Contacts of the helix formed by residues 786 - 807 (chain C) in PDB entry 3LZB
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 GLY 786 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784C ASN 4.1 1.6 + - - -
785C ILE* 1.3 78.9 - - - +
787C SER* 1.3 66.9 + - - -
788C GLN* 3.1 4.3 - - - -
789C TYR* 3.2 14.8 + - - +
790C LEU* 3.1 22.3 + - - +
957C ILE* 4.0 1.1 - - - -
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Residues in contact with SER 787 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786C GLY* 1.3 73.1 - - - +
788C GLN* 1.3 62.2 + - - +
790C LEU 3.6 0.2 + - - -
791C LEU* 3.2 30.0 + - - +
951C PRO* 3.6 31.6 + - - +
952C GLN* 3.1 25.1 + - - -
955C LEU* 3.8 16.8 - - - +
957C ILE* 3.5 25.7 - - - +
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Residues in contact with GLN 788 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786C GLY* 3.1 0.8 - - - -
787C SER* 1.3 80.9 + - - +
789C TYR* 1.3 68.2 + - + +
791C LEU* 3.7 0.5 + - - -
792C ASN* 3.1 66.2 + - - +
948C ALA* 2.8 30.5 + - - +
949C ARG 5.7 0.2 - - - -
951C PRO* 3.8 18.9 - - + +
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Residues in contact with TYR 789 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777C TYR* 5.6 1.6 - + - -
785C ILE* 3.9 15.0 - - + -
786C GLY* 3.2 16.4 + - - +
788C GLN* 1.3 87.3 - - + +
790C LEU* 1.3 67.2 + - - +
792C ASN* 3.2 7.4 + - - +
793C TRP* 3.0 43.0 + + + +
824C PRO* 3.2 37.4 - - + +
825C GLN* 2.7 31.1 + - + +
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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
----------------------------------------------------------
778C VAL* 5.2 1.6 - - + -
785C ILE* 3.8 10.3 - - + +
786C GLY 3.1 14.5 + - - +
789C TYR* 1.3 80.7 - - - +
791C LEU* 1.3 63.6 + - - +
793C TRP* 3.4 29.2 + - + +
794C CYS* 3.3 24.1 + - - -
883C LEU* 3.8 31.2 - - + +
884C MET* 4.6 5.4 - - - +
886C PHE* 3.9 27.6 - - + -
914C ILE* 4.2 7.4 - - + -
955C LEU* 3.6 20.9 - - + -
957C ILE* 4.0 19.3 - - + -
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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 SER 3.2 10.6 + - - +
788C GLN 4.3 1.3 - - - +
790C LEU* 1.3 73.1 - - - +
792C ASN* 1.3 61.9 + - - +
794C CYS* 3.0 19.2 + - - +
795C VAL* 3.1 18.0 + - - +
884C MET* 4.1 11.7 - - + -
919C VAL* 4.8 4.5 - - + -
944C PHE* 3.7 30.1 - - + +
947C MET* 4.3 23.6 - - + +
948C ALA* 4.1 15.7 - - + +
951C PRO* 3.2 40.2 - - + +
954C TYR* 4.7 2.9 - - + -
955C LEU* 3.7 22.2 - - + -
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Residues in contact with ASN 792 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788C GLN* 3.1 54.1 + - - +
789C TYR* 3.2 8.2 + - - +
791C LEU* 1.3 73.8 - - - +
793C TRP* 1.3 61.8 + - + +
795C VAL* 3.2 6.9 + - - +
796C GLN* 2.8 45.1 + - - +
825C GLN* 6.2 2.9 - - - +
948C ALA* 3.4 13.3 - - - +
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Residues in contact with TRP 793 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774C LEU* 3.9 27.1 - - + -
777C TYR* 3.8 33.0 - + - -
778C VAL* 3.7 17.9 - - + -
785C ILE* 3.9 19.7 - - + -
789C TYR* 3.0 28.6 + + + +
790C LEU* 3.5 37.7 - - + +
792C ASN* 1.3 78.3 - - + +
794C CYS* 1.3 57.8 + - - +
796C GLN* 3.7 13.2 - - - +
797C ILE* 2.8 37.8 + - - +
821C VAL* 6.0 0.4 - - + -
824C PRO* 3.0 29.8 + - + -
825C GLN* 4.6 1.0 - - - +
827C VAL* 3.9 25.0 - - + +
883C LEU* 4.0 14.1 - - + -
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Residues in contact with CYS 794 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790C LEU 3.3 10.1 + - - -
791C LEU* 3.0 13.2 + - - +
793C TRP* 1.3 80.9 - - - +
795C VAL* 1.3 58.2 + - - +
797C ILE* 4.7 4.0 - - - -
798C ALA* 3.2 14.0 + - - +
876C TYR* 2.7 26.5 + - - +
880C VAL* 3.8 19.3 - - - -
883C LEU* 4.4 8.3 - - - -
884C MET* 3.4 33.4 - - - -
944C PHE* 3.5 27.8 - - + -
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Residues in contact with VAL 795 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791C LEU 3.1 14.2 + - - +
792C ASN* 3.5 9.0 - - - +
794C CYS* 1.3 71.3 - - - +
796C GLN* 1.3 63.6 + - + +
798C ALA* 3.3 5.8 + - - +
799C LYS* 2.8 63.1 + - + +
941C ILE* 4.5 4.7 - - + +
944C PHE* 3.5 37.5 - - + +
945C SER* 3.4 20.4 - - - +
948C ALA* 4.2 8.1 - - + -
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Residues in contact with GLN 796 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749C HIS* 3.3 43.5 + - + +
792C ASN* 2.8 34.0 + - - +
793C TRP* 3.7 7.2 - - - +
795C VAL* 1.3 78.0 - - + +
797C ILE* 1.3 63.2 + - - +
799C LYS* 3.4 7.1 + - + +
800C GLY* 3.0 18.9 + - - -
825C GLN* 2.9 28.2 + - - +
826C HIS* 3.3 1.4 - - - -
827C VAL* 2.7 42.6 + - + -
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Residues in contact with ILE 797 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774C LEU* 4.1 14.4 - - + -
793C TRP 2.8 28.8 + - - +
794C CYS* 3.9 5.2 - - - +
795C VAL 3.2 0.2 - - - -
796C GLN* 1.3 77.1 - - - +
798C ALA* 1.3 57.6 + - - +
801C MET* 3.0 27.6 + - + +
814C LEU* 4.1 22.4 - - + -
819C VAL* 3.9 34.1 - - + -
827C VAL* 4.3 5.2 - - + -
829C ILE* 3.2 14.4 - - + +
876C TYR* 3.7 23.3 - - + -
879C THR* 4.2 11.4 - - + -
880C VAL* 6.2 0.9 - - + -
883C LEU* 4.1 14.1 - - + -
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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
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794C CYS 3.2 16.5 + - - +
795C VAL* 3.7 4.5 - - - +
796C GLN 3.2 0.2 - - - -
797C ILE* 1.3 75.4 - - - +
799C LYS* 1.3 60.6 + - - +
800C GLY 3.2 0.2 - - - -
801C MET* 3.7 5.4 - - - +
802C ASN* 2.7 32.6 + - - +
876C TYR* 3.8 19.5 - - + +
937C PHE* 4.0 6.7 - - + +
940C LEU* 4.3 8.1 - - + -
941C ILE* 3.8 28.4 - - + +
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Residues in contact with LYS 799 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747C ASN* 4.4 6.9 + - - +
749C HIS* 4.0 23.6 + - + +
795C VAL* 2.8 55.7 + - + +
796C GLN* 3.7 5.4 - - + +
798C ALA* 1.3 72.7 - - - +
800C GLY* 1.3 59.5 + - - +
802C ASN* 3.4 1.7 + - - +
803C TYR* 2.9 28.2 + - - +
941C ILE* 3.8 29.8 - - + -
945C SER* 4.9 1.3 - - - -
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Residues in contact with GLY 800 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747C ASN* 4.0 6.3 - - - -
749C HIS* 3.8 6.0 - - - +
750C VAL* 3.5 21.2 - - - +
796C GLN 3.0 11.6 + - - -
798C ALA 3.2 0.2 - - - -
799C LYS* 1.3 77.4 - - - +
801C MET* 1.3 59.9 + - - +
803C TYR* 3.1 4.9 + - - +
804C LEU* 3.1 20.7 + - - +
829C ILE* 3.5 22.0 - - - -
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Residues in contact with MET 801 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797C ILE* 3.0 25.1 + - + +
798C ALA 3.7 0.7 - - - +
800C GLY* 1.3 75.5 - - - +
802C ASN* 1.3 58.3 + - - +
804C LEU* 3.4 19.7 + - + +
805C GLU* 2.8 28.1 + - - +
809C LEU 5.8 0.7 - - - +
811C HIS* 4.0 17.5 - - + +
814C LEU* 3.7 24.2 - - + -
829C ILE* 4.0 12.8 - - + -
872C ASP* 3.7 39.7 - - + +
876C TYR* 4.6 0.2 - - + -
937C PHE* 3.4 40.0 - - + -
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Residues in contact with ASN 802 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798C ALA 2.7 21.5 + - - +
799C LYS 3.7 4.0 - - - +
801C MET* 1.3 71.6 - - - +
803C TYR* 1.3 58.5 + - - +
805C GLU* 4.2 11.3 + - - +
806C ASP* 2.9 52.5 + - - +
936C LYS* 6.0 1.2 - - - +
937C PHE* 3.9 11.6 - - + +
938C ARG* 4.1 23.6 - - - +
941C ILE* 3.5 24.2 - - + +
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Residues in contact with TYR 803 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744C SER 3.9 0.7 + - - -
745C VAL* 3.9 15.5 - - + -
746C ASP* 2.9 40.3 + - - +
747C ASN* 3.6 35.0 - - + +
750C VAL* 4.1 10.1 - - + -
799C LYS 2.9 14.2 + - - +
800C GLY 3.1 7.6 + - - +
802C ASN* 1.3 74.8 - - - +
804C LEU* 1.3 56.1 + - + +
806C ASP* 2.9 13.3 + - + +
807C ARG* 2.6 83.2 + - + +
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Residues in contact with LEU 804 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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745C VAL* 4.3 5.2 - - + -
750C VAL* 4.2 14.4 - - + -
800C GLY 3.1 13.6 + - - +
801C MET* 3.6 29.4 - - + +
803C TYR* 1.3 78.8 - - + +
805C GLU* 1.3 66.0 + - - +
807C ARG* 3.1 4.8 + - - -
808C ARG 2.9 4.9 + - - -
809C LEU* 2.8 59.4 + - + +
811C HIS* 4.4 4.0 - - + +
829C ILE* 4.4 10.1 - - + -
832C PHE* 3.7 46.9 - - + -
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Residues in contact with GLU 805 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801C MET 2.8 20.8 + - - +
802C ASN* 3.7 12.1 + - - +
803C TYR 3.2 0.2 - - - -
804C LEU* 1.3 70.5 - - - +
806C ASP* 1.3 61.6 + - - +
808C ARG* 2.7 29.3 + - - +
809C LEU 4.1 0.6 + - - -
869C HIS* 3.6 49.5 + - + +
870C GLN* 5.0 2.3 - - - +
936C LYS* 3.0 37.4 + - - -
937C PHE* 3.8 22.6 - - + +
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Residues in contact with ASP 806 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802C ASN* 2.9 36.3 + - - +
803C TYR* 3.4 12.7 - - + +
805C GLU* 1.3 79.8 - - - +
807C ARG* 1.3 63.0 + - + +
808C ARG* 3.3 9.4 + - - +
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Residues in contact with ARG 807 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741C VAL* 4.6 7.3 + - - +
744C SER* 2.9 41.4 + - - -
745C VAL* 3.7 8.9 - - - +
803C TYR* 2.6 76.6 + - + +
804C LEU* 3.1 8.0 + - - +
806C ASP* 1.3 73.7 - - + +
808C ARG* 1.3 76.6 + - - +
809C LEU* 3.5 23.1 + - + +
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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