Contacts of the helix formed by residues 780 - 799 (chain A) in PDB entry 3KSY
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 HIS 780 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762A GLU* 3.6 31.1 + - + +
763A TRP 3.5 27.4 - - - +
764A HIS* 3.3 10.7 - - - +
778A THR 4.4 0.2 - - - -
779A LEU* 1.3 72.6 - - - +
781A PRO* 1.3 79.4 - - + +
782A ILE* 3.1 40.7 - - + +
783A GLU* 3.0 14.9 + - + +
784A ILE* 3.0 11.9 + - - +
1038A PRO* 3.2 32.7 - - + +
1039A GLY* 4.6 0.2 - - - -
1040A VAL 3.9 13.2 - - - -
1041A ARG 4.6 6.0 + - - -
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Residues in contact with PRO 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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779A LEU 3.6 6.2 - - - +
780A HIS* 1.3 96.7 - - + +
782A ILE* 1.3 62.8 + - - +
784A ILE* 3.1 15.2 + - + +
785A ALA* 3.3 10.3 + - - +
854A ARG* 3.6 30.3 - - + +
857A GLU* 4.1 6.7 - - + +
858A ILE* 4.1 21.2 - - + +
861A VAL* 5.1 2.0 - - + -
1037A SER* 4.2 0.4 - - - +
1038A PRO* 3.5 26.7 - - + -
1040A VAL* 3.9 24.9 - - + +
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Residues in contact with ILE 782 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A GLU* 3.4 24.0 - - + -
780A HIS* 3.1 29.6 - - + +
781A PRO* 1.3 78.6 - - - +
783A GLU* 1.3 57.8 + - - +
785A ALA* 3.4 2.3 + - - +
786A ARG* 3.0 44.9 + - - +
861A VAL* 3.3 37.9 - - + +
864A GLU* 4.7 4.0 - - - +
1040A VAL* 3.5 21.8 - - + +
1041A ARG 4.0 2.2 - - - +
1042A PRO* 3.8 32.5 - - + -
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Residues in contact with GLU 783 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761A VAL* 3.7 17.0 - - - +
762A GLU* 3.2 44.6 + - + +
763A TRP* 6.1 1.1 - - + -
764A HIS* 5.8 0.4 - - + -
779A LEU* 6.0 0.2 - - + -
780A HIS* 3.0 14.0 + - + +
782A ILE* 1.3 79.1 - - - +
784A ILE* 1.3 64.7 + - + +
786A ARG* 3.4 21.7 + - - +
787A GLN* 3.0 57.8 + - - +
984A GLU* 4.2 1.7 - - - +
987A ILE* 3.5 25.7 - - + +
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Residues in contact with ILE 784 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776A LEU* 3.7 28.3 - - + +
779A LEU* 3.5 49.4 - - + +
780A HIS 3.0 11.4 + - - +
781A PRO* 3.4 8.3 - - + +
783A GLU* 1.3 77.8 - - + +
785A ALA* 1.3 56.6 + - - +
787A GLN* 3.5 2.2 + - - +
788A LEU* 3.0 41.7 + - + +
834A TRP* 5.5 1.1 - - + -
858A ILE* 3.8 27.4 - - + -
987A ILE* 5.1 1.8 - - + -
991A PHE* 3.4 25.3 - - + -
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Residues in contact with ALA 785 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781A PRO 3.3 6.1 + - - +
782A ILE 3.8 1.6 - - - +
784A ILE* 1.3 75.9 - - - +
786A ARG* 1.3 55.7 + - - +
788A LEU 3.2 0.2 + - - -
789A THR* 2.7 42.5 + - - -
858A ILE* 4.0 13.9 - - + +
861A VAL* 3.6 36.1 - - + -
862A PHE* 3.5 26.0 - - + -
865A LEU* 4.3 1.1 - - + -
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Residues in contact with ARG 786 (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 PRO* 3.9 25.7 + - - +
760A THR 3.1 27.5 + - - -
761A VAL* 3.7 5.4 - - - +
762A GLU* 4.1 19.2 + - - +
782A ILE* 3.0 29.5 + - - +
783A GLU* 3.6 30.1 + - - +
785A ALA* 1.3 77.0 - - - +
787A GLN* 1.3 60.1 + - + +
789A THR* 3.4 2.1 - - - -
790A LEU* 2.9 35.2 + - + +
861A VAL* 5.2 1.9 - - + +
865A LEU* 4.0 13.4 - - + +
981A LEU* 3.8 37.6 - - + +
1042A PRO* 4.5 17.8 - - - +
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Residues in contact with GLN 787 (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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783A GLU* 3.0 39.5 + - - +
784A ILE 3.9 2.5 - - - +
786A ARG* 1.3 77.1 - - - +
788A LEU* 1.3 59.2 + - - +
790A LEU* 3.7 16.6 - - - +
791A LEU* 3.0 29.6 + - - +
982A ARG 3.4 12.1 + - - -
983A VAL* 4.0 1.7 - - - +
984A GLU* 3.0 42.4 + - - +
987A ILE* 3.5 30.5 - - + -
988A LYS* 4.3 16.2 - - - +
991A PHE* 4.9 3.8 - - + -
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Residues in contact with LEU 788 (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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784A ILE* 3.0 34.9 + - + +
785A ALA 3.7 2.7 - - - +
787A GLN* 1.3 73.5 - - - +
789A THR* 1.3 60.9 + - - +
791A LEU* 4.1 3.1 - - + -
792A GLU* 2.8 41.0 + - - +
827A HIS* 4.3 15.5 - - + -
831A LEU* 3.8 31.2 - - + -
834A TRP* 5.9 0.2 - - + -
835A PHE* 4.8 6.1 - - + -
858A ILE* 5.2 0.4 - - + -
862A PHE* 3.6 27.6 - - + -
867A ASN* 4.3 0.7 - - - -
991A PHE* 3.4 41.5 - - + -
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Residues in contact with THR 789 (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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785A ALA 2.7 26.6 + - - -
786A ARG 3.4 4.9 - - - -
788A LEU* 1.3 70.7 - - - +
790A LEU* 1.3 59.9 + - - +
792A GLU 3.8 0.7 - - - -
793A SER* 2.9 32.2 + - - -
862A PHE* 3.4 8.7 - - - -
865A LEU* 3.6 16.3 - - + +
867A ASN* 3.0 29.9 + - + +
927A VAL* 4.1 1.2 - - - +
979A TYR* 3.3 46.9 - - + +
981A LEU* 5.2 1.8 - - + -
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Residues in contact with LEU 790 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786A ARG* 2.9 18.3 + - + +
787A GLN* 3.7 20.4 - - - +
789A THR* 1.3 75.1 - - - +
791A LEU* 1.3 64.7 + - - +
793A SER* 3.1 4.9 + - - -
794A ASP* 3.0 35.6 + - - +
978A PRO* 6.4 0.2 - - + -
979A TYR* 3.9 32.1 - - + +
981A LEU* 3.9 33.7 - - + +
982A ARG 4.3 1.6 - - - +
983A VAL* 3.6 35.4 - - + +
988A LYS* 6.1 3.6 - - + -
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Residues in contact with LEU 791 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787A GLN 3.0 17.0 + - - +
788A LEU* 3.5 6.5 - - + +
790A LEU* 1.3 80.5 - - - +
792A GLU* 1.3 60.7 + - - +
794A ASP* 3.5 7.4 + - - +
795A LEU* 3.3 41.4 + - + +
827A HIS* 3.3 33.9 - - + +
988A LYS* 4.0 18.4 - - + +
991A PHE* 3.9 27.1 - - + -
992A GLU* 3.8 33.4 - - + +
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Residues in contact with GLU 792 (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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788A LEU* 2.8 29.4 + - - +
789A THR 4.1 2.2 - - - +
791A LEU* 1.3 72.3 - - - +
793A SER* 1.3 58.2 + - - +
795A LEU* 3.6 11.2 + - + +
796A TYR* 3.1 26.7 + - - +
824A MET* 5.1 2.2 - - + +
827A HIS* 3.3 29.1 + - + +
831A LEU* 3.5 7.6 - - - +
862A PHE* 4.8 0.2 - - - -
867A ASN* 3.5 10.4 - - - +
869A ASN* 2.9 26.0 + - - +
870A GLY* 3.2 19.5 + - - -
873A GLU* 2.7 29.4 - - - +
927A VAL* 3.8 10.1 - - + +
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Residues in contact with SER 793 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789A THR 2.9 20.2 + - - -
790A LEU* 3.1 6.0 + - - -
792A GLU* 1.3 76.2 - - - +
794A ASP* 1.3 62.7 + - - +
796A TYR* 3.3 6.8 + - - +
797A ARG* 2.9 29.6 + - - +
926A CYS 5.1 2.1 + - - -
927A VAL* 3.9 8.4 - - - +
977A GLN 5.3 1.0 + - - -
978A PRO* 5.0 5.5 - - - +
979A TYR* 3.3 34.4 + - - -
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Residues in contact with ASP 794 (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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790A LEU* 3.0 23.3 + - - +
791A LEU* 3.8 5.2 - - - +
793A SER* 1.3 78.2 - - - +
795A LEU* 1.3 60.4 + - + +
797A ARG* 3.3 27.4 + - - +
798A ALA* 2.8 31.0 + - - +
978A PRO* 6.0 1.9 - - - +
983A VAL* 6.0 1.6 - - - +
988A LYS* 4.8 14.2 - - - -
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Residues in contact with LEU 795 (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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791A LEU* 3.3 36.3 + - + +
792A GLU* 3.7 11.4 - - - +
793A SER 3.3 0.4 - - - -
794A ASP* 1.3 78.3 - - + +
796A TYR* 1.3 62.6 + - - +
798A ALA* 3.3 9.2 + - + +
799A VAL* 3.3 26.3 + - - +
820A ASN* 4.8 3.8 - - - +
823A LYS* 3.9 39.3 - - + +
824A MET* 4.1 24.1 - - + +
827A HIS* 3.9 25.8 - - + +
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Residues in contact with TYR 796 (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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792A GLU 3.1 15.8 + - - +
793A SER* 3.6 6.1 - - - +
794A ASP 3.2 0.2 - - - -
795A LEU* 1.3 75.9 - - - +
797A ARG* 1.3 67.7 + - + +
799A VAL* 3.3 11.6 + - - +
824A MET* 4.0 11.6 - - - -
926A CYS 4.9 2.2 - - - -
927A VAL* 4.3 7.9 - - + -
928A PRO* 3.3 52.8 - - + +
930A PHE* 3.4 39.0 - + - -
933A TYR* 3.9 6.3 + + - -
971A ILE* 2.8 45.8 + - + +
974A TYR* 4.0 13.5 - - + -
975A GLN* 3.0 30.6 + - + -
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Residues in contact with ARG 797 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793A SER* 2.9 16.8 + - - +
794A ASP* 3.7 26.2 + - - +
796A TYR* 1.3 77.3 - - + +
798A ALA* 1.3 64.7 + - - +
799A VAL 3.2 2.4 + - - +
800A GLN* 5.5 1.6 + - - -
975A GLN* 3.5 52.2 + - + +
976A ASN 5.2 0.7 - - - -
978A PRO* 5.2 17.4 - - - +
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Residues in contact with ALA 798 (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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794A ASP 2.8 18.4 + - - +
795A LEU* 3.6 10.3 - - + +
796A TYR 3.2 0.2 - - - -
797A ARG* 1.3 81.0 - - - +
799A VAL* 1.3 59.4 + - - +
800A GLN* 3.1 14.5 + - - +
820A ASN* 2.7 37.7 + - + +
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Residues in contact with VAL 799 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795A LEU 3.3 16.4 - - - +
796A TYR 3.5 10.8 - - - +
797A ARG 3.2 2.9 - - - +
798A ALA* 1.3 74.8 - - - +
800A GLN* 1.3 64.1 + - - +
801A PRO* 3.8 5.0 - - + +
803A GLU* 4.8 3.8 - - - +
804A LEU* 3.7 29.4 - - + -
820A ASN* 3.9 9.6 - - - +
821A LEU* 4.1 18.2 - - + +
824A MET* 4.0 24.5 - - + -
930A PHE* 3.7 17.9 - - + -
971A ILE* 5.2 2.4 - - + +
975A GLN* 3.3 20.3 + - - +
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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