Contacts of the helix formed by residues 758 - 780 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756B SER 4.1 1.2 + - - -
757B PRO* 1.3 76.1 - - - +
759B LYS* 1.3 63.3 + - - +
760B GLU* 3.6 11.6 + - - +
761B ASP* 3.1 43.4 + - - +
762B LEU* 3.2 15.2 + - - +
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Residues in contact with LYS 759 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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758B SER* 1.3 69.7 - - - +
760B GLU* 1.3 65.9 + - - +
762B LEU* 3.2 24.5 + - + +
763B LEU* 3.0 38.1 + - + +
813B GLY 5.2 3.4 - - - -
816B PRO* 4.4 17.9 - - + -
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Residues in contact with GLU 760 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758B SER* 3.6 9.9 + - - +
759B LYS* 1.3 75.8 - - - +
761B ASP* 1.3 66.6 + - - +
763B LEU* 3.2 10.4 + - + +
764B VAL* 2.9 40.5 + - + +
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Residues in contact with ASP 761 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752B ILE* 4.5 10.6 - - + +
757B PRO* 3.9 15.0 - - + +
758B SER* 3.1 41.7 + - - +
760B GLU* 1.3 78.5 - - - +
762B LEU* 1.3 63.9 + - - +
764B VAL* 3.4 7.7 + - - +
765B LEU* 3.3 20.6 + - - +
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Residues in contact with LEU 762 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752B ILE* 4.1 10.5 - - + -
757B PRO* 4.3 13.9 - - + +
758B SER 3.6 14.4 - - - +
759B LYS* 3.2 24.0 + - + +
761B ASP* 1.3 76.4 - - - +
763B LEU* 1.3 58.1 + - + +
765B LEU* 4.8 1.3 - - - +
766B ARG* 3.2 25.6 + - - +
813B GLY 3.8 20.2 - - - +
814B LEU* 3.6 21.5 - - + -
816B PRO* 4.0 25.1 - - + +
817B LEU* 3.5 38.1 - - + +
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Residues in contact with LEU 763 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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759B LYS* 3.0 36.6 + - + +
760B GLU* 3.2 8.9 + - + +
762B LEU* 1.3 76.8 - - + +
764B VAL* 1.3 65.7 + - + +
766B ARG* 3.5 29.3 + - - +
767B LYS* 3.1 24.8 + - - +
816B PRO* 5.2 4.7 - - + -
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Residues in contact with VAL 764 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748B GLN* 5.3 7.4 - - - +
760B GLU* 2.9 32.3 + - + +
761B ASP* 3.7 7.4 - - - +
763B LEU* 1.3 76.4 - - + +
765B LEU* 1.3 61.2 + - - +
767B LYS* 3.6 10.9 - - + +
768B THR* 3.2 24.4 + - - +
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Residues in contact with LEU 765 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745B ILE* 4.7 8.5 - - + -
748B GLN* 3.7 31.9 - - + +
749B LEU* 4.1 20.6 - - - +
752B ILE* 3.2 30.5 - - + -
761B ASP 3.3 12.9 + - - +
762B LEU 4.2 0.2 - - - +
764B VAL* 1.3 76.5 - - - +
766B ARG* 1.3 56.2 + - - +
767B LYS 3.1 1.6 - - - -
768B THR* 2.9 14.9 + - + -
769B VAL* 2.8 50.1 + - + +
802B PHE* 4.6 7.9 - - + -
817B LEU* 3.8 23.8 - - + -
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Residues in contact with ARG 766 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762B LEU 3.2 16.0 + - - +
763B LEU* 3.6 26.3 - - - +
765B LEU* 1.3 77.2 - - - +
767B LYS* 1.3 61.2 + - - +
769B VAL* 3.5 4.8 + - - -
770B LYS* 3.0 33.5 + - - +
816B PRO* 3.2 46.1 + - - +
817B LEU* 3.8 8.6 - - + +
818B VAL 5.2 6.8 + - - -
819B PHE* 3.7 19.5 - - + -
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Residues in contact with LYS 767 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763B LEU 3.1 13.3 + - - +
764B VAL* 3.6 10.5 - - + +
765B LEU 3.1 0.6 - - - -
766B ARG* 1.3 78.8 - - - +
768B THR* 1.3 59.7 + - - +
770B LYS* 3.0 9.3 + - - +
771B SER* 2.8 34.5 + - - +
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Residues in contact with THR 768 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713B PHE* 3.5 41.3 - - + -
745B ILE* 4.4 10.1 - - + -
748B GLN* 4.7 14.2 + - - +
764B VAL* 3.2 14.9 + - - +
765B LEU* 2.9 18.7 + - + -
767B LYS* 1.3 74.4 - - - +
769B VAL* 1.3 56.9 + - - +
771B SER* 3.3 10.0 + - - -
772B PHE* 3.1 26.9 + - - +
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Residues in contact with VAL 769 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745B ILE* 4.1 15.9 - - + -
765B LEU* 2.8 43.4 + - + +
766B ARG* 3.9 5.2 - - - +
768B THR* 1.3 73.7 - - - +
770B LYS* 1.3 56.8 + - - +
772B PHE* 3.3 2.1 + - - +
773B LEU* 2.8 46.6 + - + +
798B LEU* 5.2 5.8 - - + -
802B PHE* 3.9 39.7 - - + -
817B LEU* 5.2 0.9 - - + -
819B PHE* 4.0 14.8 - - + -
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Residues in contact with LYS 770 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766B ARG* 3.0 26.1 + - - +
767B LYS* 3.0 5.6 + - - +
769B VAL* 1.3 73.5 - - - +
771B SER* 1.3 62.1 + - - +
773B LEU* 3.7 4.7 - - + +
774B ALA* 2.9 30.6 + - + +
819B PHE* 3.9 28.5 - - + -
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Residues in contact with SER 771 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713B PHE* 5.2 2.5 - - - -
717B TYR* 3.7 31.5 + - - -
767B LYS* 2.8 23.2 + - - +
768B THR* 3.4 10.4 - - - -
769B VAL 3.3 0.2 - - - -
770B LYS* 1.3 76.5 - - - +
772B PHE* 1.3 58.4 + - - +
774B ALA* 3.4 6.8 - - - +
775B VAL* 2.9 32.6 + - - +
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Residues in contact with PHE 772 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713B PHE* 4.1 10.1 - + + -
717B TYR* 4.8 1.8 - + - -
720B LEU* 4.2 5.6 - - + -
738B LEU* 3.3 40.8 - - + -
741B SER* 3.3 26.0 - - - -
742B HIS* 4.0 17.3 - - + -
745B ILE* 3.4 25.1 - - + -
768B THR 3.1 15.4 + - - +
769B VAL 3.7 4.0 - - - +
771B SER* 1.3 76.4 - - - +
773B LEU* 1.3 53.2 + - - +
775B VAL* 2.9 13.2 + - + +
776B CYS* 2.7 49.3 + - - +
794B LEU* 4.2 4.5 - - + -
798B LEU* 3.5 29.4 - - + -
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Residues in contact with LEU 773 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769B VAL* 2.8 42.2 + - + +
770B LYS* 3.7 7.0 - - + +
772B PHE* 1.3 75.8 - - - +
774B ALA* 1.3 51.8 + - - +
776B CYS* 3.2 6.4 + - - +
777B GLN* 2.8 34.9 + - - +
795B LEU* 3.6 28.6 - - + +
798B LEU* 4.2 26.2 - - + +
799B LEU* 4.5 16.2 - - + -
802B PHE* 6.0 1.3 - - + -
819B PHE* 3.7 33.0 - - + -
825B LEU* 5.5 4.2 - - + +
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Residues in contact with ALA 774 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717B TYR* 6.0 0.2 - - - +
721B LYS* 6.1 1.6 - - - +
770B LYS* 2.9 19.5 + - + +
771B SER* 3.4 8.1 - - - +
773B LEU* 1.3 75.0 - - - +
775B VAL* 1.3 58.8 + - + +
777B GLN* 3.8 6.0 - - - +
778B GLN* 2.9 42.6 + - + +
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Residues in contact with VAL 775 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717B TYR* 3.6 28.9 - - + +
720B LEU* 3.6 40.4 - - + -
721B LYS* 4.6 11.7 - - + +
724B ILE* 4.3 14.1 - - + -
738B LEU* 4.4 7.2 - - + -
771B SER 2.9 17.9 + - - +
772B PHE* 2.9 14.5 + - + +
774B ALA* 1.3 75.4 - - + +
776B CYS* 1.3 57.8 + - - +
778B GLN* 3.5 8.6 + - - +
779B CYS* 2.9 30.9 + - - +
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Residues in contact with CYS 776 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738B LEU* 3.6 25.6 - - - -
772B PHE* 2.7 42.0 + - - +
773B LEU* 3.7 3.6 - - - +
775B VAL* 1.3 73.8 - - - +
777B GLN* 1.3 62.7 - - - +
779B CYS* 3.0 17.6 + - - +
780B LEU* 3.2 11.3 + - - +
791B ALA* 3.5 11.2 - - + +
794B LEU* 4.2 17.0 - - - -
795B LEU* 3.6 26.2 - - + -
798B LEU* 4.8 2.9 - - + -
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Residues in contact with GLN 777 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773B LEU 2.8 20.3 + - - +
774B ALA* 3.9 7.0 - - - +
776B CYS* 1.3 72.0 - - - +
778B GLN* 1.3 62.0 + - + +
780B LEU* 3.1 26.9 + - + +
781B SER* 4.3 1.6 + - - -
795B LEU* 4.1 2.3 - - - +
822B ASP* 4.8 5.8 + - - +
824B GLY 3.9 4.0 + - - -
825B LEU* 3.5 55.3 - - + +
828B GLU* 3.0 31.1 + - - +
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Residues in contact with GLN 778 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721B LYS* 4.5 16.0 + - - +
724B ILE* 3.4 50.3 - - + +
774B ALA* 2.9 32.9 + - + +
775B VAL* 4.3 2.1 - - - +
777B GLN* 1.3 71.9 - - + +
779B CYS* 1.3 61.6 + - - +
781B SER* 3.3 20.9 + - - -
782B ASN 4.3 1.4 + - - -
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Residues in contact with CYS 779 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720B LEU* 4.7 4.0 - - - -
724B ILE* 4.6 13.2 - - - -
734B VAL* 4.3 10.1 - - - -
738B LEU* 4.3 13.2 - - + -
775B VAL* 2.9 32.5 + - - +
776B CYS* 3.0 8.9 + - - +
778B GLN* 1.3 72.9 - - - +
780B LEU* 1.3 61.6 + - - +
781B SER 3.1 2.7 - - - -
782B ASN* 3.1 26.5 + - - +
787B VAL* 3.9 25.7 - - + +
788B LYS* 4.1 2.1 - - - -
791B ALA* 3.7 15.7 - - + -
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Residues in contact with LEU 780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776B CYS 3.2 6.6 + - - +
777B GLN* 3.1 23.4 + - + +
779B CYS* 1.3 75.1 - - - +
781B SER* 1.3 58.0 + - - +
782B ASN 3.4 0.2 - - - -
788B LYS* 3.0 47.1 - - - +
791B ALA* 4.1 1.6 - - + -
792B PHE* 3.9 26.2 - - + +
795B LEU* 3.6 20.4 - - + -
825B LEU* 4.8 1.1 - - + -
828B GLU* 4.2 36.6 - - + +
829B LEU* 4.6 7.0 - - + -
832B PHE* 4.6 17.8 - - + -
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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