Contacts of the helix formed by residues 966 - 982 (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 SER 966 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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923A GLU* 3.6 22.4 + - - +
965A THR* 1.3 76.1 + - - +
967A SER* 1.3 64.1 + - - +
968A ARG* 2.9 13.0 - - - +
969A ILE* 3.1 29.5 + - - +
970A ARG* 3.0 19.4 + - - +
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Residues in contact with SER 967 (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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963A ARG* 5.3 0.7 - - - -
965A THR 3.6 1.2 + - - -
966A SER* 1.3 72.4 - - - +
968A ARG* 1.3 60.6 + - - +
970A ARG* 3.4 31.3 - - - +
971A PHE* 2.8 50.8 + - - -
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Residues in contact with ARG 968 (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* 3.2 25.4 + - - +
927A GLU* 2.4 44.1 + - - -
966A SER* 2.9 10.7 - - - +
967A SER* 1.3 82.2 + - - +
969A ILE* 1.3 80.1 + - - +
971A PHE* 2.9 20.0 + - - +
972A MSE 2.9 23.3 + - + +
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Residues in contact with ILE 969 (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* 3.4 40.2 - - + +
926A LEU* 3.5 33.4 - - + -
927A GLU* 4.2 7.2 - - + +
930A CYS* 5.7 0.4 - - - -
965A THR* 4.6 7.2 - - - -
966A SER* 3.1 21.0 + - - +
968A ARG* 1.3 99.9 - - - +
970A ARG* 1.3 57.1 + - - +
972A MSE 3.6 20.8 - - + +
973A LEU* 2.8 37.5 + - + +
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Residues in contact with ARG 970 (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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960A VAL* 3.4 50.4 + - + -
963A ARG* 2.8 67.7 + - - +
965A THR* 2.5 37.1 + - - +
966A SER 3.0 9.5 + - - +
967A SER* 3.4 36.5 - - - +
968A ARG 3.0 0.2 - - - -
969A ILE* 1.3 78.4 - - - +
971A PHE* 1.3 59.3 + - + +
973A LEU* 3.8 9.0 - - - +
974A GLN* 3.0 37.5 + - + +
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Residues in contact with PHE 971 (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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967A SER* 2.8 38.4 + - - -
968A ARG* 2.9 9.2 + - - +
970A ARG* 1.3 75.4 - - + +
972A MSE 1.3 66.3 + - - +
974A GLN* 3.3 20.7 + - + +
975A ASP* 3.0 28.9 + - - +
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Residues in contact with MSE 972 (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* 3.5 47.1 - - + +
930A CYS* 3.7 27.1 - - + +
931A ARG* 4.3 13.2 - - + +
968A ARG* 2.9 32.1 + - + +
969A ILE* 3.6 20.9 - - - +
971A PHE* 1.3 77.6 - - - +
973A LEU* 1.3 63.7 + - - +
975A ASP* 3.0 22.6 + - - +
976A VAL* 3.3 11.4 + - - +
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Residues in contact with LEU 973 (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* 4.3 15.5 - - + -
929A LEU* 4.9 3.1 - - + -
930A CYS* 3.7 19.7 - - - -
956A MSE 4.2 30.2 - - + +
959A ILE* 3.6 33.2 - - + -
960A VAL* 3.8 20.6 - - + -
965A THR* 5.1 1.1 - - - +
969A ILE* 2.8 44.2 + - + +
970A ARG* 3.8 6.3 - - - +
972A MSE 1.3 72.3 - - - +
974A GLN* 1.3 60.4 + - - +
975A ASP 3.1 0.6 + - - -
976A VAL* 3.1 5.9 + - - +
977A ILE* 3.1 28.8 + - + +
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Residues in contact with GLN 974 (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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960A VAL* 4.1 27.3 - - + +
970A ARG* 3.0 28.5 + - - +
971A PHE* 3.6 24.8 - - + +
972A MSE 3.3 0.2 - - - -
973A LEU* 1.3 75.9 - - - +
975A ASP* 1.3 58.4 + - - +
977A ILE* 3.8 12.0 - - + +
978A ASP* 2.9 40.3 + - - +
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Residues in contact with ASP 975 (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 THR* 6.1 0.2 - - - +
971A PHE* 3.0 14.5 + - - +
972A MSE 3.0 16.1 + - - +
974A GLN* 1.3 77.3 - - - +
976A VAL* 1.3 61.5 + - + +
978A ASP* 3.2 11.8 + - - +
979A LEU* 2.9 30.0 + - - +
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Residues in contact with VAL 976 (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* 3.8 28.3 - - + -
933A LEU* 3.8 33.0 - - + -
934A THR* 3.9 18.8 - - - +
953A PHE* 3.6 22.1 - - + -
956A MSE 5.1 5.8 - - - -
972A MSE 3.5 13.9 - - - +
973A LEU* 3.1 4.8 + - - +
975A ASP* 1.3 77.2 - - + +
977A ILE* 1.3 63.4 - - - +
979A LEU* 3.3 7.6 - - + +
980A ARG* 3.1 18.7 + - - +
984A TRP* 4.4 9.2 - - + -
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Residues in contact with ILE 977 (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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953A PHE* 4.2 28.3 - - + +
956A MSE 4.4 11.0 - - + -
957A GLU* 4.0 40.2 - - + +
960A VAL* 4.5 5.8 - - + -
973A LEU 3.1 21.4 + - - +
974A GLN* 3.9 11.0 - - + +
976A VAL* 1.3 75.8 - - - +
978A ASP* 1.3 66.6 + - - +
980A ARG* 4.0 0.9 - - - +
981A LEU* 3.1 41.6 + - + +
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Residues in contact with ASP 978 (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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974A GLN* 2.9 30.8 + - - +
975A ASP* 3.2 13.0 + - - +
977A ILE* 1.3 80.9 - - - +
979A LEU* 1.3 62.2 + - - +
981A LEU* 3.3 12.6 + - - +
982A CYS* 3.0 30.4 + - - +
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Residues in contact with LEU 979 (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 THR* 4.1 35.0 - - + +
975A ASP 2.9 13.5 + - - +
976A VAL* 3.3 12.6 - - - +
978A ASP* 1.3 74.3 - - - +
980A ARG* 1.3 55.8 + - - +
982A CYS* 2.7 28.0 + - - +
984A TRP* 3.0 62.3 + - + +
985A VAL 3.7 18.6 - - - +
986A SER* 4.5 8.1 - - - +
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Residues in contact with ARG 980 (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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941A ASP* 3.5 18.3 + - - +
946A LYS* 3.5 10.1 + - - +
949A MSE 3.6 10.8 - - - +
950A ASP* 2.4 54.4 + - - +
953A PHE* 3.6 40.7 - - + +
954A ASN* 5.6 0.8 + - - -
976A VAL 3.1 11.5 + - - +
977A ILE 4.0 2.7 - - - +
979A LEU* 1.3 73.3 - - - +
981A LEU* 1.3 58.5 + - - +
982A CYS 2.7 5.4 + - - -
983A ASN* 2.6 29.1 + - - +
984A TRP* 3.3 35.8 - - + +
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Residues in contact with LEU 981 (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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977A ILE* 3.1 36.4 + - + +
978A ASP* 3.6 11.7 - - - +
980A ARG* 1.3 81.9 - - + +
982A CYS* 1.3 58.5 + - - +
983A ASN* 3.3 8.1 + - - +
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Residues in contact with CYS 982 (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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978A ASP* 3.0 19.5 + - - +
979A LEU* 2.7 12.4 + - - +
980A ARG 2.7 0.4 + - - -
981A LEU* 1.3 81.1 - - - +
983A ASN* 1.3 76.5 + - - +
984A TRP 3.2 1.8 - - - -
985A VAL* 3.1 31.5 + - - +
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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
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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