Contacts of the helix formed by residues 899 - 915 (chain B) 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 ARG 899 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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789B HIS* 3.1 74.6 + - + +
792B LYS* 3.7 28.4 - - - +
794B ILE* 3.5 23.7 - - + +
835B LEU* 3.6 22.2 - - + +
840B SEP 3.8 28.5 + - - -
898B THR* 1.3 76.4 - - - +
900B SER* 1.3 55.3 + - - +
901B ILE* 3.0 0.4 - - - +
902B ASP* 2.9 23.0 + - - +
903B ILE* 3.8 1.4 + - + -
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Residues in contact with SER 900 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859B GLU* 4.2 2.1 + - - -
898B THR* 2.6 25.2 + - - -
899B ARG* 1.3 78.0 - - - +
901B ILE* 1.3 61.5 + - - +
902B ASP 3.2 0.2 - - - -
903B ILE* 3.1 24.7 + - - +
904B PHE 3.3 6.2 + - - -
965B PRO* 3.6 36.0 + - - +
968B ARG* 3.2 26.3 + - - -
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Residues in contact with ILE 901 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794B ILE* 3.3 28.7 - - + -
796B ARG* 4.9 11.2 - - + +
842B PHE* 5.4 5.4 - - + -
856B ARG* 5.4 0.2 - - - -
857B ALA* 3.1 34.2 + - + +
859B GLU* 4.3 8.5 + - + +
860B LEU* 3.2 44.0 - - + -
897B LEU* 5.7 3.8 - - + -
898B THR 3.1 20.1 + - - +
899B ARG 2.9 1.0 + - - +
900B SER* 1.3 80.1 + - - +
902B ASP* 1.3 66.7 + - - +
903B ILE 3.6 0.2 + - - -
904B PHE* 3.7 3.8 + - - +
905B SER* 3.5 17.7 + - - -
968B ARG* 4.0 4.9 - - - +
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Residues in contact with ASP 902 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785B VAL* 4.3 3.5 - - + +
788B LEU* 6.1 0.2 - - - +
789B HIS* 2.8 35.5 + - + +
794B ILE* 3.4 10.6 - - - +
795B HIS* 3.0 29.7 + - - +
796B ARG* 3.0 27.7 + - - -
798B LEU* 4.0 15.5 - - + +
899B ARG 2.9 4.7 + - - +
901B ILE* 1.3 77.6 - - - +
903B ILE* 1.3 55.2 + - - +
905B SER* 2.8 8.8 + - - -
906B MET* 2.7 37.5 + - - +
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Residues in contact with ILE 903 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789B HIS* 4.1 8.7 - - + -
899B ARG 4.3 2.2 - - - +
900B SER* 3.1 22.5 + - - +
902B ASP* 1.3 75.6 - - - +
904B PHE* 1.3 52.9 + - - +
906B MET* 3.7 20.7 - - + +
907B GLY* 2.7 31.5 + - - -
960B MET* 3.6 36.5 - - + +
968B ARG* 4.3 5.8 - - + -
969B PRO* 3.3 24.9 - - + +
970B THR* 4.1 2.0 - - - -
971B ALA* 3.7 36.1 - - + +
974B VAL* 4.6 3.4 - - + -
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Residues in contact with PHE 904 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855B TRP 4.5 0.4 - - - -
856B ARG 3.2 21.5 - - - -
857B ALA* 3.5 24.7 - - + -
858B PRO* 3.7 18.4 - - + -
900B SER 3.3 3.0 + - - -
901B ILE 3.8 9.2 - - - +
902B ASP 3.2 0.2 - - - -
903B ILE* 1.3 78.9 - - - +
905B SER* 1.3 61.2 + - - +
907B GLY* 3.0 3.3 + - - -
908B CYS* 2.9 43.2 + - - -
921B PHE* 3.4 28.9 - + - -
931B ILE* 3.7 21.5 - - + -
960B MET 3.4 10.9 + - - -
961B ILE* 3.3 37.7 - - - +
962B ASP 4.5 1.3 - - - -
963B HIS* 5.6 0.2 - - - -
968B ARG* 4.0 16.2 - - - +
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Residues in contact with SER 905 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796B ARG 6.0 0.7 - - - -
797B ASP 5.8 0.2 + - - -
798B LEU* 3.6 30.6 + - - +
855B TRP* 3.2 27.9 - - - -
901B ILE 3.5 4.8 + - - -
902B ASP* 2.8 29.6 + - - -
904B PHE* 1.3 79.7 - - - +
906B MET* 1.3 55.6 + - - +
908B CYS* 3.2 7.2 + - - +
909B VAL* 3.0 33.1 + - - +
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Residues in contact with MET 906 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781B ILE* 3.6 22.7 - - + -
782B ALA* 3.7 27.6 - - - -
785B VAL* 3.3 42.8 - - + -
798B LEU* 4.5 6.7 - - + +
902B ASP 2.7 18.5 + - - +
903B ILE* 3.7 22.7 - - + +
905B SER* 1.3 69.3 + - - +
907B GLY* 1.3 60.4 + - - +
909B VAL* 3.1 7.2 + - + +
910B PHE* 2.9 54.1 + - + -
960B MET* 3.9 8.5 - - + -
971B ALA* 4.7 4.7 - - + -
974B VAL* 5.2 2.2 - - + -
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Residues in contact with GLY 907 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903B ILE 2.7 19.2 + - - -
904B PHE 3.0 4.9 + - - -
906B MET* 1.3 74.6 - - - +
908B CYS* 1.3 58.9 + - - +
910B PHE* 3.5 4.2 - - - +
911B TYR* 3.5 14.6 + - - +
957B ILE* 3.6 14.7 - - - +
960B MET* 3.6 29.3 - - - +
961B ILE* 3.5 9.2 - - - -
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Residues in contact with CYS 908 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855B TRP* 3.5 25.0 - - + -
904B PHE* 2.9 41.5 + - - -
905B SER* 3.5 9.0 - - - +
906B MET 3.1 0.2 - - - -
907B GLY* 1.3 75.8 - - - +
909B VAL* 1.3 60.5 + - - +
911B TYR* 3.2 5.4 + - - +
912B TYR* 2.9 26.7 + - - +
919B HIS* 3.9 21.5 - - - +
920B PRO* 4.0 12.7 - - + +
921B PHE* 4.2 11.2 - - - -
961B ILE* 4.2 5.2 - - - -
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Residues in contact with VAL 909 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752B LEU* 3.7 19.1 - - + -
781B ILE* 4.0 12.6 - - + -
798B LEU* 4.6 2.0 - - + +
799B LYS* 4.2 8.5 - - - +
800B PRO* 4.2 13.0 - - + -
803B ILE* 3.6 32.8 - - + -
855B TRP* 4.0 15.5 - - + -
905B SER 3.0 21.9 + - - +
906B MET* 3.6 11.7 - - + +
908B CYS* 1.3 74.8 - - - +
910B PHE* 1.3 58.3 + - + +
912B TYR* 3.3 8.1 + - + +
913B ILE* 2.9 28.8 + - + +
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Residues in contact with PHE 910 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778B LEU* 3.5 63.0 - - + -
781B ILE* 4.3 6.5 - - + -
782B ALA* 4.3 6.7 - - + -
906B MET* 2.9 48.2 + - + -
907B GLY 3.5 11.4 - - - +
908B CYS 3.2 0.4 - - - -
909B VAL* 1.3 79.7 - - + +
911B TYR* 1.3 57.8 + - - +
913B ILE* 3.3 4.5 + - - +
914B LEU* 3.0 32.4 + - - +
956B LEU* 4.3 6.1 - - + -
957B ILE* 4.0 16.4 - - + -
960B MET* 3.6 30.3 - - + -
974B VAL* 4.1 4.7 - - + -
979B LEU* 5.6 0.7 - - + -
980B PHE* 4.0 14.1 - + - -
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Residues in contact with TYR 911 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907B GLY 3.5 3.9 + - - +
908B CYS 3.2 2.5 + - - +
910B PHE* 1.3 79.4 - - - +
912B TYR* 1.3 51.1 + - - +
914B LEU* 4.4 1.6 - - - +
915B SER* 2.5 50.8 + - - -
918B LYS* 3.5 28.0 - - + +
919B HIS 3.9 10.1 - - - -
920B PRO* 3.5 37.7 - - + -
937B SER* 3.8 8.9 + - - -
938B LEU* 3.5 33.4 - - + -
939B ASP 3.5 4.7 + - - -
940B GLU* 3.0 35.1 + - - +
941B MET* 3.9 29.8 - - + -
957B ILE* 3.8 11.3 - - + +
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Residues in contact with TYR 912 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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752B LEU* 4.5 7.4 - - + -
753B GLN* 3.2 21.7 - - + +
756B VAL* 3.7 26.7 - - + +
757B GLU* 2.7 37.2 + - + +
800B PRO* 3.4 30.5 - - + -
855B TRP* 3.7 25.8 - + + -
908B CYS 2.9 13.7 + - - +
909B VAL* 3.4 10.3 - - - +
911B TYR* 1.3 76.1 - - - +
913B ILE* 1.3 61.0 + - - +
916B LYS 3.4 0.5 + - - -
917B GLY* 3.0 58.5 + - - -
918B LYS 3.1 17.4 + - - +
919B HIS* 5.8 0.2 - - + -
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Residues in contact with ILE 913 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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752B LEU* 3.6 36.3 - - + -
756B VAL* 4.5 8.5 - - + +
772B TYR* 4.0 18.6 + - - +
774B PRO* 4.1 17.7 - - + +
777B LEU* 4.3 14.8 - - + -
778B LEU* 3.4 30.7 - - + -
781B ILE* 3.8 19.1 - - + -
909B VAL* 2.9 18.6 + - + +
910B PHE* 3.6 6.1 - - - +
911B TYR 3.2 0.2 - - - -
912B TYR* 1.3 76.7 - - + +
914B LEU* 1.3 62.9 + - - +
916B LYS* 3.2 12.0 + - - -
943B CYS* 3.6 11.6 - - - -
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Residues in contact with LEU 914 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774B PRO* 3.8 27.1 - - + -
775B ILE* 4.9 3.6 - - + -
778B LEU* 4.0 28.5 - - + -
910B PHE 3.0 17.5 + - - +
911B TYR* 4.1 2.9 - - - +
913B ILE* 1.3 76.7 - - - +
915B SER* 1.3 58.5 + - - +
941B MET* 3.6 24.2 - - + -
942B LYS 3.4 4.9 + - - -
943B CYS* 3.2 31.0 + - + +
944B LEU* 3.9 24.9 + - + -
953B ALA* 3.9 28.3 - - + -
957B ILE* 4.3 9.2 - - + -
979B LEU* 5.1 0.9 - - + -
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Residues in contact with SER 915 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911B TYR* 2.5 40.1 + - - -
912B TYR 3.5 1.0 + - - -
914B LEU* 1.3 72.5 - - - +
916B LYS* 1.3 68.9 + - - +
918B LYS* 2.9 47.2 + - - +
940B GLU 3.2 21.8 - - - -
941B MET* 4.2 0.4 - - - +
942B LYS* 3.2 22.5 - - - -
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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