SER* 1.3 73.7 - - - +
760A GLU* 1.3 75.0 + - - +
762A LEU* 3.4 12.4 + - + +
763A LEU* 3.1 46.6 + - + +
816A PRO* 3.9 27.2 - - + +
509B GLU* 4.9 10.4 + - - +
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Residues in contact with GLU 760 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758A SER* 3.3 9.1 + - - +
759A LYS* 1.3 94.5 + - - +
761A ASP* 1.3 61.8 + - - +
763A LEU* 3.7 10.1 - - + +
764A VAL* 2.9 37.3 + - + +
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Residues in contact with ASP 761 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752A ILE* 3.9 13.8 - - + +
756A SER 5.2 0.3 - - - +
757A PRO* 4.1 13.7 - - + +
758A SER* 2.9 38.5 + - - +
759A LYS 3.4 0.2 - - - -
760A GLU* 1.3 80.8 - - - +
762A LEU* 1.3 63.3 + - - +
764A VAL* 3.3 4.8 + - - +
765A LEU* 3.1 21.8 + - - +
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Residues in contact with LEU 762 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752A ILE* 3.8 29.8 - - + -
757A PRO* 4.0 13.2 - - + +
758A SER 3.2 15.1 + - - +
759A LYS* 3.5 13.7 - - + +
760A GLU 3.3 0.2 - - - -
761A ASP* 1.3 79.9 - - - +
763A LEU* 1.3 58.6 + - + +
765A LEU 3.3 1.4 + - - -
766A ARG* 2.9 24.7 + - - +
813A GLY 3.1 26.9 - - - +
814A LEU* 4.0 14.8 - - + -
816A PRO* 3.8 25.4 - - + -
817A LEU* 3.4 22.5 - - + +
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Residues in contact with LEU 763 (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 LYS* 3.1 40.4 + - + +
760A GLU* 4.2 8.3 - - + +
761A ASP 3.3 0.2 - - - -
762A LEU* 1.3 77.3 - - + +
764A VAL* 1.3 62.0 + - + +
766A ARG* 3.8 25.9 - - - +
767A LYS* 3.1 26.7 + - - +
816A PRO* 4.1 20.2 - - + -
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Residues in contact with VAL 764 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A GLN* 5.5 4.7 - - - +
760A GLU* 2.9 25.6 + - + +
761A ASP* 3.8 4.5 - - - +
763A LEU* 1.3 72.9 - - - +
765A LEU* 1.3 65.9 + - - +
767A LYS* 3.4 5.5 + - - +
768A THR* 2.9 34.2 + - - +
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Residues in contact with LEU 765 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745A ILE* 4.7 6.5 - - + +
748A GLN* 3.6 33.9 - - + +
749A LEU* 4.0 35.7 - - + +
752A ILE* 3.8 31.6 - - + -
761A ASP 3.1 6.5 + - - -
762A LEU 3.7 6.3 - - - +
764A VAL* 1.3 78.6 - - - +
766A ARG* 1.3 56.9 + - - +
768A THR* 3.1 8.6 + - + -
769A VAL* 2.9 43.1 + - + +
802A PHE* 4.4 4.5 - - + -
817A LEU* 3.9 17.5 - - + -
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Residues in contact with ARG 766 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A LEU 2.9 16.7 + - - +
763A LEU* 3.8 24.5 - - - +
764A VAL 3.3 0.2 - - - -
765A LEU* 1.3 75.3 - - - +
767A LYS* 1.3 61.3 + - - +
769A VAL* 3.2 1.4 + - - -
770A LYS* 2.8 47.9 + - - +
815A GLN 5.1 0.2 + - - -
816A PRO* 2.6 38.3 + - - +
817A LEU* 3.8 8.9 - - + +
818A VAL 3.2 23.0 + - - -
819A PHE* 3.5 36.1 - - + -
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Residues in contact with LYS 767 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763A LEU 3.1 15.5 + - - +
764A VAL* 3.9 5.6 - - - +
765A LEU 3.3 0.4 - - - -
766A ARG* 1.3 82.1 - - - +
768A THR* 1.3 61.0 + - - +
770A LYS* 3.4 12.6 + - + +
771A SER* 3.1 26.7 + - - -
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Residues in contact with THR 768 (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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713A PHE* 3.8 37.6 - - + -
745A ILE* 4.4 9.0 - - + -
748A GLN* 4.3 18.3 + - - +
764A VAL* 2.9 21.0 + - - +
765A LEU* 3.1 13.9 + - + -
767A LYS* 1.3 76.7 - - - +
769A VAL* 1.3 57.5 + - - +
771A SER* 3.0 22.3 + - - -
772A PHE* 3.0 15.1 + - - +
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Residues in contact with VAL 769 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745A ILE* 3.9 20.6 - - + -
765A LEU* 2.9 32.1 + - + +
766A ARG* 3.8 3.6 - - - +
768A THR* 1.3 72.7 - - - +
770A LYS* 1.3 60.9 + - - +
772A PHE* 3.2 0.7 + - - +
773A LEU* 2.9 44.0 + - + +
798A LEU* 5.4 2.9 - - + -
802A PHE* 3.6 43.1 - - + -
819A PHE* 3.6 24.7 - - + -
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Residues in contact with LYS 770 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766A ARG* 2.8 39.8 + - - +
767A LYS* 3.9 15.1 - - + +
769A VAL* 1.3 71.9 - - - +
771A SER* 1.3 61.0 + - - +
773A LEU* 3.9 5.8 - - - +
774A ALA* 3.0 30.0 + - + +
819A PHE* 3.4 29.3 - - + -
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Residues in contact with SER 771 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713A PHE* 4.0 7.6 - - - -
717A TYR* 3.8 30.0 + - - -
767A LYS* 3.1 15.9 + - - -
768A THR* 3.0 17.7 + - - -
770A LYS* 1.3 80.0 - - - +
772A PHE* 1.3 56.1 + - - +
774A ALA* 3.5 7.7 - - - +
775A VAL* 3.0 31.4 + - - +
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Residues in contact with PHE 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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713A PHE* 3.9 12.1 - + + -
717A TYR* 5.2 1.3 - + - -
720A LEU* 4.3 7.6 - - + -
738A LEU* 3.5 40.6 - - + -
741A SER* 3.3 26.7 - - - -
742A HIS* 4.2 15.3 - - + -
745A ILE* 3.6 22.0 - - + -
768A THR 3.0 16.8 + - - +
769A VAL 3.2 1.8 + - - +
771A SER* 1.3 76.0 + - - +
773A LEU* 1.3 59.4 + - - +
775A VAL* 3.0 12.1 + - + +
776A CYS* 2.8 49.1 + - - -
794A LEU* 4.2 4.5 - - + -
798A LEU* 3.6 26.5 - - + -
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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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769A VAL* 2.9 29.9 + - + +
770A LYS* 3.9 4.0 - - - +
772A PHE* 1.3 74.7 - - - +
774A ALA* 1.3 57.8 + - - +
776A CYS* 3.8 4.9 - - - +
777A GLN* 2.9 31.5 + - - +
795A LEU* 3.9 23.0 - - + +
798A LEU* 3.7 35.4 - - + -
799A LEU* 4.4 18.6 - - + +
802A PHE* 5.9 1.6 - - + -
819A PHE* 3.9 39.0 - - + -
825A LEU* 5.5 7.0 - - + +
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Residues in contact with ALA 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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721A LYS* 5.9 2.9 - - - +
770A LYS* 3.0 21.2 + - + +
771A SER* 3.5 9.0 - - - +
773A LEU* 1.3 75.9 - - - +
775A VAL* 1.3 56.6 + - - +
777A GLN* 3.3 8.6 + - - +
778A GLN* 2.9 40.0 + - - +
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Residues in contact with VAL 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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717A TYR* 3.5 29.2 - - + +
720A LEU* 3.8 36.3 - - + -
721A LYS* 4.6 11.4 - - + +
724A ILE* 4.1 13.4 - - + +
738A LEU* 4.3 5.6 - - + -
771A SER 3.0 19.0 + - - +
772A PHE* 3.0 11.8 + - + +
774A ALA* 1.3 70.5 - - - +
776A CYS* 1.3 60.4 + - - +
778A GLN* 3.2 8.8 + - - +
779A CYS* 2.9 38.3 + - - -
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Residues in contact with CYS 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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738A LEU* 3.7 12.1 - - - -
772A PHE* 2.8 56.9 + - - +
773A LEU* 4.8 0.2 - - - -
775A VAL* 1.3 68.2 - - - +
777A GLN* 1.3 68.9 + - - +
779A CYS* 3.0 11.7 + - - -
780A LEU 3.2 8.3 + - - -
791A ALA* 3.4 19.0 - - + +
794A LEU* 4.0 16.6 - - - -
795A LEU* 3.6 30.8 - - + +
798A LEU* 4.7 4.0 - - - -
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Residues in contact with GLN 777 (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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773A LEU 2.9 18.4 + - - +
774A ALA* 3.5 9.0 - - - +
776A CYS* 1.3 78.4 - - - +
778A GLN* 1.3 68.9 + - + +
780A LEU* 3.2 20.3 + - + +
781A SER* 4.4 0.9 + - - -
795A LEU* 3.8 9.7 - - - +
822A ASP* 4.7 8.2 + - - +
824A GLY* 4.2 2.2 - - - -
825A LEU* 3.6 49.1 - - + +
828A GLU* 2.7 31.5 + - - +
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Residues in contact with GLN 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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721A LYS* 3.3 26.3 + - - +
724A ILE* 3.6 46.2 - - + +
725A GLU* 5.9 0.2 + - - -
774A ALA* 2.9 28.5 + - - +
775A VAL* 3.2 1.5 + - - +
777A GLN* 1.3 78.9 - - + +
779A CYS* 1.3 56.0 + - - +
781A SER* 3.1 28.6 + - - -
782A ASN 4.3 0.7 + - - -
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Residues in contact with CYS 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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720A LEU* 4.7 3.8 - - - -
724A ILE* 4.5 13.9 - - - -
734A VAL* 4.3 13.9 - - - -
738A LEU* 4.2 16.6 - - + -
775A VAL* 2.9 37.5 + - - +
776A CYS* 3.0 7.1 + - - +
778A GLN* 1.3 71.4 - - - +
780A LEU* 1.3 63.0 + - - +
781A SER 3.1 1.8 - - - -
782A ASN* 3.0 26.4 + - - +
787A VAL* 3.6 17.2 - - + +
788A LYS* 4.2 3.8 - - - -
791A ALA* 3.8 11.9 - - + -
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Residues in contact with LEU 780 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776A CYS 3.2 8.0 + - - +
777A GLN* 3.2 18.7 + - - +
779A CYS* 1.3 76.2 - - - +
781A SER* 1.3 57.0 + - - +
782A ASN 3.4 0.2 - - - -
788A LYS* 3.2 52.1 + - - +
791A ALA* 4.2 1.8 - - + -
792A PHE* 4.0 28.0 - - + +
795A LEU* 4.2 15.3 - - + -
825A LEU* 4.9 3.6 - - + -
828A GLU* 3.9 40.8 - - + +
829A LEU* 4.8 5.8 - - + -
832A PHE* 4.6 11.9 - - + -
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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