Contacts of the helix formed by residues 60 - 73 (chain C) in PDB entry 1WUR
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 60 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56C GLU 5.1 0.4 + - - -
58C LEU 3.3 0.4 - - - -
59C LEU* 1.3 80.7 - - + +
61C THR* 1.3 57.7 + - - +
62C PRO* 3.6 1.3 - - - -
63C GLU* 3.3 36.3 + - + +
64C ARG* 3.0 59.2 + - + +
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Residues in contact with THR 61 (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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42C ALA* 6.0 0.7 - - + -
46C LEU* 4.2 19.5 - - + -
57C GLY 3.4 2.3 + - - -
58C LEU* 3.3 35.9 - - + +
60C LYS* 1.3 74.9 - - - +
62C PRO* 1.3 65.8 - - + +
64C ARG* 3.0 26.2 + - + +
65C VAL* 2.8 49.3 + - + +
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Residues in contact with PRO 62 (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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39C GLN* 3.3 39.5 - - + +
42C ALA* 3.7 18.5 - - + +
43C ALA* 4.0 13.7 - - + +
46C LEU* 4.2 8.7 - - + -
58C LEU 3.3 13.5 - - - +
59C LEU 3.7 11.0 - - - +
61C THR* 1.3 92.3 - - + +
63C GLU* 1.3 56.9 + - + +
65C VAL* 4.0 1.7 - - + +
66C ALA* 3.1 27.7 + - - +
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Residues in contact with GLU 63 (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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39C GLN* 3.8 28.4 + - - +
60C LYS* 3.3 40.6 + - - +
61C THR 3.1 0.4 - - - -
62C PRO* 1.3 79.0 - - + +
64C ARG* 1.3 65.1 + - + +
66C ALA* 3.4 2.8 + - - +
67C LYS* 3.2 49.4 + - + +
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Residues in contact with ARG 64 (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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57C GLY 3.2 17.4 + - - -
60C LYS* 3.0 45.3 + - + +
61C THR* 3.0 36.7 + - + +
63C GLU* 1.3 78.4 - - + +
65C VAL* 1.3 58.9 + - + +
67C LYS* 3.7 6.8 + - - +
68C ALA* 3.0 29.0 + - - +
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Residues in contact with VAL 65 (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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42C ALA* 4.4 17.5 - - + -
61C THR* 2.8 42.2 + - + +
62C PRO* 4.0 4.3 - - + +
64C ARG* 1.3 70.3 - - + +
66C ALA* 1.3 60.9 + - - +
68C ALA* 4.0 5.4 - - - -
69C TRP* 3.0 49.5 + - + +
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Residues in contact with ALA 66 (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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35C LEU* 3.7 26.2 - - + +
38C LEU* 3.8 24.7 - - + +
39C GLN* 3.7 17.9 - - + +
62C PRO 3.1 19.9 + - - +
63C GLU 3.6 5.4 - - - +
64C ARG 3.3 0.4 - - - -
65C VAL* 1.3 77.8 - - - +
67C LYS* 1.3 63.7 + - + +
69C TRP 3.4 0.5 + - - -
70C ALA* 3.1 21.3 + - - +
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Residues in contact with LYS 67 (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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35C LEU* 4.3 25.2 - - + +
39C GLN* 5.8 1.4 + - - -
63C GLU* 3.2 42.6 + - - +
64C ARG* 4.1 5.6 - - - +
66C ALA* 1.3 73.2 - - + +
68C ALA* 1.3 64.6 + - - +
70C ALA* 3.3 8.7 + - - +
71C PHE* 3.1 22.7 + - - +
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Residues in contact with ALA 68 (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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64C ARG 3.0 21.0 + - - +
65C VAL* 3.4 9.6 - - - +
67C LYS* 1.3 75.4 - - - +
69C TRP* 1.3 62.9 + - + +
71C PHE* 3.1 9.2 + - - +
72C LEU* 2.9 39.4 + - + +
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Residues in contact with TRP 69 (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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38C LEU* 4.7 13.0 - - + -
65C VAL* 3.0 42.9 + - + +
66C ALA 4.1 2.9 - - - +
68C ALA* 1.3 78.5 - - + +
70C ALA* 1.3 55.7 + - - +
72C LEU* 4.1 11.8 - - + +
73C THR* 2.7 54.3 + - + +
107C MET* 3.7 36.1 - - + +
112C LEU* 3.8 41.3 - - + -
146C LEU* 3.9 23.1 - - + -
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Residues in contact with ALA 70 (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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33C VAL* 4.7 13.7 - - + -
35C LEU* 3.9 18.6 - - + -
38C LEU* 5.1 0.4 - - - +
66C ALA 3.1 14.6 + - - +
67C LYS* 3.5 11.0 - - - +
68C ALA 3.2 0.2 - - - -
69C TRP* 1.3 75.9 - - - +
71C PHE* 1.3 62.1 + - - +
73C THR* 3.5 4.0 + - - -
74C ARG* 3.2 8.5 + - - +
77C ARG* 2.8 28.9 + - - +
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Residues in contact with PHE 71 (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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67C LYS 3.1 11.6 + - - +
68C ALA* 3.1 9.8 + - - +
70C ALA* 1.3 76.7 - - - +
72C LEU* 1.3 78.5 + - + +
73C THR 3.1 2.9 + - - -
74C ARG* 3.1 51.4 - - - +
144C ARG* 3.5 42.4 - - - -
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Residues in contact with LEU 72 (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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68C ALA* 2.9 29.2 + - + +
69C TRP* 4.0 20.4 - - + +
70C ALA 3.4 0.4 - - - -
71C PHE* 1.3 92.2 - - + +
73C THR* 1.3 62.0 + - + +
74C ARG 3.6 0.2 - - - -
105C TYR* 6.3 3.6 - - + -
107C MET* 3.6 38.5 - - + +
144C ARG* 3.0 31.0 - - + +
145C ARG* 3.4 4.2 + - - +
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Residues in contact with THR 73 (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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33C VAL* 4.8 3.5 - - - +
69C TRP* 2.7 44.6 + - + +
70C ALA* 3.5 6.8 + - - -
72C LEU* 1.3 81.2 - - - +
74C ARG* 1.3 62.4 + - - +
75C GLY 3.1 7.6 + - - -
76C TYR* 3.3 38.6 + - + -
77C ARG* 3.6 17.5 + - - -
144C ARG 3.3 6.3 - - - -
145C ARG* 5.1 2.5 - - - -
146C LEU* 5.1 7.9 - - + -
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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