Contacts of the helix formed by residues 966 - 974 (chain B) in PDB entry 2A73
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 ALA 966 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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961B GLN* 3.4 15.8 - - + +
963B THR* 3.3 22.0 + - - +
965B VAL* 1.3 78.5 - - - +
967B GLN* 1.3 57.9 + - - +
968B MET 3.1 2.9 - - - +
969B THR* 3.8 6.8 - - - +
970B GLU* 2.8 43.3 + - - +
1295B SER 5.0 1.3 - - - +
1296B LEU* 4.4 15.5 - - + +
1297B LEU* 4.2 9.6 - - + -
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Residues in contact with GLN 967 (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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957B ARG* 6.0 1.1 - - - +
959B LEU* 4.9 15.3 - - + -
961B GLN* 3.1 21.3 - - + +
966B ALA* 1.3 76.5 - - - +
968B MET* 1.3 63.0 + - - +
970B GLU* 3.4 0.7 + - - +
971B ASP* 2.8 60.5 + - - +
980B HIS 4.1 10.5 + - - -
981B LEU* 3.8 21.0 - - - +
1238B ARG* 4.0 10.4 + - - -
1242B GLY 3.6 20.4 - - - +
1243B GLY* 4.9 4.1 - - - -
1297B LEU* 3.9 17.6 - - + +
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Residues in contact with MET 968 (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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964B PRO 3.8 21.5 - - - +
965B VAL* 3.8 21.3 - - + -
966B ALA 3.1 1.4 - - - +
967B GLN* 1.3 85.7 - - - +
969B THR* 1.3 57.6 + - - +
971B ASP* 3.0 1.4 + - - +
972B ALA* 2.7 36.2 + - - +
981B LEU* 3.8 22.8 - - + +
1238B ARG* 4.6 4.5 - - - +
1244B TYR* 4.1 28.7 - - + -
1250B THR* 4.2 17.0 - - - +
1254B PHE* 3.9 44.2 - - + +
1257B LEU* 4.5 5.4 - - + -
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Residues in contact with THR 969 (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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965B VAL* 3.0 26.2 - - - +
966B ALA* 3.3 11.2 + - - +
968B MET* 1.3 78.5 - - - +
970B GLU* 1.3 65.5 + - - +
971B ASP 3.2 0.2 + - - -
972B ALA* 3.5 1.0 + - - +
973B VAL* 3.4 23.5 + - + +
1002B ALA* 4.5 6.0 - - + +
1005B TYR* 3.4 17.3 - - + -
1006B LEU* 3.9 36.8 - - + -
1015B PHE* 4.9 9.0 - - + -
1254B PHE* 3.8 10.3 - - - -
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Residues in contact with GLU 970 (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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966B ALA* 2.8 22.5 + - - +
967B GLN 3.5 5.6 - - - +
969B THR* 1.3 77.5 - - - +
971B ASP* 1.3 65.9 + - - +
973B VAL* 3.7 4.0 + - - +
974B ASP* 3.6 20.3 + - - +
977B ARG* 4.4 12.4 + - - +
1015B PHE* 4.2 28.1 - - + -
1019B LYS* 5.2 3.2 + - - +
1294B ALA 5.2 0.9 - - - +
1295B SER* 3.4 30.3 - - - +
1297B LEU* 3.4 26.0 - - + +
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Residues in contact with ASP 971 (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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967B GLN* 2.8 50.0 + - - +
968B MET 3.0 3.1 + - - +
970B GLU* 1.3 80.7 - - - +
972B ALA* 1.3 67.1 + - - +
973B VAL 3.0 2.7 + - - -
974B ASP 3.0 21.8 + - - +
977B ARG* 3.1 43.3 - - - +
978B LEU* 3.5 9.1 + - - -
980B HIS* 3.9 14.2 - - - +
981B LEU* 4.1 13.2 - - + +
1297B LEU* 5.9 0.2 - - - +
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Residues in contact with ALA 972 (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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968B MET 2.7 20.3 + - - +
971B ASP* 1.3 72.2 - - - +
973B VAL* 1.3 60.2 + - - +
978B LEU* 3.9 13.1 - - - +
981B LEU* 4.2 2.2 - - + +
998B PRO* 3.6 26.5 - - + -
999B THR* 2.9 29.1 + - - +
1002B ALA* 3.6 25.8 - - + -
1026B LEU* 3.8 4.7 - - - +
1254B PHE* 4.0 4.0 - - + -
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Residues in contact with VAL 973 (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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969B THR 3.4 17.0 + - - +
970B GLU 3.9 4.5 - - - +
971B ASP 3.0 0.6 - - - -
972B ALA* 1.3 80.4 - - - +
974B ASP* 1.3 66.5 + - - +
975B ALA 3.9 0.3 + - - -
999B THR* 4.7 0.4 - - + -
1002B ALA* 4.8 8.7 - - + -
1003B VAL* 5.4 2.2 - - + -
1006B LEU* 4.3 7.6 - - + -
1012B TRP* 4.3 15.5 - - + -
1015B PHE* 4.1 21.5 - - + -
1019B LYS* 3.9 37.5 - - + +
1022B GLY 4.7 1.7 - - - -
1023B ALA* 4.0 19.2 + - + -
1026B LEU* 3.4 15.3 - - - +
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Residues in contact with ASP 974 (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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970B GLU 3.6 11.2 + - - +
971B ASP 3.0 17.0 + - - +
973B VAL* 1.3 88.1 - - - +
975B ALA* 1.3 65.6 + - - +
976B GLU* 4.7 5.9 + - - +
977B ARG* 4.0 28.9 + - + +
978B LEU* 3.2 13.9 + - - +
1019B LYS* 5.3 9.2 - - - +
1026B LEU* 3.8 2.3 - - - +
5D BMA 4.2 14.9 + - - -
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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