Contacts of the helix formed by residues 961 - 980 (chain B) in PDB entry 3O33
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 LYS 961 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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900B LEU* 3.3 11.7 - - - +
960B SER* 1.3 84.8 + - - +
962B PRO* 1.3 77.3 - - + +
963B GLU* 3.9 26.7 - - - +
964B ASP* 2.9 50.8 + - - +
965B PHE* 3.9 1.6 + - - -
872C ASP* 3.3 29.8 + - - +
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Residues in contact with PRO 962 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900B LEU* 3.7 2.7 - - + -
904B ASP* 3.7 33.9 - - + +
961B LYS* 1.3 88.5 - - + +
963B GLU* 1.3 72.9 - - - +
964B ASP 2.9 1.4 + - - -
965B PHE* 3.1 18.3 + - + -
966B VAL* 3.0 28.0 + - + +
1005B TYR* 3.7 27.4 - - + +
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Residues in contact with GLU 963 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961B LYS* 3.2 26.7 + - - +
962B PRO* 1.3 90.5 - - - +
964B ASP* 1.3 61.2 - - - +
965B PHE 3.5 0.2 - - - -
966B VAL* 3.8 9.3 - - + +
967B ALA* 3.1 24.3 + - - +
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Residues in contact with ASP 964 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958B MET* 3.9 6.3 - - + +
959B TYR* 3.8 27.0 - - + -
960B SER* 2.8 37.4 + - - -
961B LYS* 2.9 39.8 + - - +
963B GLU* 1.3 80.6 - - - +
965B PHE* 1.3 60.9 + - - +
967B ALA* 3.6 9.8 + - - +
968B ASP* 3.6 10.0 + - - +
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Residues in contact with PHE 965 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900B LEU* 3.9 25.6 - - + -
904B ASP 3.8 10.5 - - - -
908B CYS* 3.5 46.4 - - + -
911B LEU* 4.0 15.9 - - + -
948B ILE* 4.7 2.5 - - + -
959B TYR* 3.8 26.2 - + + -
961B LYS 4.2 0.2 - - - -
962B PRO* 3.4 27.4 - - + -
964B ASP* 1.3 76.7 - - - +
966B VAL* 1.3 94.0 + - + +
967B ALA 3.2 0.2 - - - -
968B ASP* 3.1 3.9 + - - +
969B PHE* 3.1 30.8 + + - -
1005B TYR* 3.5 25.8 - + - -
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Residues in contact with VAL 966 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962B PRO* 3.0 26.6 + - + +
963B GLU* 3.9 9.4 - - + +
965B PHE* 1.3 93.6 - - + +
967B ALA* 1.3 61.8 + - - +
969B PHE* 3.2 8.1 + - - +
970B ARG* 3.0 57.2 + - - +
997B PHE* 4.3 5.2 - - + -
1001B LEU* 3.7 32.5 - - + -
1005B TYR* 5.3 2.0 - - + -
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Residues in contact with ALA 967 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963B GLU 3.1 18.8 + - - +
964B ASP* 3.7 7.2 - - - +
965B PHE 3.2 0.2 - - - -
966B VAL* 1.3 78.8 - - - +
968B ASP* 1.3 59.6 + - - +
970B ARG* 3.5 7.5 + - - +
971B LEU* 3.0 28.1 + - - +
974B GLN* 4.8 2.3 + - - -
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Residues in contact with ASP 968 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943B MET* 3.2 40.7 - - - +
948B ILE* 3.8 13.5 - - + -
951B ARG* 2.9 23.0 + - - -
958B MET* 5.2 1.7 - - - +
959B TYR* 2.6 36.7 + - - +
964B ASP 3.6 5.2 + - - +
965B PHE 3.1 8.4 + - - +
967B ALA* 1.3 79.6 - - - +
969B PHE* 1.3 65.0 + - - +
971B LEU* 3.2 17.1 + - - +
972B ILE* 3.3 2.8 + - - +
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Residues in contact with PHE 969 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908B CYS* 3.9 22.4 - - - -
911B LEU* 3.9 17.3 - - + -
912B LEU* 3.4 41.3 - - + -
915B LEU* 3.5 35.2 - - + -
945B LEU* 3.9 6.3 - - + -
948B ILE* 3.6 14.1 - - + +
965B PHE* 3.1 32.4 + + - -
966B VAL 3.2 7.2 + - - +
968B ASP* 1.3 73.9 - - - +
970B ARG* 1.3 62.6 - - - +
972B ILE* 3.1 22.9 + - + +
973B PHE* 3.3 12.8 - - + -
997B PHE* 3.4 33.2 - + + -
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Residues in contact with ARG 970 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
966B VAL* 3.0 33.7 + - - +
967B ALA* 3.9 6.8 - - - +
969B PHE* 1.3 73.8 - - - +
971B LEU* 1.3 60.7 + - - +
973B PHE* 3.2 11.7 + - + +
974B GLN* 2.9 44.7 + - + +
994B GLU* 5.4 4.9 - - - +
997B PHE* 4.1 8.5 - - + -
998B GLU* 3.0 43.2 + - - +
1001B LEU* 3.8 12.9 - - - +
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Residues in contact with LEU 971 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941B ASN* 3.4 42.0 - - + +
942B PRO 4.5 0.2 - - - +
943B MET* 3.8 26.5 - - + -
967B ALA 3.0 14.6 + - - +
968B ASP* 3.2 17.2 + - - +
970B ARG* 1.3 77.0 - - - +
972B ILE* 1.3 57.7 + - - +
974B GLN* 3.8 18.4 - - + +
975B ASN* 2.9 47.4 + - - +
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Residues in contact with ILE 972 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924B PHE* 3.9 35.0 - - + +
943B MET* 3.6 30.3 - - + +
944B ASP 3.6 24.2 - - - -
945B LEU* 3.7 18.2 - - + +
948B ILE* 3.8 18.4 - - + -
968B ASP 3.5 9.9 - - - +
969B PHE* 3.1 13.7 + - + +
971B LEU* 1.3 79.1 - - - +
973B PHE* 1.3 72.4 + - + +
975B ASN* 3.9 4.0 - - - +
976B CYS* 3.2 21.1 + - - +
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Residues in contact with PHE 973 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915B LEU* 4.2 15.0 - - + -
924B PHE* 5.6 2.0 - + - -
969B PHE* 3.3 23.6 - + + -
970B ARG* 3.2 13.8 + - + +
972B ILE* 1.3 88.2 - - + +
974B GLN* 1.3 65.8 + - + +
976B CYS* 3.4 5.9 + - - +
977B ALA* 3.1 24.8 + - - +
990B GLY* 3.7 20.5 - - - +
993B LEU* 3.7 26.9 - - + -
994B GLU* 3.6 58.3 - - + +
997B PHE* 3.9 29.2 - + + -
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Residues in contact with GLN 974 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967B ALA 4.8 2.2 + - - -
970B ARG* 2.9 41.2 + - + +
971B LEU* 3.3 21.7 + - + +
973B PHE* 1.3 73.2 - - + +
975B ASN* 1.3 62.4 + - - +
977B ALA* 3.4 5.3 + - - +
978B GLU* 2.9 34.1 + - - +
994B GLU* 6.1 1.1 - - - +
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Residues in contact with ASN 975 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935B TYR* 3.6 18.3 + - - +
939B ILE* 3.4 26.8 - - + +
941B ASN* 2.9 24.5 + - - +
942B PRO* 3.5 14.3 - - - +
943B MET* 3.5 10.6 + - - +
971B LEU* 2.9 34.5 + - - +
972B ILE* 3.9 4.3 - - - +
974B GLN* 1.3 78.0 - - - +
976B CYS* 1.3 58.0 + - - +
978B GLU* 3.6 1.8 - - - +
979B PHE* 2.9 34.8 + - - +
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Residues in contact with CYS 976 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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924B PHE* 3.5 29.4 - - + -
935B TYR* 5.5 1.3 - - - -
972B ILE 3.2 12.4 + - - +
973B PHE* 3.5 12.1 - - - +
975B ASN* 1.3 78.9 - - - +
977B ALA* 1.3 57.6 + - - +
980B ASN* 3.0 51.1 + - - +
986B VAL* 3.5 25.4 - - - -
987B ALA* 4.0 8.5 - - - -
990B GLY* 3.7 11.2 - - - -
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Residues in contact with ALA 977 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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973B PHE 3.1 14.0 + - - +
974B GLN* 4.0 5.2 - - - +
976B CYS* 1.3 81.5 - - - +
978B GLU* 1.3 62.0 + - - +
980B ASN 3.6 12.7 - - - +
987B ALA* 5.6 5.4 - - - +
991B ILE* 6.1 5.4 - - + -
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Residues in contact with GLU 978 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938B ILE* 4.5 15.0 - - + +
939B ILE* 4.0 17.7 - - + -
974B GLN* 2.9 20.7 + - - +
975B ASN* 3.6 4.8 - - - +
977B ALA* 1.3 80.4 - - - +
979B PHE* 1.3 60.5 + - - +
980B ASN 4.7 0.9 - - - +
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Residues in contact with PHE 979 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932B VAL* 3.5 33.7 - - + -
933B PRO 3.6 13.2 - - - -
934B ASP* 4.1 4.9 - - + -
935B TYR* 3.4 46.4 - + + -
938B ILE* 4.3 21.3 - - + -
939B ILE* 4.2 6.7 - - + -
975B ASN 2.9 16.3 + - - +
976B CYS 4.5 0.2 - - - +
978B GLU* 1.3 79.5 - - - +
980B ASN* 1.3 85.2 + - - +
981B GLU* 3.9 8.1 + - - +
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Residues in contact with ASN 980 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
935B TYR* 5.6 1.0 - - - -
976B CYS* 3.0 30.6 + - - +
977B ALA 3.6 14.2 - - - +
978B GLU 4.7 0.9 - - - +
979B PHE* 1.3 101.7 - - - +
981B GLU* 1.3 65.8 + - - +
982B PRO* 3.5 4.2 - - - +
984B SER* 3.7 14.3 + - - +
986B VAL* 3.4 36.3 - - - +
987B ALA* 4.1 11.0 - - + +
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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
------------------------------------------------------------
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