Contacts of the helix formed by residues 971 - 980 (chain B) in PDB entry 4Q0W
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 PRO 971 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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965B LYS* 4.3 15.0 - - - +
969B GLY 3.4 8.7 - - - +
970B TRP* 1.3 88.0 - - + +
972B HIS* 1.3 65.0 + - - +
973B GLU* 4.3 17.9 - - + +
974B LYS* 3.1 27.3 + - + +
975B SER* 3.3 10.3 + - - -
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Residues in contact with HIS 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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958B ASP 5.5 0.9 - - - -
961B ARG* 3.8 65.1 + - + +
962B SER* 4.1 9.8 + - - -
965B LYS* 4.3 22.0 - - + +
970B TRP 4.6 0.2 - - - -
971B PRO* 1.3 73.0 - - - +
973B GLU* 1.3 57.9 + - - +
975B SER* 3.2 4.7 + - - -
976B ASP* 2.8 35.2 + - - +
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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
----------------------------------------------------------
971B PRO* 4.3 13.7 - - + -
972B HIS* 1.3 77.7 - - - +
974B LYS* 1.3 65.1 + - + +
976B ASP* 3.3 12.2 + - - +
977B GLU* 3.1 22.7 + - - +
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Residues in contact with LYS 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 TRP* 3.6 53.9 - - + +
971B PRO* 3.1 27.2 + - + +
973B GLU* 1.3 80.6 - - + +
975B SER* 1.3 65.6 + - - +
977B GLU* 3.3 23.5 + - - +
978B ILE* 3.7 14.0 + - + +
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Residues in contact with SER 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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961B ARG* 4.4 19.6 + - - -
964B MET* 3.5 17.4 - - - +
970B TRP* 3.5 27.1 - - - +
971B PRO 3.3 8.5 + - - -
972B HIS 3.2 9.3 + - - -
974B LYS* 1.3 77.9 - - - +
976B ASP* 1.3 58.5 + - - +
978B ILE* 3.1 4.7 + - - +
979B LEU* 2.9 47.4 + - - +
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Residues in contact with ASP 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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957B LEU* 3.5 11.9 - - - +
961B ARG* 2.7 48.2 + - - +
972B HIS* 2.8 22.3 + - - +
973B GLU* 3.4 10.8 - - - +
975B SER* 1.3 73.9 - - - +
977B GLU* 1.3 65.9 + - - +
979B LEU 4.3 0.7 - - - +
980B ILE* 2.9 53.3 + - + +
981B PRO* 3.9 0.2 - - - +
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Residues in contact with GLU 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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67B TYR* 4.2 1.6 + - - -
973B GLU 3.1 12.5 + - - +
974B LYS* 3.6 15.5 - - - +
975B SER 3.2 0.6 - - - -
976B ASP* 1.3 76.8 - - - +
978B ILE* 1.3 64.8 + - + +
981B PRO* 3.6 15.1 - - - +
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Residues in contact with ILE 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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59B PHE* 4.0 9.4 - - + -
63B CYS* 3.7 31.4 - - + -
67B TYR* 2.5 39.7 + - + +
970B TRP* 3.5 36.6 - - + -
974B LYS* 4.0 15.5 - - + +
975B SER 3.1 5.1 + - - +
976B ASP 3.1 0.4 - - - -
977B GLU* 1.3 82.8 - - + +
979B LEU* 1.3 58.4 + - - +
981B PRO* 3.4 7.5 - - - +
982B LEU* 4.4 0.2 - - - +
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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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59B PHE* 3.9 21.3 - - + -
63B CYS* 4.4 3.4 - - - -
782B PHE* 3.6 35.4 - - + -
955B PRO* 5.7 1.1 - - + -
957B LEU* 3.8 19.1 - - + -
960B LEU* 3.6 36.6 - - + +
964B MET* 5.4 0.7 - - + -
975B SER* 2.9 29.9 + - - +
978B ILE* 1.3 75.6 - - - +
980B ILE* 1.3 62.6 + - - +
981B PRO* 3.2 2.5 - - - -
982B LEU* 2.8 38.9 + - + +
983B ILE* 3.5 10.3 - - + +
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Residues in contact with ILE 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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957B LEU* 3.8 23.8 - - + -
961B ARG* 5.1 1.3 - - - +
976B ASP* 2.9 44.9 + - + +
979B LEU* 1.3 76.5 - - - +
981B PRO* 1.3 66.8 - - + +
982B LEU 2.9 1.4 + - - -
983B ILE* 3.0 28.0 + - + +
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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
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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