Contacts of the helix formed by residues 773 - 791 (chain A) in PDB entry 3LJ1
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 773 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772A TYR* 1.3 73.6 - - - +
774A PRO* 1.3 75.1 - - - +
775A ILE* 3.5 19.8 - - - +
776A SER* 3.2 41.4 + - - -
777A LEU* 3.6 11.2 + - - +
820A GLU* 6.4 0.2 - - + -
821A ASN* 5.4 0.8 + - - -
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Residues in contact with PRO 774 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772A TYR* 3.4 16.5 - - + +
773A ASN* 1.3 93.0 - - - +
775A ILE* 1.3 61.5 + - - +
777A LEU* 3.4 10.8 + - + +
778A LEU* 3.0 28.4 + - - +
913A ILE* 4.1 15.0 - - + -
914A LEU* 3.8 16.4 - - + -
943A CYS* 4.4 20.6 - - + -
944A LEU* 4.1 24.0 - - + -
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Residues in contact with ILE 775 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A ASN* 3.3 15.3 - - - +
774A PRO* 1.3 76.1 - - - +
776A SER* 1.3 64.9 + - - +
778A LEU* 3.3 8.7 + - + +
779A ARG* 3.0 21.6 + - + +
914A LEU* 4.9 5.6 - - + -
944A LEU* 4.4 14.8 - - + -
949A LEU* 3.7 32.1 - - + -
979A LEU* 3.8 37.7 - - + +
980A PHE* 3.8 24.9 - - + -
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Residues in contact with SER 776 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A ASN* 3.2 33.7 + - - -
774A PRO 3.2 0.2 - - - -
775A ILE* 1.3 75.2 - - - +
777A LEU* 1.3 60.6 + - - +
779A ARG* 3.1 9.4 + - - +
780A GLN* 2.8 39.9 + - - +
820A GLU* 2.7 42.0 + - - +
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Residues in contact with LEU 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752A LEU* 4.5 7.6 - - + -
755A LEU* 4.0 14.1 - - + -
772A TYR* 3.4 35.2 - - + +
773A ASN 3.6 11.6 + - - +
774A PRO* 3.4 9.1 + - + +
775A ILE 3.4 0.4 - - - -
776A SER* 1.3 79.6 - - - +
778A LEU* 1.3 58.8 + - - +
780A GLN* 3.4 16.4 + - - +
781A ILE* 2.9 36.3 + - - +
822A LEU* 4.1 24.7 - - + -
824A ILE* 3.8 26.1 - - + +
913A ILE* 4.3 14.8 - - + -
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Residues in contact with LEU 778 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774A PRO 3.0 20.2 - - - +
775A ILE* 3.3 11.9 + - + +
776A SER 3.2 0.4 - - - -
777A LEU* 1.3 72.2 - - - +
779A ARG* 1.3 65.6 + - - +
781A ILE* 3.2 3.1 + - - +
782A ALA* 2.9 20.1 + - - +
910A PHE* 3.5 53.0 - - + +
913A ILE* 3.4 37.2 - - + -
914A LEU* 3.9 30.7 - - + -
979A LEU* 4.4 15.3 - - + -
980A PHE* 3.8 8.1 - - + -
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Residues in contact with ARG 779 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A ASN* 5.3 2.6 - - - +
775A ILE* 3.0 13.4 + - + +
776A SER* 3.4 9.3 - - - +
778A LEU* 1.3 76.1 - - - +
780A GLN* 1.3 76.8 + - - +
782A ALA* 3.3 2.4 + - - +
783A SER* 2.8 52.8 + - - -
817A THR* 4.8 10.9 + - - -
820A GLU* 3.6 27.9 + - - -
975A LEU* 3.5 16.8 - - + +
980A PHE* 3.4 33.8 - - + -
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Residues in contact with GLN 780 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A ASN* 3.1 33.9 + - - +
776A SER* 2.8 38.5 + - - +
777A LEU* 3.6 14.7 - - - +
779A ARG* 1.3 92.0 - - - +
781A ILE* 1.3 67.2 + - - +
783A SER* 3.2 5.2 + - - -
784A GLY 3.0 18.4 + - - -
820A GLU* 4.3 7.8 - - - +
822A LEU 3.3 19.1 + - - -
823A ARG* 3.4 12.1 - - - -
824A ILE* 2.8 32.0 + - + +
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Residues in contact with ILE 781 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752A LEU* 4.4 0.9 - - + -
777A LEU 2.9 25.0 + - - +
778A LEU* 3.6 5.6 - - - +
780A GLN* 1.3 73.1 - - - +
782A ALA* 1.3 63.6 + - - +
784A GLY* 3.3 1.2 + - - -
785A VAL* 3.1 27.8 + - + +
798A LEU* 5.6 2.2 - - + -
803A ILE* 3.9 35.2 - - + -
824A ILE* 3.6 25.8 - - + +
826A ILE* 3.8 9.4 - - + +
906A MET* 3.6 26.9 - - + -
909A VAL* 3.9 7.2 - - + -
910A PHE* 4.3 3.1 - - + -
913A ILE* 3.8 26.0 - - + -
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Residues in contact with ALA 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 LEU 2.9 13.2 + - - +
779A ARG* 3.5 4.5 - - - +
781A ILE* 1.3 74.6 - - - +
783A SER* 1.3 66.3 + - - +
784A GLY 3.1 0.3 + - - -
785A VAL* 3.2 1.7 + - - +
786A ALA* 2.8 26.3 + - - +
906A MET* 3.7 21.9 - - - -
910A PHE* 4.3 1.3 - - + -
971A ALA* 4.6 4.2 - - - +
974A VAL* 4.2 16.4 - - + -
975A LEU* 3.4 26.7 - - + -
980A PHE* 5.1 0.9 - - + -
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Residues in contact with SER 783 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A HIS* 3.3 25.1 + - - -
727A ASN* 3.6 8.9 + - - -
779A ARG* 2.8 36.6 + - - -
780A GLN 3.4 5.8 - - - -
782A ALA* 1.3 71.8 - - - +
784A GLY* 1.3 60.8 + - - +
786A ALA* 3.5 3.1 - - - +
787A HIS* 3.3 17.7 + - - +
975A LEU* 3.6 16.5 - - - +
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Residues in contact with GLY 784 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A HIS* 3.7 19.7 + - - -
727A ASN* 4.0 7.9 - - - -
728A VAL* 4.4 2.9 - - - +
780A GLN 3.0 13.2 + - - -
781A ILE 3.7 2.9 - - - -
783A SER* 1.3 75.4 + - - +
785A VAL* 1.3 64.4 + - - +
787A HIS* 3.1 6.6 + - - +
788A LEU* 3.1 23.6 + - - +
826A ILE* 4.1 11.7 - - - -
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Residues in contact with VAL 785 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781A ILE* 3.1 19.2 + - + +
782A ALA 3.8 0.7 - - - +
784A GLY* 1.3 71.1 - - - +
786A ALA* 1.3 66.3 + - - +
788A LEU* 3.0 12.1 + - + +
789A HIS* 2.9 55.7 + - + +
795A HIS* 6.4 0.4 - - + -
798A LEU* 3.8 18.4 - - + -
826A ILE* 3.8 15.0 - - + +
902A ASP* 4.3 6.5 - - + +
906A MET* 3.3 35.9 - - + -
971A ALA* 4.3 2.0 - - + -
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Residues in contact with ALA 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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782A ALA 2.8 16.7 + - - +
783A SER 3.5 7.0 - - - +
785A VAL* 1.3 78.5 - - - +
787A HIS* 1.3 55.9 + - - +
789A HIS* 3.5 3.1 + - - +
790A SER* 3.0 30.0 + - - -
971A ALA* 3.6 22.1 - - + +
972A MET* 4.1 22.5 - - + +
975A LEU* 4.0 19.1 - - + -
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Residues in contact with HIS 787 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A GLU 4.6 1.8 - - - -
722A SER* 3.4 28.0 + - - -
724A ASP* 5.4 3.8 - - + +
725A HIS* 3.6 37.7 + + + +
728A VAL* 4.6 2.6 - - - +
783A SER 3.3 10.4 + - - +
784A GLY 3.1 11.3 + - - +
785A VAL 3.1 0.6 - - - -
786A ALA* 1.3 79.1 - - - +
788A LEU* 1.3 62.7 + - - +
790A SER* 2.6 28.6 + - - -
791A LEU* 3.2 38.4 + - + +
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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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722A SER* 3.3 34.8 - - - +
728A VAL* 4.3 8.3 - - + -
784A GLY 3.1 14.1 + - - +
785A VAL* 3.0 17.1 + - + +
787A HIS* 1.3 76.6 - - - +
789A HIS* 1.3 64.3 + - + +
791A LEU* 3.2 10.9 + - - -
792A LYS 3.2 0.2 + - - -
793A ILE* 2.8 47.0 + - + +
795A HIS* 4.6 22.0 - - + -
826A ILE* 4.6 10.8 - - + -
829A PHE* 3.6 30.5 - - + -
902A ASP* 6.1 0.2 - - - +
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Residues in contact with HIS 789 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785A VAL* 2.9 39.2 + - + +
786A ALA* 3.8 6.1 - - - +
788A LEU* 1.3 77.9 - - + +
790A SER* 1.3 58.7 + - - +
792A LYS 3.0 13.6 + - - +
793A ILE 3.5 18.2 - - - +
794A ILE* 4.8 0.7 - - - -
899A ARG* 3.1 77.1 + - + +
902A ASP* 2.7 26.5 + - + -
903A ILE* 4.1 11.8 - - + +
971A ALA* 4.0 13.4 + - + +
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Residues in contact with SER 790 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786A ALA 3.0 16.0 + - - -
787A HIS* 2.6 27.6 + - - -
789A HIS* 1.3 76.1 - - - +
791A LEU* 1.3 64.1 + - - +
792A LYS* 3.2 7.9 + - - +
972A MET* 5.3 9.4 - - - -
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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
----------------------------------------------------------
721A GLU* 3.5 35.8 - - + +
722A SER* 3.6 12.8 - - - +
787A HIS* 3.2 42.1 + - + +
788A LEU 3.2 7.8 + - - +
790A SER* 1.3 82.3 + - - +
792A LYS* 1.3 71.7 + - - +
793A ILE* 3.3 16.8 + - + +
834A LYS* 3.6 14.6 - - - -
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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) + - + + + + + -
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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