Contacts of the helix formed by residues 776 - 797 (chain A) in PDB entry 4BIC
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 ASN 776 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A LEU* 2.8 29.1 + - + +
775A ASP* 1.4 78.5 - - - +
777A GLU* 1.3 60.4 + - - +
778A GLN* 3.1 18.3 + - - +
779A THR* 3.0 43.3 + - - +
780A ILE* 3.2 18.2 + - - +
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Residues in contact with GLU 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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774A LYS 3.7 16.8 - - - +
775A ASP 3.8 2.0 + - - -
776A ASN* 1.3 73.0 - - - +
778A GLN* 1.3 58.8 + - - +
779A THR 3.5 0.2 - - - -
780A ILE* 3.9 7.0 - - + -
781A GLY* 3.0 25.3 + - - -
906A SER 4.8 0.9 - - - +
907A MET* 3.5 22.9 - - + +
908A SER* 2.9 51.4 + - - -
911A ALA* 3.5 12.1 - - - +
937A PHE* 3.7 19.6 - - + -
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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
----------------------------------------------------------
776A ASN* 3.1 10.1 - - - +
777A GLU* 1.3 73.9 - - - +
779A THR* 1.4 55.4 + - - +
781A GLY* 3.4 1.6 + - - -
782A PHE* 2.8 37.3 + - - +
940A VAL 5.9 1.4 + - - -
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Residues in contact with THR 779 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770A TRP* 4.6 6.3 - - + -
773A LEU* 3.6 29.9 - - + +
776A ASN* 3.0 36.5 + - - -
778A GLN* 1.4 73.8 - - - +
780A ILE* 1.4 62.2 + - - +
782A PHE* 3.2 7.6 + - - +
783A TYR* 3.1 49.8 + - + -
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Residues in contact with ILE 780 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A LEU* 3.1 40.8 - - + +
774A LYS* 4.2 1.3 - - - +
776A ASN 3.2 14.6 + - - +
777A GLU* 4.1 6.3 - - - +
779A THR* 1.4 74.1 - - - +
781A GLY* 1.3 53.4 + - - +
783A TYR* 3.4 1.0 + - - -
784A THR* 2.7 49.9 + - - +
871A ILE* 3.7 23.8 - - + -
874A MET* 4.0 20.7 - - + +
875A ALA* 4.2 11.2 - - + +
907A MET* 3.9 25.1 - - + -
937A PHE* 4.2 13.7 - - + -
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Residues in contact with GLY 781 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777A GLU 3.0 18.5 + - - -
778A GLN* 3.8 0.9 - - - -
780A ILE* 1.3 75.4 - - - +
782A PHE* 1.4 56.3 + - - +
784A THR* 4.3 0.2 - - - -
785A LYS* 3.0 32.9 + - - +
937A PHE* 4.2 11.8 - - - -
938A LEU* 3.6 21.5 - - - +
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Residues in contact with PHE 782 (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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778A GLN 2.8 23.1 + - - +
779A THR* 3.2 7.4 + - - +
781A GLY* 1.4 72.5 - - - +
783A TYR* 1.3 86.9 + + - +
785A LYS* 4.1 3.2 + - - +
786A GLN* 3.3 34.6 + - - +
815A SER 4.9 2.5 - - - -
816A GLY* 3.3 36.6 - - - -
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Residues in contact with TYR 783 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A LEU* 5.3 2.5 - - + -
770A TRP* 3.6 28.7 - + - -
773A LEU* 5.5 0.2 - - + -
779A THR* 3.1 40.9 + - + +
780A ILE 4.2 1.3 - - - +
782A PHE* 1.3 104.5 - + - +
784A THR* 1.3 64.6 + - - +
785A LYS 3.4 0.4 - - - -
786A GLN* 3.4 11.8 + - - +
787A ILE* 3.2 27.8 + - - +
811A ILE* 3.7 33.5 - - + +
813A THR* 5.6 1.7 - - - -
816A GLY* 3.4 16.4 - - - -
818A LEU* 3.6 23.1 - - + +
874A MET* 4.5 13.7 - - + -
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Residues in contact with THR 784 (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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780A ILE* 2.7 36.1 + - - +
781A GLY* 4.0 2.9 - - - -
783A TYR* 1.3 73.7 - - - +
785A LYS* 1.3 65.6 + - - +
786A GLN 3.3 0.3 + - - -
787A ILE* 3.3 6.6 + - - +
788A LEU* 3.1 31.6 + - + +
867A LEU* 4.5 5.8 - - + -
871A ILE* 3.7 27.2 - - + +
874A MET* 3.2 21.3 - - - +
914A PHE* 3.9 17.3 - - + -
937A PHE* 5.2 1.3 - - + -
938A LEU* 4.2 6.3 - - + -
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Residues in contact with LYS 785 (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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781A GLY 3.0 18.5 + - - +
782A PHE* 4.3 4.9 - - - +
784A THR* 1.3 74.3 - - - +
786A GLN* 1.4 52.3 + - + +
788A LEU* 3.4 4.2 + - - +
789A GLU* 2.8 59.3 + - - +
933A LEU* 3.5 19.4 - - + +
938A LEU* 4.1 30.7 - - + +
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Residues in contact with GLN 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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735A LYS* 5.4 1.6 - - - +
736A ASN* 3.2 34.8 + - - +
782A PHE* 3.3 37.8 + - - +
783A TYR* 3.4 13.1 + - - +
784A THR 3.2 0.6 - - - -
785A LYS* 1.4 75.7 - - + +
787A ILE* 1.4 64.6 + - - +
789A GLU* 3.2 9.5 + - - +
790A GLY 3.0 18.9 + - - -
816A GLY 2.9 21.3 + - - -
817A VAL* 3.4 6.9 - - - +
818A LEU* 2.7 35.8 + - + -
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Residues in contact with ILE 787 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A LEU* 4.7 0.9 - - + -
783A TYR 3.2 17.7 + - - +
784A THR* 3.3 4.7 + - - +
786A GLN* 1.4 72.7 - - - +
788A LEU* 1.4 52.5 + - - +
790A GLY* 3.3 2.4 + - - -
791A LEU* 2.8 46.9 + - + +
804A ILE* 4.3 15.7 - - + -
809A VAL* 4.3 12.6 - - + -
818A LEU* 3.6 28.3 - - + -
820A ILE* 3.7 12.3 - - + +
867A LEU* 3.7 23.3 - - + -
870A THR* 4.0 25.8 - - + -
874A MET* 4.1 15.3 - - + -
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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 THR* 3.1 16.9 + - + +
785A LYS 3.4 8.3 - - - +
787A ILE* 1.4 76.7 - - - +
789A GLU* 1.3 52.6 + - - +
791A LEU* 3.6 5.5 - - + +
792A LYS* 2.7 36.2 + - - +
864A ILE* 4.5 4.0 - - + -
867A LEU* 3.7 24.7 - - + -
914A PHE* 3.8 19.3 - - + -
929A ALA* 3.8 34.9 - - + +
932A LEU* 3.8 17.3 - - + -
933A LEU* 3.7 10.8 - - + -
938A LEU* 3.7 29.2 - - + -
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Residues in contact with GLU 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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734A HIS* 3.7 17.0 + - + +
735A LYS* 3.0 25.3 + - - +
736A ASN* 3.5 14.4 - - - +
785A LYS* 2.8 52.2 + - - +
786A GLN* 3.2 10.2 + - - +
788A LEU* 1.3 71.5 - - - +
790A GLY* 1.3 60.4 + - - +
792A LYS* 3.6 9.0 + - + +
793A TYR 3.2 16.1 + - - -
933A LEU* 4.2 13.6 - - + +
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Residues in contact with GLY 790 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734A HIS* 4.3 1.3 - - - -
736A ASN* 4.0 8.4 - - - +
737A ILE* 3.6 16.1 - - - +
786A GLN 3.0 12.3 + - - -
787A ILE 3.6 2.7 - - - -
789A GLU* 1.3 75.2 - - - +
791A LEU* 1.4 57.9 + - - +
793A TYR* 3.3 5.0 + - - +
794A LEU* 3.1 30.5 + - - +
820A ILE* 3.7 19.3 - - - -
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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
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787A ILE* 2.8 41.0 + - + +
788A LEU* 3.7 5.4 - - - +
790A GLY* 1.4 68.3 - - - +
792A LYS* 1.3 61.7 + - - +
794A LEU* 3.3 9.8 + - + +
795A HIS* 2.9 44.5 + - + +
801A HIS* 4.3 5.6 - - + -
804A ILE* 3.8 26.0 - - + -
820A ILE* 3.8 1.3 - - + +
863A ASP* 3.8 47.6 - - + +
864A ILE* 4.5 8.7 - - + -
867A LEU* 4.4 13.9 - - + -
929A ALA* 4.9 3.8 - - + -
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Residues in contact with LYS 792 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788A LEU 2.7 22.0 + - - +
789A GLU* 3.7 8.3 - - + +
790A GLY 3.4 0.2 - - - -
791A LEU* 1.3 71.6 - - - +
793A TYR* 1.3 55.1 + - - +
795A HIS* 3.8 2.6 - - - -
796A ASP* 2.8 64.8 + - - +
929A ALA* 4.0 16.2 - - + +
930A ASN* 3.1 38.7 + - - +
933A LEU* 3.8 21.5 - - + -
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Residues in contact with TYR 793 (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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731A HIS 3.9 4.7 + - - -
732A LEU* 3.4 31.1 - - + +
733A LYS 2.9 37.2 + - - -
734A HIS* 3.5 37.9 - + + +
737A ILE* 3.6 19.3 - - + -
789A GLU 3.2 6.9 + - - +
790A GLY 3.3 8.7 - - - +
792A LYS* 1.3 81.1 - - - +
794A LEU* 1.3 63.8 + - + +
796A ASP* 3.4 5.8 + - + +
797A ASN* 2.8 52.2 + - - -
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Residues in contact with LEU 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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732A LEU* 4.0 27.1 - - + -
737A ILE* 4.2 5.6 - - + -
790A GLY 3.1 15.3 + - - +
791A LEU* 3.3 15.2 + - + +
793A TYR* 1.3 88.5 - - + +
795A HIS* 1.3 60.1 + - + +
797A ASN* 3.0 10.4 + - - +
798A GLN 3.2 0.2 + - - -
799A ILE* 2.8 55.5 + - + +
801A HIS* 4.3 27.8 - - + +
820A ILE* 4.7 7.4 - - + -
823A PHE* 3.9 26.2 - - + -
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Residues in contact with HIS 795 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791A LEU* 2.9 30.6 + - + +
792A LYS* 3.8 4.5 - - - +
794A LEU* 1.3 76.2 - - + +
796A ASP* 1.4 59.7 + - - +
798A GLN* 2.9 17.8 + - - -
799A ILE 3.2 19.1 - - - -
800A VAL* 4.5 0.2 - - - -
860A LYS* 3.1 79.8 + - + +
863A ASP* 2.7 33.6 + - + +
864A ILE* 4.2 13.4 - - + +
928A CYS* 6.3 0.2 - - - +
929A ALA* 4.4 12.3 + - + +
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Residues in contact with ASP 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 LYS* 2.8 53.7 + - - +
793A TYR* 3.7 7.3 - - + +
795A HIS* 1.4 76.4 - - - +
797A ASN* 1.3 61.7 + - - +
798A GLN* 3.1 17.8 + - - +
860A LYS* 4.9 3.4 + - - +
930A ASN* 4.3 7.4 - - - +
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Residues in contact with ASN 797 (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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732A LEU* 4.5 3.4 - - + +
793A TYR* 2.8 57.1 + - - -
794A LEU* 3.0 4.4 + - - +
796A ASP* 1.3 79.3 - - - +
798A GLN* 1.3 68.7 + - - +
799A ILE* 3.3 20.2 + - + +
828A ARG* 3.1 36.8 + - - +
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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