Contacts of the helix formed by residues 919 - 941 (chain A) in PDB entry 6VSB
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 919 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717A ASN* 5.4 2.0 + - - -
718A PHE* 3.8 24.3 - - + -
915A VAL* 3.1 18.4 + - - +
916A LEU 3.2 3.1 - - - +
918A GLU* 1.3 89.1 - - - +
920A GLN* 1.3 64.6 + - - +
921A LYS 3.2 3.1 - - - -
922A LEU* 3.1 23.4 + - + +
923A ILE* 3.0 28.7 + - + +
1109A PHE* 4.8 12.9 - - - -
1D NAG 6.1 3.4 + - - +
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Residues in contact with GLN 920 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A GLY* 3.4 28.8 + - - +
800A PHE* 4.8 5.7 - - + -
899A ALA* 3.4 28.6 - - + +
916A LEU* 2.6 24.6 + - + +
917A TYR* 3.3 29.9 + - - +
918A GLU 3.5 0.8 + - - -
919A ASN* 1.3 73.1 - - - +
921A LYS* 1.3 63.9 + - - +
923A ILE* 3.4 6.9 + - - +
924A ALA* 3.1 22.7 + - - +
1129C VAL* 4.9 0.7 - - - +
1130C ILE* 3.8 31.2 - - + +
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Residues in contact with LYS 921 (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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918A GLU 5.3 0.4 + - - -
919A ASN 3.2 1.0 - - - -
920A GLN* 1.3 79.0 - - - +
922A LEU* 1.3 64.2 + - - +
924A ALA* 3.4 6.0 + - + +
925A ASN* 3.1 34.8 + - - +
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Residues in contact with LEU 922 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A ASN* 4.5 13.7 - - - +
718A PHE* 4.8 7.9 - - + -
919A ASN* 3.1 33.8 + - + +
921A LYS* 1.3 78.5 - - - +
923A ILE* 1.3 64.7 + - - +
925A ASN* 3.2 7.0 + - - +
926A GLN* 3.0 51.2 + - - +
1D NAG 3.8 20.9 - - - +
2D NAG 3.3 33.4 - - + +
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Residues in contact with ILE 923 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718A PHE* 3.4 28.3 - - + -
720A ILE* 4.1 20.9 - - + +
800A PHE* 3.5 25.6 - - + -
902A MET* 5.0 2.5 - - + -
906A PHE* 3.5 32.1 - - + -
916A LEU* 3.7 28.3 - - + +
919A ASN* 3.0 21.6 + - + +
920A GLN* 3.7 4.9 - - - +
922A LEU* 1.3 77.1 - - - +
924A ALA* 1.3 57.3 + - - +
926A GLN* 3.2 5.6 + - - +
927A PHE* 2.8 28.1 + - - +
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Residues in contact with ALA 924 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A GLY 4.3 4.3 - - - +
799A GLY* 3.5 26.5 - - - +
800A PHE* 3.8 24.2 - - + -
920A GLN 3.1 16.3 + - - +
921A LYS* 3.8 5.8 - - + +
922A LEU 3.3 0.2 - - - -
923A ILE* 1.3 77.2 - - - +
925A ASN* 1.3 65.4 + - - +
927A PHE* 3.4 2.0 + - - +
928A ASN* 3.0 31.6 + - - -
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Residues in contact with ASN 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 LYS* 3.1 24.9 + - - +
922A LEU* 3.6 7.3 - - - +
923A ILE 3.2 0.2 - - - -
924A ALA* 1.3 79.8 - - - +
926A GLN* 1.3 63.3 + - - +
928A ASN* 3.9 7.5 + - - +
929A SER* 3.0 26.0 + - - -
2D NAG 4.4 26.3 + - + +
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Residues in contact with GLN 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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718A PHE* 3.6 14.2 + - - +
719A THR* 3.3 11.4 - - - +
720A ILE* 3.1 43.9 + - + +
922A LEU* 3.0 54.7 + - + +
923A ILE* 5.3 1.1 - - - -
925A ASN* 1.3 75.7 - - - +
927A PHE* 1.3 57.7 + - - +
929A SER* 3.7 4.9 - - - -
930A ALA* 2.9 31.4 + - - +
1D NAG 4.0 17.0 + - - +
2D NAG 4.6 9.6 - - + -
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Residues in contact with PHE 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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720A ILE* 4.0 12.0 - - + +
722A VAL* 4.4 3.4 - - + -
800A PHE* 3.4 30.5 - + + -
801A ASN 4.6 3.6 - - - -
802A PHE* 3.4 39.3 - + - -
805A ILE* 5.6 0.7 - - + -
902A MET* 5.2 0.2 - - + -
923A ILE 2.8 17.7 + - - +
924A ALA 3.6 3.6 - - - +
926A GLN* 1.3 76.5 - - - +
928A ASN* 1.3 72.4 + - - +
930A ALA* 3.0 7.5 + - - +
931A ILE* 2.9 52.0 + - + +
1050A MET* 4.7 4.7 - - - -
1052A PHE* 4.3 8.1 - + - -
1065A VAL* 3.6 42.2 - - + -
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Residues in contact with ASN 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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799A GLY 3.4 19.4 + - - -
800A PHE 3.9 0.2 - - - -
801A ASN* 2.8 44.0 + - + +
924A ALA 3.0 22.0 + - - +
925A ASN* 3.9 8.2 + - - +
927A PHE* 1.3 86.3 - - - +
929A SER* 1.3 57.6 + - - +
931A ILE* 2.9 23.3 + - - +
932A GLY* 2.9 12.8 + - - -
1E NAG 5.4 0.8 + - - -
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Residues in contact with SER 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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925A ASN 3.0 18.1 + - - -
926A GLN* 3.7 4.9 - - - -
928A ASN* 1.3 75.7 - - - +
930A ALA* 1.3 56.8 + - - +
932A GLY* 4.1 2.7 - - - +
933A LYS* 3.3 36.3 + - - +
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Residues in contact with ALA 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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720A ILE 4.6 1.1 - - - +
721A SER* 4.4 9.6 - - - -
722A VAL* 3.3 41.2 - - + +
926A GLN 2.9 18.7 + - - +
927A PHE* 3.3 8.3 - - - +
928A ASN 3.0 0.2 - - - -
929A SER* 1.3 78.5 - - - +
931A ILE* 1.3 64.8 + - - +
932A GLY 3.3 0.2 - - - -
933A LYS* 3.2 19.7 + - - +
934A ILE 3.4 6.2 + - - -
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Residues in contact with ILE 931 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A VAL* 3.8 25.6 - - + -
801A ASN 5.1 9.0 - - - +
804A GLN* 4.3 27.1 - - + +
805A ILE* 4.9 10.3 - - + -
818A ILE* 4.6 10.8 - - + +
927A PHE* 2.9 43.4 + - + +
928A ASN* 2.9 9.6 + - - +
930A ALA* 1.3 75.9 - - - +
932A GLY* 1.3 63.0 + - - +
934A ILE* 3.0 16.8 + - + +
935A GLN* 3.1 10.6 + - - +
1052A PHE* 5.8 1.3 - - + -
1063A LEU* 4.5 19.5 - - + -
1065A VAL* 5.4 1.3 - - + -
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Residues in contact with GLY 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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804A GLN* 4.6 5.6 - - - -
928A ASN 2.9 13.4 + - - -
929A SER* 4.1 2.9 - - - -
931A ILE* 1.3 78.0 - - - +
933A LYS* 1.3 60.8 + - - +
935A GLN* 3.3 17.1 + - - +
936A ASP* 3.1 26.1 + - - -
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Residues in contact with LYS 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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929A SER* 3.3 27.3 + - - +
930A ALA* 3.2 13.6 + - - +
931A ILE 3.2 0.8 - - - -
932A GLY* 1.3 74.9 - - - +
934A ILE* 1.3 58.1 + - + +
936A ASP* 3.1 4.6 + - - +
937A SER* 2.6 38.9 + - - -
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Residues in contact with ILE 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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722A VAL* 3.6 37.0 - - + +
723A THR* 5.3 0.2 - - - -
724A THR* 3.6 36.6 - - + +
818A ILE* 4.9 11.9 - - + -
930A ALA 3.4 1.3 + - - +
931A ILE* 3.0 11.3 + - + +
933A LYS* 1.3 81.1 - - + +
935A GLN* 1.3 64.6 + - - +
937A SER* 4.2 10.1 - - - -
938A LEU* 3.1 39.6 + - + +
1063A LEU* 4.0 16.4 - - + -
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Residues in contact with GLN 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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804A GLN* 2.4 47.7 + - - +
817A PHE* 3.0 38.1 - - + -
818A ILE* 5.2 9.1 - - + +
821A LEU* 3.4 12.6 - - + +
931A ILE 3.1 8.4 + - - +
932A GLY* 3.3 13.0 + - - +
934A ILE* 1.3 76.9 - - - +
936A ASP* 1.3 69.9 + - - +
938A LEU* 5.4 1.1 - - - -
939A SER* 3.2 23.3 + - - -
2E NAG 5.2 4.3 - - - +
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Residues in contact with ASP 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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932A GLY 3.1 13.6 + - - +
933A LYS* 3.8 5.2 - - - +
934A ILE 3.1 0.4 - - - -
935A GLN* 1.3 96.7 + - - +
937A SER* 1.3 65.3 + - - +
938A LEU 3.2 1.6 - - - -
939A SER* 3.3 11.7 + - - -
940A SER* 3.1 21.3 + - - -
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Residues in contact with SER 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 LYS* 2.6 24.0 + - - -
934A ILE* 3.9 13.1 - - - +
936A ASP* 1.3 73.9 - - - +
938A LEU* 1.3 66.6 + - - +
940A SER* 4.8 0.7 - - - -
941A THR* 3.3 32.6 + - - -
944A ALA* 5.3 0.3 - - - +
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Residues in contact with LEU 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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724A THR* 5.0 15.7 - - + +
726A ILE* 5.8 2.0 - - + -
818A ILE* 4.7 8.1 - - + -
821A LEU* 3.5 25.1 - - + -
822A LEU* 4.3 20.4 - - + -
825A LYS* 2.7 38.2 + - + -
934A ILE* 3.1 36.1 + - + +
935A GLN* 5.7 0.4 - - - -
937A SER* 1.3 81.7 - - - +
939A SER* 1.3 54.7 + - - +
940A SER 3.3 0.5 + - - -
941A THR 3.9 2.4 - - - +
944A ALA* 3.7 26.7 - - + +
945A LEU* 4.9 10.8 - - + -
1061A VAL* 5.9 2.7 - - + -
1063A LEU* 6.0 0.4 - - + -
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Residues in contact with SER 939 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821A LEU* 3.8 17.6 - - - +
825A LYS* 4.2 6.7 + - - +
935A GLN* 3.2 20.0 + - - -
936A ASP* 3.3 11.2 + - - -
938A LEU* 1.3 79.4 - - - +
940A SER* 1.3 58.1 + - - +
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Residues in contact with SER 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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825A LYS* 4.7 2.5 + - - -
936A ASP 3.1 16.2 + - - -
937A SER* 4.1 1.0 + - - -
938A LEU 4.4 0.2 - - - -
939A SER* 1.3 81.1 - - - +
941A THR* 1.3 69.0 + - - +
942A ALA* 3.2 4.9 + - - +
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Residues in contact with THR 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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825A LYS* 3.6 9.1 + - - -
937A SER* 3.3 23.8 + - - +
938A LEU 3.9 0.7 - - - +
940A SER* 1.3 78.4 + - - +
942A ALA* 1.3 75.1 + - - +
943A SER* 5.0 1.3 - - - +
944A ALA* 3.4 24.3 - - - +
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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