Contacts of the helix formed by residues 780 - 798 (chain C) in PDB entry 1XD2
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762C GLU* 3.5 51.0 + - + +
763C TRP* 3.8 16.7 - - - +
764C HIS* 3.6 13.9 - - + +
779C LEU* 1.3 73.0 - - - +
781C PRO* 1.3 82.3 - - + +
782C ILE* 3.1 30.3 + - + +
783C GLU* 3.1 5.7 + - + +
784C ILE* 3.0 22.1 + - - +
1038C PRO* 3.6 24.8 + - + +
1039C GLY 3.1 27.3 + - - -
1041C ARG 5.5 1.4 + - - -
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Residues in contact with PRO 781 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779C LEU 3.4 5.3 - - - +
780C HIS* 1.3 93.2 - - - +
782C ILE* 1.3 63.1 + - - +
784C ILE* 3.2 13.5 + - + +
785C ALA* 3.2 22.5 + - - +
854C ARG* 4.0 23.6 - - + +
857C GLU* 4.0 15.7 - - + +
858C ILE* 4.1 20.2 - - + +
861C VAL* 5.1 2.0 - - - -
1038C PRO* 3.5 20.4 - - + -
1039C GLY 3.7 15.0 - - - +
1040C VAL* 4.2 9.2 - - + -
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Residues in contact with ILE 782 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762C GLU* 4.2 8.3 - - + +
780C HIS* 3.1 28.0 + - + +
781C PRO* 1.3 77.7 - - - +
783C GLU* 1.3 58.4 + - - +
785C ALA* 3.3 3.8 + - - +
786C ARG* 3.0 61.5 + - + +
861C VAL* 4.2 16.7 - - + +
1040C VAL* 3.5 43.3 - - + +
1041C ARG 3.7 3.8 - - - +
1042C PRO* 3.6 25.6 - - + -
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Residues in contact with GLU 783 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761C VAL* 3.3 22.6 - - + +
762C GLU* 2.8 46.0 + - - +
779C LEU* 6.1 0.9 - - + -
780C HIS* 3.1 11.1 + - + +
782C ILE* 1.3 76.7 - - - +
784C ILE* 1.3 61.1 + - + +
786C ARG* 3.0 31.7 + - - +
787C GLN* 2.8 61.2 + - + +
982C ARG 4.4 1.0 - - - +
987C ILE* 3.7 22.7 - - + -
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Residues in contact with ILE 784 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775C ASP 4.6 0.2 - - - +
776C LEU* 3.6 33.2 - - + +
779C LEU* 3.8 28.5 - - + +
780C HIS 3.0 17.6 + - - +
781C PRO* 3.2 9.8 + - + +
783C GLU* 1.3 72.7 - - - +
785C ALA* 1.3 66.3 + - - +
788C LEU* 3.1 40.8 + - + +
834C TRP* 5.4 3.1 - - + -
835C PHE* 5.7 0.4 - - + -
858C ILE* 3.8 28.0 - - + -
987C ILE* 5.3 0.7 - - - -
991C PHE* 3.5 34.4 - - + -
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Residues in contact with ALA 785 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781C PRO 3.2 6.8 + - - +
782C ILE 3.6 2.7 - - - +
784C ILE* 1.3 80.6 - - - +
786C ARG* 1.3 53.0 + - - +
789C THR* 2.6 39.1 + - - -
858C ILE* 3.9 10.5 - - + +
861C VAL* 3.3 38.6 - - + -
862C PHE* 3.5 24.1 - - + -
865C LEU* 4.2 1.3 - - + -
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Residues in contact with ARG 786 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759C PRO* 3.5 29.9 + - - +
760C THR 2.8 27.3 + - - -
761C VAL* 4.1 0.8 - - - +
762C GLU* 3.6 9.9 + - - +
782C ILE* 3.0 37.0 + - + +
783C GLU* 3.0 34.6 + - - +
784C ILE 3.3 0.2 - - - -
785C ALA* 1.3 76.7 - - - +
787C GLN* 1.3 61.2 + - - +
789C THR* 3.1 4.0 + - - -
790C LEU* 2.9 31.8 + - - +
861C VAL* 5.3 1.1 - - + -
865C LEU* 4.0 16.3 - - + +
981C LEU* 3.7 33.4 - - + +
1042C PRO* 4.3 18.4 - - - +
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Residues in contact with GLN 787 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761C VAL* 4.9 0.2 - - - +
783C GLU* 2.8 45.4 + - - +
784C ILE 4.4 1.1 - - - +
786C ARG* 1.3 75.4 - - - +
788C LEU* 1.3 58.0 + - - +
790C LEU* 3.3 12.2 + - - +
791C LEU* 2.9 28.3 + - - +
982C ARG 3.0 22.8 + - - -
983C VAL* 3.6 9.9 - - - +
984C GLU* 3.0 33.1 + - - +
987C ILE* 3.4 38.4 - - + -
988C LYS* 4.7 9.1 + - - +
991C PHE* 4.8 4.7 - - + -
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Residues in contact with LEU 788 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784C ILE* 3.1 40.6 + - + +
785C ALA 4.0 1.8 - - - +
787C GLN* 1.3 74.2 - - - +
789C THR* 1.3 56.4 + - - +
791C LEU* 3.5 5.1 - - + +
792C GLU* 2.7 45.8 + - - +
827C HIS* 3.8 19.5 - - + -
831C LEU* 3.5 40.4 - - + -
834C TRP* 5.6 0.2 - - + -
835C PHE* 4.9 4.9 - - + -
862C PHE* 4.2 15.0 - - + -
867C ASN* 4.4 0.2 - - - -
991C PHE* 3.7 35.2 - - + -
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Residues in contact with THR 789 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785C ALA 2.6 25.3 + - - -
786C ARG 3.4 4.9 - - - -
788C LEU* 1.3 76.7 - - - +
790C LEU* 1.3 55.1 + - - +
792C GLU* 4.0 0.3 - - - +
793C SER* 2.8 31.9 + - - -
862C PHE* 3.5 8.1 - - - -
865C LEU* 3.6 15.6 - - + +
867C ASN* 2.9 32.5 + - + +
927C VAL* 4.2 0.7 - - + +
979C TYR* 3.5 43.1 - - + +
981C LEU* 4.7 2.0 - - + -
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Residues in contact with LEU 790 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786C ARG 2.9 14.2 + - - +
787C GLN* 3.6 17.0 - - - +
789C THR* 1.3 74.8 - - - +
791C LEU* 1.3 66.9 + - - +
793C SER* 3.2 5.6 + - - -
794C ASP* 3.0 35.6 + - - +
979C TYR* 4.1 20.9 - - + +
981C LEU* 3.8 36.3 - - + +
982C ARG 3.8 6.3 - - - +
983C VAL* 3.4 43.5 - - + -
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Residues in contact with LEU 791 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787C GLN 2.9 17.5 + - - +
788C LEU* 3.5 7.6 - - + +
790C LEU* 1.3 76.9 - - - +
792C GLU* 1.3 62.7 + - - +
794C ASP* 3.3 8.7 + - + +
795C LEU* 3.2 30.4 + - + +
827C HIS* 3.6 31.4 - - + +
988C LYS* 3.9 29.4 - - + +
991C PHE* 3.9 32.5 - - + +
992C GLU* 3.8 24.7 - - + +
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Residues in contact with GLU 792 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788C LEU* 2.7 28.3 + - - +
789C THR 4.0 2.5 - - - +
791C LEU* 1.3 70.6 - - - +
793C SER* 1.3 65.6 + - - +
795C LEU* 3.3 9.5 + - + +
796C TYR* 3.0 22.9 + - - +
824C MET* 5.3 1.2 - - - +
827C HIS* 2.9 35.2 + - + +
831C LEU* 3.5 7.1 - - - +
862C PHE* 4.6 0.7 - - - -
867C ASN* 2.7 32.4 + - - +
869C ASN* 3.4 28.0 + - - +
870C GLY* 3.5 6.1 + - - -
873C GLU* 3.2 13.5 - - - +
927C VAL* 3.9 11.0 - - + +
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Residues in contact with SER 793 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789C THR 2.8 22.7 + - - -
790C LEU* 3.2 6.9 + - - -
792C GLU* 1.3 72.9 - - - +
794C ASP* 1.3 59.6 + - - +
796C TYR* 3.2 5.6 + - - +
797C ARG* 2.9 46.3 + - - +
926C CYS 5.0 1.6 + - - -
927C VAL* 3.8 11.9 - - - +
977C GLN 5.0 2.9 + - - -
978C PRO* 5.7 0.3 - - - +
979C TYR* 3.5 33.5 + - - -
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Residues in contact with ASP 794 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790C LEU* 3.0 24.6 + - - +
791C LEU* 3.5 8.9 - - + +
793C SER* 1.3 74.8 - - - +
795C LEU* 1.3 67.0 + - + +
797C ARG* 3.1 17.8 + - - +
798C ALA* 3.0 24.7 + - - +
988C LYS* 4.3 16.7 + - - +
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Residues in contact with LEU 795 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791C LEU* 3.2 21.3 + - + +
792C GLU* 3.7 9.6 - - + +
794C ASP* 1.3 78.1 - - + +
796C TYR* 1.3 61.6 + - - +
798C ALA* 3.5 11.3 + - + +
799C VAL* 3.4 18.4 + - - +
820C ASN 4.7 2.3 - - - +
823C LYS* 4.1 37.7 - - + +
824C MET* 3.5 29.8 - - + +
827C HIS* 3.5 44.6 - - + +
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Residues in contact with TYR 796 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792C GLU 3.0 13.6 + - - +
793C SER* 3.4 10.8 - - - +
795C LEU* 1.3 72.9 - - - +
797C ARG* 1.3 62.9 + - + +
798C ALA 3.1 6.0 + - - -
799C VAL* 3.2 13.8 + - - +
824C MET* 4.3 7.6 - - + +
926C CYS 5.1 3.4 - - - -
927C VAL* 4.3 9.6 - - + -
928C PRO* 3.3 45.7 - - + +
930C PHE* 3.5 36.8 - + - -
933C TYR* 4.2 5.4 - + - -
971C ILE* 2.8 32.7 + - + +
974C TYR* 3.4 26.5 - - + +
975C GLN* 2.9 41.4 + - + -
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Residues in contact with ARG 797 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLN 5.8 0.2 + - - -
750C HIS* 4.5 20.4 + - - -
752C ILE* 5.1 5.7 - - - +
793C SER* 2.9 38.4 + - - +
794C ASP* 3.1 16.1 + - - +
796C TYR* 1.3 78.3 - - + +
798C ALA* 1.3 58.4 + - - +
799C VAL 3.5 0.4 - - - -
800C GLN* 4.1 7.1 + - - -
974C TYR 5.2 0.7 - - - +
975C GLN* 2.5 60.1 + - + +
976C ASN 3.3 10.1 + - - -
977C GLN 3.2 23.7 + - - +
978C PRO* 4.1 18.1 - - - +
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Residues in contact with ALA 798 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794C ASP 3.0 14.6 + - - +
795C LEU* 3.9 9.0 - - + +
796C TYR 3.1 1.0 - - - -
797C ARG* 1.3 77.7 - - - +
799C VAL* 1.3 63.6 + - - +
800C GLN* 3.2 14.6 + - - +
820C ASN* 3.3 33.6 + - + +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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