Contacts of the helix formed by residues 922 - 943 (chain A) in PDB entry 3LXK
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 ASP 922 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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920A ARG 3.9 3.5 + - - +
921A LEU* 1.3 74.1 - - - +
923A ALA* 1.3 63.9 + - - +
924A SER* 3.3 14.9 + - - -
925A ARG* 3.0 32.2 + - - +
926A LEU* 3.2 11.6 + - - +
1023A TYR* 4.3 5.2 - - - -
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Residues in contact with ALA 923 (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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922A ASP* 1.3 74.7 - - - +
924A SER* 1.3 56.4 + - - +
926A LEU* 3.2 14.0 + - - +
927A LEU* 2.9 37.6 + - + +
1021A PHE* 4.3 12.9 - - + -
1023A TYR* 4.7 1.2 + - - -
1067A PRO* 4.5 14.4 - - + -
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Residues in contact with SER 924 (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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922A ASP* 3.2 15.3 + - - -
923A ALA* 1.3 78.6 - - - +
925A ARG* 1.3 57.6 + - - +
927A LEU* 3.3 12.4 + - - +
928A LEU* 2.9 28.2 + - - +
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Residues in contact with ARG 925 (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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921A LEU* 3.7 15.8 - - + +
922A ASP* 3.0 27.6 + - - +
924A SER* 1.3 77.5 - - - +
926A LEU* 1.3 56.1 - - - +
928A LEU* 3.2 20.6 + - - +
929A TYR* 2.9 62.9 + - + +
960A GLU* 3.1 54.6 + - - +
961A ALA* 4.4 8.9 - - - +
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Residues in contact with LEU 926 (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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914A LEU* 3.8 25.6 - - + -
921A LEU* 5.0 3.4 - - + -
922A ASP 3.2 11.5 + - - +
923A ALA* 3.2 9.6 + - - +
925A ARG* 1.3 76.6 - - - +
927A LEU* 1.3 52.2 + - - +
929A TYR* 3.4 11.7 + - + +
930A SER* 2.7 37.5 + - - -
1020A LEU* 3.4 36.7 - - + +
1021A PHE* 3.7 36.1 - - + -
1023A TYR* 3.5 31.2 - - + +
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Residues in contact with LEU 927 (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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923A ALA* 2.9 29.8 + - + +
924A SER* 3.6 10.5 - - - +
925A ARG 3.2 0.2 - - - -
926A LEU* 1.3 73.2 - - - +
928A LEU* 1.3 61.1 + - - +
930A SER* 3.3 5.5 + - - +
931A SER* 2.9 29.3 + - - -
1021A PHE* 4.0 10.8 - - + -
1067A PRO* 5.7 3.1 - - + -
1070A VAL* 3.8 28.0 - - + -
1095A LEU* 4.5 26.4 - - + +
1098A LEU* 3.7 43.1 - - + +
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Residues in contact with LEU 928 (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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924A SER 2.9 14.9 + - - +
925A ARG* 3.4 30.1 - - - +
927A LEU* 1.3 74.0 - - - +
929A TYR* 1.3 66.2 + - + +
931A SER* 3.2 9.1 + - - -
932A GLN* 3.0 47.6 + - + +
961A ALA* 3.5 31.2 - - + +
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Residues in contact with TYR 929 (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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910A LEU* 4.2 9.9 - - + -
913A PHE* 3.7 18.8 - + - -
914A LEU* 4.3 15.3 - - + -
921A LEU* 3.7 8.2 - - + +
925A ARG* 2.9 45.1 + - + +
926A LEU* 3.6 9.4 - - + +
928A LEU* 1.3 75.7 - - + +
930A SER* 1.3 58.0 + - - +
932A GLN* 3.2 10.3 + - - +
933A ILE* 2.9 37.0 + - + +
957A VAL* 5.7 0.2 - - + -
959A SER 4.7 1.1 - - - -
960A GLU 2.5 35.0 + - - -
961A ALA* 4.3 0.9 - - - -
962A HIS 4.2 6.5 - - - -
963A VAL* 3.7 34.0 - - + +
1020A LEU* 3.9 26.0 - - + -
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Residues in contact with SER 930 (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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926A LEU 2.7 21.1 + - - -
927A LEU* 3.4 10.5 - - - -
929A TYR* 1.3 76.9 - - - +
931A SER* 1.3 57.1 + - - +
933A ILE* 3.5 2.6 + - - +
934A CYS* 2.9 29.6 + - - +
1013A PHE* 3.7 5.3 - - - -
1017A LEU* 3.3 31.5 - - - +
1020A LEU* 3.4 14.7 - - - +
1021A PHE* 3.9 7.3 - - - -
1095A LEU* 3.7 16.9 - - - +
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Residues in contact with SER 931 (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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927A LEU 2.9 17.2 + - - -
928A LEU* 3.6 10.3 - - - -
930A SER* 1.3 76.0 - - - +
932A GLN* 1.3 59.7 + - - +
934A CYS* 3.3 2.9 + - - +
935A LYS* 2.9 45.3 + - - +
1092A GLY* 4.7 2.5 + - - -
1095A LEU* 4.1 18.6 - - - +
1096A ASP* 2.6 32.0 + - - -
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Residues in contact with GLN 932 (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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882A PHE* 3.5 48.5 - - + +
928A LEU* 3.0 35.6 + - + +
929A TYR* 3.2 10.6 + - - +
931A SER* 1.3 73.9 - - - +
933A ILE* 1.3 65.5 + - - +
935A LYS* 3.2 4.6 + - + +
936A GLY 3.0 18.7 + - - -
961A ALA 2.9 23.7 + - - +
962A HIS* 3.3 11.2 + - - +
963A VAL* 2.9 34.3 + - + +
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Residues in contact with ILE 933 (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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882A PHE* 5.6 0.2 - - - -
910A LEU* 4.2 18.8 - - + -
929A TYR 2.9 22.5 + - - +
930A SER* 3.9 3.6 - - - +
932A GLN* 1.3 74.0 - - - +
934A CYS* 1.3 57.5 + - - +
936A GLY* 3.2 2.9 + - - -
937A MET* 2.9 29.9 + - + +
950A LEU* 4.2 23.1 - - + -
955A ILE* 4.2 18.6 - - + -
963A VAL* 3.9 12.8 - - + -
964A LYS 6.1 0.2 - - - -
965A ILE* 3.9 9.6 - - + +
1013A PHE* 3.8 21.8 - - + -
1016A VAL* 3.9 23.3 - - + -
1020A LEU* 4.1 14.6 - - + -
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Residues in contact with CYS 934 (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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930A SER 2.9 18.1 + - - +
931A SER 3.5 5.2 - - - +
932A GLN 3.3 0.2 - - - -
933A ILE* 1.3 76.4 - - - +
935A LYS* 1.3 58.8 + - - +
937A MET* 3.3 2.8 + - - +
938A GLU* 2.9 27.4 + - - +
1013A PHE* 3.9 10.5 - - + -
1088A PHE* 3.3 40.9 - - - +
1091A LEU* 3.8 13.0 - - - -
1092A GLY* 3.5 22.7 - - - -
1095A LEU* 3.7 11.4 - - + -
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Residues in contact with LYS 935 (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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882A PHE* 3.8 35.1 - - + -
931A SER* 2.9 36.9 + - - +
932A GLN* 3.6 6.1 - - - +
934A CYS* 1.3 75.6 - - + +
936A GLY* 1.3 65.2 + - - +
938A GLU* 3.2 15.9 + - - +
939A TYR* 2.9 25.3 + - - +
1092A GLY* 5.8 5.6 - - - -
1096A ASP* 3.9 18.3 + - - -
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Residues in contact with GLY 936 (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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880A SER* 4.8 1.3 - - - -
882A PHE* 3.8 23.3 - - - +
883A ILE* 4.2 7.1 - - - +
932A GLN 3.0 11.1 + - - -
933A ILE 3.2 3.8 + - - -
935A LYS* 1.3 76.1 - - - +
937A MET* 1.3 57.3 + - - +
939A TYR* 3.3 6.2 + - - +
940A LEU* 2.9 28.9 + - - +
965A ILE* 3.8 14.8 - - - -
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Residues in contact with MET 937 (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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933A ILE* 2.9 21.7 + - + +
934A CYS 3.7 4.5 - - - +
936A GLY* 1.3 74.0 - - - +
938A GLU* 1.3 63.8 + - - +
940A LEU* 3.4 17.8 + - + +
941A GLY* 3.0 20.8 + - - -
945A CYS 5.7 0.9 - - - +
947A HIS* 4.1 11.4 - - + -
950A LEU* 3.9 31.0 - - + -
965A ILE* 3.5 20.6 - - + -
1009A ASP* 3.5 39.7 - - + +
1088A PHE* 3.6 35.4 - - + -
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Residues in contact with GLU 938 (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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934A CYS* 2.9 16.4 + - - +
935A LYS* 3.2 16.6 + - - +
937A MET* 1.3 75.2 - - - +
939A TYR* 1.3 63.1 + - - +
941A GLY* 3.4 1.2 + - - -
942A SER* 3.0 23.0 + - - -
1088A PHE* 4.0 16.8 - - + +
1089A SER* 3.6 39.9 + - - +
1092A GLY* 5.6 3.6 - - - -
1093A PRO* 6.0 0.3 - - - +
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Residues in contact with TYR 939 (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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877A ALA 3.7 6.4 + - - -
878A LEU* 3.5 25.8 - - + +
879A HIS* 2.9 43.8 + - - +
880A SER* 3.6 26.2 - - - +
883A ILE* 4.1 10.1 - - + -
935A LYS 2.9 13.1 + - - +
936A GLY* 3.4 7.9 - - - +
938A GLU* 1.3 77.2 - - - +
940A LEU* 1.3 63.5 + - - +
942A SER* 2.7 29.4 + - - -
943A ARG* 3.2 31.2 + - + +
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Residues in contact with LEU 940 (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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878A LEU* 3.5 36.6 - - + -
883A ILE* 4.4 7.2 - - + -
936A GLY 2.9 18.2 + - - +
937A MET* 3.6 23.1 - - + +
938A GLU 3.4 0.2 - - - -
939A TYR* 1.3 73.4 - - - +
941A GLY* 1.3 57.5 + - - +
943A ARG* 3.0 13.2 + - - +
945A CYS* 3.0 55.9 + - + +
947A HIS* 3.8 42.2 - - + -
965A ILE* 5.1 1.3 - - + -
968A PHE* 3.8 11.2 - - + -
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Residues in contact with GLY 941 (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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937A MET* 3.0 16.3 + - - +
938A GLU* 3.9 2.0 - - - -
940A LEU* 1.3 76.0 - - - +
942A SER* 1.3 56.2 + - - +
944A ARG* 3.0 11.6 + - - -
945A CYS 3.9 4.9 + - - -
1006A ARG* 2.9 49.4 + - - -
1088A PHE* 6.2 0.9 - - - -
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Residues in contact with SER 942 (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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938A GLU* 3.0 14.7 + - - -
939A TYR* 2.7 27.8 + - - -
941A GLY* 1.3 75.2 - - - +
943A ARG* 1.3 74.9 + - - +
944A ARG* 3.2 7.1 + - - +
1006A ARG* 5.2 0.2 - - - +
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Residues in contact with ARG 943 (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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877A ALA* 4.9 8.6 + - - +
878A LEU* 3.8 28.0 - - + -
939A TYR* 3.3 33.7 + - + +
940A LEU 3.0 8.3 + - - +
942A SER* 1.3 93.5 + - - +
944A ARG* 1.3 70.9 + - - +
945A CYS* 3.3 5.8 + - + +
973A LEU* 4.3 11.7 - - + +
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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
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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