Contacts of the helix formed by residues 966 - 977 (chain C) in PDB entry 5Y3R
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 PHE 966 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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934C LEU* 3.4 31.9 - - + -
938C VAL* 4.0 12.3 - - + -
959C TYR* 5.6 1.3 - + - -
962C TYR* 3.0 61.9 - + - -
963C LYS* 2.8 13.2 + - + -
965C THR* 1.3 93.6 + - + +
967C PRO* 1.3 72.4 - - + +
968C VAL 3.0 0.7 - - - -
969C LEU* 3.6 22.0 - - + -
970C LEU* 2.9 41.8 + - + +
984C TYR* 6.2 0.7 - + - -
988C VAL* 4.9 11.9 - - + -
1009C LEU* 5.7 2.5 - - + -
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Residues in contact with PRO 967 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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963C LYS 2.9 24.2 - - - +
964C ARG* 2.8 33.0 - - - +
965C THR 2.7 0.4 - - - -
966C PHE* 1.3 78.5 - - + +
968C VAL* 1.3 57.7 + - - +
970C LEU* 4.7 0.6 - - + +
971C ARG* 2.7 46.9 + - + +
1009C LEU* 4.0 12.8 - - + -
1013C ILE* 4.1 27.8 - - + -
1024C THR* 5.9 2.9 - - + -
1027C ASP* 5.2 2.7 - - - +
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Residues in contact with VAL 968 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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917C LEU* 3.9 35.7 - - + +
918C ALA* 6.0 0.2 - - - -
927C LYS* 4.0 4.7 - - - +
964C ARG* 4.3 2.5 - - - +
965C THR* 2.3 43.9 + - - +
967C PRO* 1.3 67.0 - - - +
969C LEU* 1.3 70.8 + - + +
971C ARG* 2.8 27.2 + - + +
972C LEU* 2.9 44.9 + - + +
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Residues in contact with LEU 969 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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917C LEU* 5.3 3.4 - - + -
927C LYS* 4.9 8.3 + - - +
931C CYS* 3.6 20.9 - - + -
934C LEU* 3.5 29.8 - - + -
966C PHE* 3.1 26.4 + - + +
968C VAL* 1.3 88.7 - - + +
970C LEU* 1.3 79.2 + - + +
972C LEU* 4.7 0.7 - - - +
973C ALA* 2.9 28.6 + - - +
980C THR* 3.4 16.4 - - + +
984C TYR* 3.4 39.9 - - + -
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Residues in contact with LEU 970 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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966C PHE* 2.9 38.5 + - + +
967C PRO* 4.7 0.7 - - + +
969C LEU* 1.3 99.7 - - + +
971C ARG* 1.3 70.0 + - - +
973C ALA* 3.9 0.5 - - - +
974C CYS 4.1 0.2 + - - -
981C ARG* 3.0 57.1 - - + +
984C TYR* 3.5 8.3 - - + -
985C GLU* 3.4 33.7 - - + +
988C VAL* 3.7 13.0 - - + -
1026C ARG* 5.1 0.2 + - - -
1031C ARG* 3.1 26.0 - - - +
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Residues in contact with ARG 971 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762C TYR* 5.0 11.1 + - - -
964C ARG* 2.7 48.2 - - - +
967C PRO* 2.7 34.9 + - + +
968C VAL* 2.8 30.9 - - + +
970C LEU* 1.3 82.2 - - - +
972C LEU* 1.3 66.6 + - + +
974C CYS* 3.2 16.6 + - - +
981C ARG* 4.1 3.2 - - - +
1019C ASP* 5.1 16.6 + - - +
1021C VAL* 4.5 24.8 - - + +
1024C THR* 3.5 32.3 - - + +
1026C ARG* 6.2 0.2 - - - +
1027C ASP* 4.6 6.5 - - - +
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Residues in contact with LEU 972 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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724C GLU* 6.1 0.4 - - - +
762C TYR* 5.2 21.1 - - + -
917C LEU 3.5 10.5 - - - +
918C ALA* 5.3 3.6 - - - +
920C THR* 3.9 8.7 - - + -
927C LYS* 3.3 42.6 - - - +
968C VAL* 2.9 24.4 + - + +
971C ARG* 1.3 75.1 - - + +
973C ALA* 1.3 69.0 + - - +
974C CYS* 2.9 3.5 + - - -
975C ASP* 3.0 12.1 + - + +
976C VAL* 3.0 38.3 + - + +
1021C VAL* 6.1 3.4 - - + -
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Residues in contact with ALA 973 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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927C LYS* 6.2 0.4 - - - +
969C LEU 2.9 21.0 + - - +
972C LEU* 1.3 79.5 - - - +
974C CYS* 1.3 58.4 + - - +
976C VAL* 4.0 4.9 - - - -
977C ASP 2.2 42.5 + - - +
980C THR* 3.4 15.3 - - + -
981C ARG* 3.0 37.7 - - + +
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Residues in contact with CYS 974 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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602C MET* 6.1 4.9 - - - -
970C LEU 4.1 2.7 + - - +
971C ARG 3.2 16.5 + - - +
972C LEU* 4.8 0.4 - - - -
973C ALA* 1.3 81.3 - - - +
975C ASP* 1.3 70.0 + - - +
976C VAL 2.9 4.2 + - - +
977C ASP 3.9 2.0 + - - -
978C GLN* 4.3 9.6 + - - +
981C ARG* 4.6 6.8 - - - +
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Residues in contact with ASP 975 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723C ASP* 5.5 0.2 - - - +
724C GLU* 2.8 42.6 - - - +
725C LEU* 3.9 24.2 - - - +
972C LEU* 3.0 11.6 + - + +
974C CYS* 1.3 83.6 - - - +
976C VAL* 1.3 65.1 + - + +
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Residues in contact with VAL 976 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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920C THR* 3.7 20.6 - - + +
923C ASP* 4.9 10.3 - - + +
927C LYS* 5.2 8.1 - - + -
928C VAL* 5.7 4.9 - - + -
972C LEU* 3.0 32.2 + - + +
973C ALA* 2.9 9.9 + - - +
974C CYS 3.7 2.2 - - - +
975C ASP* 1.3 85.9 - - + +
977C ASP* 1.3 87.1 + - + +
978C GLN 4.1 0.7 + - - -
980C THR* 5.0 2.0 - - - +
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Residues in contact with ASP 977 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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928C VAL* 4.4 16.3 - - - +
973C ALA 2.2 35.7 + - - +
976C VAL* 1.3 94.3 - - + +
978C GLN* 1.3 64.9 + - - +
979C VAL* 3.3 18.6 - - + +
980C THR* 2.9 38.9 + - - +
981C ARG* 3.4 5.9 + - - +
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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