Contacts of the helix formed by residues 909 - 927 (chain B) in PDB entry 1CJT
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 LEU 909 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A ILE* 4.5 13.2 - - + -
384A ILE* 3.5 37.9 - - + +
493A HIS* 3.8 19.4 - - + +
905B ASN 3.2 1.4 + - - -
906B LYS* 3.3 32.7 + - + +
907B GLU 3.3 1.2 + - - -
908B GLY* 1.3 77.0 - - - +
910B GLU* 1.3 62.5 + - - +
912B LEU* 3.1 9.7 + - + +
913B ARG* 2.9 48.1 + - - +
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Residues in contact with GLU 910 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904B VAL 4.7 1.8 - - - +
905B ASN* 3.1 28.8 + - + +
906B LYS* 3.8 25.3 + - + +
909B LEU* 1.3 76.0 - - - +
911B CYS* 1.3 60.6 + - - +
913B ARG* 2.9 61.4 + - - +
914B LEU* 3.5 6.8 + - - +
235C ILE* 4.9 7.6 - - - +
236C GLN* 3.5 43.0 - - + +
239C ASN* 3.7 13.7 + - - +
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Residues in contact with CYS 911 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895B PHE* 3.6 10.0 - - + -
898B PHE* 4.0 25.4 - - + -
899B TYR* 3.6 21.5 - - + -
900B THR 3.8 31.9 - - - -
905B ASN* 4.4 1.6 - - - -
908B GLY* 3.3 9.3 + - - +
909B LEU 3.1 0.4 - - - -
910B GLU* 1.3 75.8 - - - +
912B LEU* 1.3 64.6 + - - +
914B LEU* 3.1 15.6 + - - +
915B LEU 3.2 8.5 + - - -
236C GLN* 3.2 27.8 - - - -
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Residues in contact with LEU 912 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A FOK 4.5 13.7 - - + -
382A ILE* 4.3 2.9 - - + -
384A ILE* 4.1 17.3 - - + -
493A HIS* 3.9 27.8 - - + +
497A LEU* 4.2 6.8 - - + +
507A TRP* 3.7 54.1 - - + +
895B PHE* 5.0 0.7 - - + -
899B TYR* 4.3 10.8 - - + -
908B GLY 3.2 13.4 + - - +
909B LEU* 3.1 10.4 + - - +
911B CYS* 1.3 76.1 - - - +
913B ARG* 1.3 66.1 + - - +
915B LEU* 3.1 14.8 + - + +
916B ASN* 3.0 23.7 + - - +
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Residues in contact with ARG 913 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A PHE* 3.6 42.1 - - + +
380A HIS 5.0 6.6 + - - +
382A ILE* 3.5 41.1 - - + +
906B LYS* 5.1 2.8 - - - +
909B LEU* 2.9 29.7 + - - +
910B GLU* 2.9 49.1 + - - +
911B CYS 3.1 0.4 - - - -
912B LEU* 1.3 78.0 - - - +
914B LEU* 1.3 60.2 + - - +
916B ASN* 3.4 5.2 - - + +
917B GLU* 3.2 23.9 + - - +
239C ASN* 3.0 35.2 + - - +
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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
----------------------------------------------------------
379A PHE* 5.3 1.8 - - + -
895B PHE* 5.0 1.6 - - + -
898B PHE* 3.8 29.8 - - + -
910B GLU 3.5 5.6 + - - +
911B CYS 3.1 10.6 + - - +
913B ARG* 1.3 77.0 - - - +
915B LEU* 1.3 65.0 + - - +
917B GLU* 3.1 8.0 + - + +
918B ILE* 3.0 28.3 + - + +
986B ILE* 4.3 8.7 - - + -
990B SER* 4.1 17.5 - - - +
992B ASN* 5.0 1.1 - - - +
994B PHE* 4.0 21.3 - - + -
235C ILE* 4.1 22.9 - - + -
281C TRP* 3.9 30.7 - - + -
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Residues in contact with LEU 915 (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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101A FOK 3.9 15.0 - - + -
497A LEU* 3.7 24.5 - - + -
507A TRP* 5.1 0.9 - - - +
892B ILE* 5.2 2.7 - - + -
895B PHE* 3.6 39.6 - - + -
911B CYS 3.2 3.4 + - - +
912B LEU* 3.1 14.1 + - + +
914B LEU* 1.3 78.1 - - - +
916B ASN* 1.3 57.6 + - - +
918B ILE* 3.1 14.0 + - + -
919B ILE* 3.0 53.8 + - + +
941B GLY 4.0 14.6 - - - +
942B SER* 4.1 17.9 - - - -
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Residues in contact with ASN 916 (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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380A HIS* 4.1 18.0 + - - +
381A LYS 3.8 20.2 + - - -
382A ILE* 4.0 17.2 - - + +
496A VAL 4.3 1.1 - - - +
497A LEU* 3.3 21.5 - - + +
498A GLY* 2.6 37.1 + - - +
912B LEU 3.0 11.3 + - - +
913B ARG* 3.4 14.4 + - - +
915B LEU* 1.3 77.8 - - - +
917B GLU* 1.3 62.2 + - - +
919B ILE* 4.1 2.0 - - - +
920B ALA* 3.1 25.9 + - - +
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Residues in contact with GLU 917 (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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378A MET 4.5 1.4 - - - +
379A PHE* 3.5 20.2 - - + -
380A HIS* 2.8 45.2 + - - +
913B ARG* 3.2 15.6 + - - +
914B LEU* 3.1 10.3 + - + +
916B ASN* 1.3 77.6 + - - +
918B ILE* 1.3 62.2 + - - +
920B ALA* 3.4 5.2 + - - +
921B ASP* 3.1 29.6 + - - +
986B ILE* 4.2 5.8 - - + -
280C ARG* 3.5 14.6 + - - +
281C TRP* 2.9 43.2 + - + +
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Residues in contact with ILE 918 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892B ILE* 4.0 18.6 - - + -
895B PHE* 5.0 4.9 - - + -
914B LEU* 3.0 20.2 + - + +
915B LEU* 3.1 16.4 + - + +
917B GLU* 1.3 74.3 - - - +
919B ILE* 1.3 72.6 + - + +
921B ASP* 3.2 3.9 + - - +
922B PHE* 3.2 51.8 + - + -
983B LEU* 3.9 18.2 - - + -
986B ILE* 3.8 34.3 - - + -
994B PHE* 4.3 18.6 - - + -
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Residues in contact with ILE 919 (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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497A LEU* 4.4 13.7 - - + +
498A GLY* 3.8 16.2 - - - +
892B ILE* 5.9 0.4 - - + -
915B LEU* 3.0 40.8 + - + +
916B ASN 4.1 0.7 - - - +
918B ILE* 1.3 82.6 - - + +
920B ALA* 1.3 52.3 + - - +
922B PHE* 3.1 10.0 + - + +
923B ASP* 2.7 50.9 + - - +
936B LYS* 4.0 13.0 - - - +
939B THR* 4.1 22.9 - - + +
941B GLY 5.4 3.4 - - - +
942B SER* 5.4 7.4 - - - +
943B THR 5.8 0.4 - - - +
944B TYR* 4.5 10.3 - - + -
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Residues in contact with ALA 920 (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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380A HIS* 3.8 32.1 - - + +
498A GLY* 4.1 5.1 - - - -
499A LEU* 4.0 20.7 - - + +
916B ASN* 3.1 20.4 + - - +
917B GLU 3.6 5.4 - - - +
918B ILE 3.2 0.2 - - - -
919B ILE* 1.3 77.3 - - - +
921B ASP* 1.3 57.6 + - - +
923B ASP* 3.3 4.1 + - - +
924B ASP* 3.0 34.1 + - - +
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Residues in contact with ASP 921 (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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380A HIS* 5.1 3.1 - - - -
917B GLU 3.1 14.3 + - - +
918B ILE* 3.2 5.8 + - - +
920B ALA* 1.3 80.7 - - - +
922B PHE* 1.3 63.5 + - - +
924B ASP* 3.5 12.6 + - - +
925B LEU* 3.8 3.3 + - - +
982B LYS* 3.5 52.3 + - + +
985B ALA* 5.9 0.9 - - - +
986B ILE* 3.4 16.0 - - + +
280C ARG* 2.8 42.1 + - - -
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Residues in contact with PHE 922 (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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890B ALA 5.8 0.2 - - - -
892B ILE* 4.6 4.9 - - + -
918B ILE* 3.2 36.5 + - + -
919B ILE* 3.1 12.7 + - + +
921B ASP* 1.3 73.4 - - + +
923B ASP* 1.3 65.4 + - - +
925B LEU* 3.1 22.4 + - - +
926B LEU* 4.2 1.4 + - - +
942B SER 6.1 0.2 - - - -
944B TYR* 3.7 42.1 + + + -
975B PHE* 4.4 4.5 - - - -
979B LEU* 3.5 53.6 - - + -
982B LYS* 3.8 17.3 - - + -
983B LEU* 4.0 17.9 - - + -
986B ILE* 6.0 0.7 - - + -
996B LEU* 4.5 19.1 - - + -
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Residues in contact with ASP 923 (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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499A LEU* 3.1 27.6 + - + +
500A ARG* 3.2 28.2 + - + +
919B ILE* 2.7 26.0 + - - +
920B ALA* 3.3 7.2 + - - +
922B PHE* 1.3 73.8 - - - +
924B ASP* 1.3 61.5 + - - +
925B LEU 3.2 1.6 + - - -
926B LEU* 3.3 23.4 + - - +
927B SER* 4.5 1.9 + - - -
936B LYS* 3.0 31.1 + - - +
944B TYR* 2.7 32.7 + - - -
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Residues in contact with ASP 924 (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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380A HIS* 4.8 6.6 + - - -
499A LEU* 3.3 25.7 - - - +
500A ARG* 6.1 0.5 - - - +
920B ALA 3.0 20.9 + - - +
921B ASP* 3.9 13.9 - - - +
922B PHE 3.2 1.4 - - - -
923B ASP* 1.3 75.6 - - - +
925B LEU* 1.3 62.1 + - - +
926B LEU 3.2 0.7 - - - -
927B SER* 3.6 21.1 + - - -
928B LYS* 4.4 6.2 - - - +
982B LYS* 4.7 8.7 - - - +
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Residues in contact with LEU 925 (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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921B ASP 3.8 8.2 + - - +
922B PHE* 3.1 11.7 + - - +
924B ASP* 1.3 74.2 - - - +
926B LEU* 1.3 62.6 + - - +
927B SER 3.0 5.4 - - - -
928B LYS* 3.0 31.6 + - + +
931B PHE* 3.3 25.8 - - + +
975B PHE* 3.8 14.4 - - + -
978B ALA* 3.7 40.4 - - + +
979B LEU* 3.7 27.8 - - + -
982B LYS* 3.7 28.5 - - + -
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Residues in contact with LEU 926 (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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500A ARG* 3.8 39.3 + - + +
922B PHE 4.4 0.7 - - - +
923B ASP* 3.4 22.4 - - - +
924B ASP 3.2 0.8 - - - -
925B LEU* 1.3 77.1 - - - +
927B SER* 1.3 58.6 + - - +
928B LYS 3.3 5.4 + - - +
931B PHE* 4.3 14.0 - - - +
932B SER* 4.6 4.9 + - - -
934B VAL* 4.0 30.7 - - + +
936B LYS* 3.9 20.4 - - + +
944B TYR* 3.7 19.1 - - - +
975B PHE* 3.8 27.4 - - + -
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Residues in contact with SER 927 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A ARG* 4.8 12.0 + - - +
923B ASP 4.5 1.9 + - - -
924B ASP* 3.6 16.7 + - - -
925B LEU 3.0 1.2 - - - -
926B LEU* 1.3 75.4 - - - +
928B LYS* 1.3 64.8 + - - +
929B PRO* 3.4 8.3 - - - +
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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
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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