Contacts of the helix formed by residues 968 - 980 (chain B) in PDB entry 5J69
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 968 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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834B THR* 3.3 39.2 - - + +
966B ILE* 4.8 1.5 - - - +
967B GLN* 1.3 80.0 + - - +
969B ASN* 1.3 60.4 + - - +
970B GLY 3.4 0.9 - - - +
971B THR* 3.1 29.9 + - + +
972B LYS* 2.9 32.3 + - - +
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Residues in contact with ASN 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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967B GLN 3.1 7.1 + - - +
968B ASP* 1.3 71.5 - - - +
970B GLY* 1.3 59.1 + - - +
972B LYS* 3.0 29.3 + - - +
973B GLU* 2.9 28.8 + - - +
976B LYS* 5.5 0.2 + - - -
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Residues in contact with GLY 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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968B ASP* 3.4 0.8 - - - +
969B ASN* 1.3 76.1 - - - +
971B THR* 1.3 65.1 + - - +
973B GLU* 2.9 18.7 + - - +
974B ALA* 3.0 12.5 + - - +
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Residues in contact with THR 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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833B LEU 4.8 0.9 - - - -
834B THR* 4.6 12.0 - - - +
837B SER* 4.2 21.1 - - - +
966B ILE* 5.4 1.6 - - - +
968B ASP* 3.1 35.6 + - + +
970B GLY* 1.3 75.1 - - - +
972B LYS* 1.3 61.1 + - - +
974B ALA* 3.1 7.6 + - - +
975B PHE* 2.9 62.0 + - - -
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Residues in contact with LYS 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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963B TYR* 3.3 24.5 - - + +
964B THR* 5.3 1.6 - - - -
966B ILE* 3.6 36.3 - - + +
967B GLN 5.2 1.8 - - - -
968B ASP 2.9 18.2 + - - +
969B ASN* 3.0 39.6 + - - +
971B THR* 1.3 77.6 + - - +
973B GLU* 1.3 56.6 + - - +
975B PHE* 3.1 2.0 + - - +
976B LYS* 2.9 59.5 + - + +
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Residues in contact with GLU 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 ASN* 2.9 18.2 + - - +
970B GLY* 2.9 12.8 + - - +
972B LYS* 1.3 76.8 - - - +
974B ALA* 1.3 57.1 + - - +
976B LYS* 3.3 31.5 + - - +
977B SER* 2.9 40.3 + - - -
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Residues in contact with ALA 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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837B SER* 5.7 4.3 - - - +
838B SER 5.5 4.9 - - - +
839B ARG* 6.4 2.0 - - + -
842B LEU* 4.2 2.1 - - + +
970B GLY 3.0 11.7 + - - +
971B THR* 3.1 12.5 + - - +
973B GLU* 1.3 76.5 - - - +
975B PHE* 1.3 64.2 + - + +
977B SER* 2.6 20.4 + - - -
978B ALA* 2.9 18.9 + - - +
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Residues in contact with PHE 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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833B LEU* 3.8 36.6 - - + -
834B THR* 5.5 3.1 - - + -
837B SER* 4.4 12.3 - - - -
838B SER 4.6 4.5 - - - -
842B LEU* 3.4 32.1 - - + -
845B PHE* 6.2 3.4 - + - -
963B TYR* 3.3 32.2 + + + +
966B ILE* 3.4 34.3 - - + -
971B THR* 2.9 49.8 + - - -
972B LYS 3.1 4.2 + - - +
974B ALA* 1.3 80.0 - - + +
976B LYS* 1.3 57.8 + - - +
978B ALA* 2.8 18.9 + - - +
979B LEU 2.9 11.1 + - - -
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Residues in contact with LYS 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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963B TYR* 3.3 21.9 - - + -
972B LYS* 2.9 41.6 + - + +
973B GLU* 3.3 40.7 + - - +
975B PHE* 1.3 76.9 - - - +
977B SER* 1.3 63.8 + - - +
979B LEU* 3.3 23.9 - - + +
980B MET* 3.4 13.7 - - - +
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Residues in contact with SER 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 GLU* 2.9 28.1 + - - +
974B ALA* 2.6 26.2 + - - -
976B LYS* 1.3 77.7 - - - +
978B ALA* 1.3 58.8 + - - +
980B MET* 4.0 8.2 + - - +
981B SER* 4.0 14.2 + - - -
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Residues in contact with ALA 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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839B ARG* 5.5 9.6 - - + +
842B LEU* 3.5 22.2 - - + -
843B LEU* 5.6 2.9 - - - +
963B TYR* 5.5 0.2 - - - +
974B ALA 2.9 11.2 + - - +
975B PHE 2.8 11.2 + - - +
977B SER* 1.3 77.0 - - - +
979B LEU* 1.3 61.7 + - - +
980B MET 3.2 1.8 - - - -
981B SER* 2.8 23.6 + - - +
982B SER* 3.5 8.1 + - - -
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Residues in contact with LEU 979 (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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846B ILE* 5.9 7.6 - - + -
851B SER* 5.8 9.2 - - - +
852B HIS* 6.0 6.5 - - + -
963B TYR* 3.4 37.6 + - + +
975B PHE 2.9 9.4 + - - +
976B LYS* 3.3 15.0 - - + +
978B ALA* 1.3 76.2 - - - +
980B MET* 1.3 86.9 + - + +
982B SER* 2.6 26.6 + - - +
1001B NAG 4.4 15.7 - - + -
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Residues in contact with MET 980 (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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976B LYS 3.4 17.9 + - - +
977B SER* 4.2 8.1 - - - +
978B ALA 3.2 0.6 - - - -
979B LEU* 1.3 95.9 - - + +
981B SER* 1.3 59.0 + - - +
982B SER 3.5 6.8 - - - +
1001B NAG 4.4 15.7 - - + -
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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