Contacts of the helix formed by residues 922 - 937 (chain A) in PDB entry 1HU3
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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886A ARG* 4.2 21.8 - - - +
890A ILE* 5.7 0.3 - - - +
920A ASN* 3.2 11.4 - - + +
921A HIS* 1.3 80.8 + - - +
923A GLU* 1.3 68.3 + - - +
924A GLU* 3.3 28.9 + - - +
925A SER* 2.6 29.4 + - - -
926A LEU* 2.9 20.0 + - - +
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Residues in contact with GLU 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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921A HIS 4.0 0.4 + - - -
922A ASP* 1.3 73.0 - - - +
924A GLU* 1.3 59.5 + - + +
926A LEU* 3.1 5.6 + - + +
927A GLU* 2.8 31.8 + - - +
965A THR* 6.0 4.0 - - + +
966A SER* 3.6 28.1 + - - +
968A ARG* 3.2 20.0 + - - +
969A ILE* 3.4 25.1 - - + +
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Residues in contact with GLU 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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887A ARG* 5.2 9.8 - - - +
890A ILE* 4.4 29.0 - - + +
922A ASP* 3.3 13.9 + - - +
923A GLU* 1.3 78.1 - - + +
925A SER* 1.3 61.8 + - - +
927A GLU* 4.0 6.1 - - - +
928A CYS* 3.0 24.3 + - - +
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Residues in contact with SER 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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886A ARG* 4.9 1.4 - - - +
890A ILE* 3.6 19.9 - - - +
917A LEU* 3.6 16.3 - - - +
920A ASN* 3.1 37.9 + - - -
922A ASP* 2.6 28.1 + - - -
924A GLU* 1.3 77.1 - - - +
926A LEU* 1.3 58.6 + - - +
928A CYS* 3.2 4.7 + - - +
929A LEU* 2.9 28.1 + - - +
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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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917A LEU 4.7 6.1 - - - +
918A LEU* 4.9 2.0 - - + -
921A HIS* 3.9 26.7 - - - +
922A ASP 2.9 15.9 + - - +
923A GLU* 3.5 7.0 - - - +
925A SER* 1.3 77.0 - - - +
927A GLU* 1.3 58.3 + - - +
929A LEU* 3.1 22.6 + - + +
930A CYS* 2.8 32.5 + - - -
959A ILE* 4.0 31.6 - - + -
965A THR* 3.9 17.0 - - + -
969A ILE* 3.5 31.9 - - + -
973A LEU* 4.3 7.9 - - + -
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Residues in contact with GLU 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 GLU 2.8 20.7 + - - +
924A GLU* 4.0 5.1 - - - +
926A LEU* 1.3 69.4 - - - +
928A CYS* 1.3 61.1 + - - +
930A CYS* 3.2 1.5 + - - +
931A ARG* 2.9 62.3 + - - +
968A ARG* 2.4 37.5 + - - -
969A ILE* 4.2 3.1 - - + +
972A MSE 3.5 29.6 - - + +
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Residues in contact with CYS 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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890A ILE* 4.1 27.1 - - + -
893A ILE* 4.3 16.2 - - - -
894A LYS* 5.3 4.7 - - - -
917A LEU* 3.8 24.7 - - + -
924A GLU 3.0 14.8 + - - +
925A SER 3.3 9.2 - - - +
927A GLU* 1.3 76.3 - - - +
929A LEU* 1.3 58.1 + - - +
931A ARG* 3.9 7.4 - - - +
932A LEU* 2.8 34.1 + - - +
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Residues in contact with LEU 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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914A VAL* 3.9 25.8 - - + +
917A LEU* 3.6 26.7 - - + +
918A LEU* 3.7 32.3 - - + -
925A SER 2.9 12.8 + - - +
926A LEU* 3.1 22.2 + - + +
928A CYS* 1.3 77.4 - - - +
930A CYS* 1.3 58.5 + - - +
932A LEU* 4.3 1.6 - - + -
933A LEU* 2.8 54.4 + - + +
956A MSE 4.3 17.3 - - + -
973A LEU* 4.9 4.0 - - + -
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Residues in contact with CYS 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* 2.8 21.3 + - - +
927A GLU* 3.6 5.2 - - - +
929A LEU* 1.3 74.6 - - - +
931A ARG* 1.3 58.9 + - - +
933A LEU* 5.0 0.2 - - - -
934A THR* 2.6 39.0 + - - -
956A MSE 6.1 0.7 - - - -
969A ILE* 5.7 0.4 - - - -
972A MSE 3.7 25.8 - - + -
973A LEU* 3.7 44.6 - - - -
976A VAL* 3.8 22.5 - - + +
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Residues in contact with ARG 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 GLU* 2.9 52.6 + - + +
928A CYS* 3.9 5.2 - - - +
930A CYS* 1.3 72.1 - - - +
932A LEU* 1.3 70.1 + - - +
934A THR* 3.3 5.6 + - - -
935A THR* 3.1 23.6 + - - -
972A MSE 4.3 10.0 - - + +
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Residues in contact with LEU 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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893A ILE* 4.5 11.4 - - + +
894A LYS* 6.1 1.3 - - - -
897A GLY* 4.5 11.4 - - - -
901A LYS* 6.4 2.0 - - - -
910A MSE 3.6 26.2 - - + +
913A CYS* 4.4 15.9 - - + -
914A VAL* 4.3 21.5 - - + -
917A LEU* 4.1 21.5 - - + -
928A CYS* 2.8 20.4 + - - +
929A LEU* 3.7 3.4 - - + +
931A ARG* 1.3 74.9 - - - +
933A LEU* 1.3 64.1 + - + +
935A THR* 2.9 17.0 + - + -
936A ILE* 2.9 28.9 + - + +
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Residues in contact with LEU 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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914A VAL* 4.1 22.4 - - + -
929A LEU* 2.8 42.0 + - + +
932A LEU* 1.3 73.4 - - + +
934A THR* 1.3 59.5 + - - +
936A ILE* 4.6 0.9 - - + -
937A GLY* 2.7 42.0 + - - +
940A LEU* 4.6 7.9 - - + -
949A MSE 4.5 18.6 - - - -
952A TYR* 5.4 0.4 - - + -
953A PHE* 3.8 10.3 - - + -
956A MSE 3.5 38.8 - - + -
976A VAL* 3.8 16.4 - - + -
984A TRP* 3.4 6.2 - - - -
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Residues in contact with THR 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 CYS* 2.6 26.7 + - - +
931A ARG* 3.7 6.3 - - - -
932A LEU 3.0 0.4 + - - -
933A LEU* 1.3 78.0 - - - +
935A THR* 1.3 65.3 + - - +
937A GLY 4.4 0.9 + - - -
975A ASP* 6.1 0.3 - - - +
976A VAL* 3.9 14.3 - - - +
979A LEU* 4.1 27.3 - - + +
984A TRP* 5.0 2.3 - - - -
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Residues in contact with THR 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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901A LYS* 3.7 32.2 + - + +
931A ARG 3.1 14.0 + - - -
932A LEU* 2.9 5.3 + - + -
934A THR* 1.3 84.0 - - - +
936A ILE* 1.3 72.0 + - + +
939A ASP* 4.5 4.7 - - - +
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Residues in contact with ILE 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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900A PHE* 3.9 24.5 - - + -
901A LYS* 4.1 12.6 - - + -
910A MSE 3.0 41.3 - - + -
932A LEU* 2.9 33.7 + - + +
933A LEU* 4.6 1.6 - - - -
935A THR* 1.3 90.1 - - + +
937A GLY* 1.3 69.0 + - - +
938A LYS* 3.4 2.9 - - - -
939A ASP* 3.0 23.4 + - - +
940A LEU* 3.1 38.1 + - + +
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Residues in contact with GLY 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 LEU* 2.7 38.0 + - - -
934A THR 4.4 1.0 + - - -
935A THR 3.6 0.8 - - - -
936A ILE* 1.3 78.2 - - - +
938A LYS* 1.3 57.7 + - - +
940A LEU* 3.2 4.9 + - - +
941A ASP* 2.9 26.3 + - - +
949A MSE 4.8 2.1 - - - +
984A TRP* 3.6 20.8 - - - -
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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