Contacts of the helix formed by residues 55 - 65 (chain C) in PDB entry 3QU3
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 55 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C LEU* 4.3 2.7 - - + -
51C ASP 3.8 9.0 - - - +
52C GLU 3.2 5.7 + - - +
53C GLU 3.0 1.0 - - - -
54C ASP* 1.3 80.0 - - - +
56C GLN* 1.3 59.7 + - - +
57C ILE 3.4 2.2 - - - -
58C PHE* 3.6 18.6 - - + -
59C LYS* 2.8 33.6 + - + +
88C ARG* 3.7 35.7 - - + +
91C TRP* 4.9 3.4 - - + -
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Residues in contact with GLN 56 (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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24C GLN 5.2 1.6 - - - +
25C TYR* 3.9 21.4 - - + -
26C GLU* 5.1 9.4 + - - +
52C GLU* 3.4 21.2 + - + +
53C GLU* 3.7 33.1 + - - +
54C ASP 3.6 2.2 + - - -
55C ALA* 1.3 77.4 - - - +
57C ILE* 1.3 57.8 + - - +
59C LYS* 3.7 6.2 - - - +
60C ALA* 3.0 26.0 + - - +
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Residues in contact with ILE 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C TRP* 3.4 30.0 - - + -
16C LEU* 4.3 3.8 - - + -
19C GLU* 4.0 10.5 - - + -
25C TYR* 4.1 23.9 - - + -
28C LEU* 4.0 26.2 - - + -
40C VAL* 5.7 2.9 - - + -
41C PRO* 5.6 12.3 - - + +
54C ASP 5.7 1.3 - - - +
56C GLN* 1.3 75.0 - - - +
58C PHE* 1.3 90.0 + - + +
60C ALA* 3.2 2.0 + - - +
61C TRP* 3.2 19.4 + - - +
95C PHE* 3.6 25.7 - - + -
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Residues in contact with PHE 58 (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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41C PRO 5.3 7.2 - - - -
45C PHE* 4.3 6.1 - + - -
50C LEU* 4.0 11.7 - - + -
54C ASP 3.3 26.5 - - - -
55C ALA* 3.4 13.5 - - + +
57C ILE* 1.3 85.9 - - + +
59C LYS* 1.3 61.2 + - - +
61C TRP* 3.5 4.9 + - - +
62C ALA* 3.3 15.2 + - - +
65C ARG* 5.0 0.3 + - - -
88C ARG 4.8 0.2 - - - -
91C TRP* 3.8 33.1 - - + +
92C LYS* 3.8 29.2 - - + -
95C PHE* 3.4 46.0 - + + -
96C ARG* 4.0 28.3 - - - -
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Residues in contact with LYS 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C GLU* 4.8 13.4 + - + +
55C ALA* 2.8 22.6 + - + +
56C GLN* 3.7 6.3 - - - +
58C PHE* 1.3 72.4 - - - +
60C ALA* 1.3 58.5 + - - +
62C ALA* 3.1 2.9 + - - +
63C VAL* 2.9 39.6 + - + +
68C TRP* 3.8 15.5 - - - -
69C PRO 5.3 1.3 + - - -
70C PRO* 5.4 5.6 + - - -
72C GLY* 5.8 1.8 - - - -
84C GLU* 3.4 38.0 + - - +
91C TRP* 3.4 33.0 - - + -
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Residues in contact with ALA 60 (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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15C TRP* 3.6 17.0 + - + -
19C GLU* 4.2 1.6 - - - +
25C TYR* 3.3 29.2 - - + +
56C GLN 3.0 13.1 + - - +
57C ILE* 3.2 9.4 + - - +
59C LYS* 1.3 77.0 - - - +
61C TRP* 1.3 55.6 + - - +
63C VAL* 3.6 6.9 + - - +
64C ALA* 2.9 28.6 + - - +
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Residues in contact with TRP 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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10C VAL* 4.9 7.4 - - + -
11C LEU 4.9 0.7 - - - -
12C PHE* 3.5 44.1 - + + -
15C TRP* 3.5 51.3 - + + -
57C ILE 3.2 7.3 + - - +
58C PHE 3.7 8.1 - - - +
59C LYS 3.2 0.4 - - - -
60C ALA* 1.3 73.4 - - - +
62C ALA* 1.3 65.3 - - - +
64C ALA* 3.1 10.4 + - + +
65C ARG* 2.9 73.2 + - + +
94C ASN* 3.2 15.8 + - - -
95C PHE* 4.1 22.0 - - + -
98C ALA* 4.1 9.9 - - + +
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Residues in contact with ALA 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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58C PHE 3.3 5.9 + - - +
59C LYS 3.1 9.0 + - - +
61C TRP* 1.3 78.4 - - - +
63C VAL* 1.3 60.4 + - - +
65C ARG* 3.0 25.4 + - - +
67C ARG* 2.9 28.4 + - + -
68C TRP* 4.1 9.2 - - + +
91C TRP* 3.4 43.1 - - + +
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Residues in contact with VAL 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLN* 5.4 1.6 - - - +
59C LYS* 2.9 29.5 + - + +
60C ALA* 3.8 6.7 - - - +
62C ALA* 1.3 75.0 - - - +
64C ALA* 1.3 59.2 + - - +
66C GLY* 3.0 17.3 + - - -
68C TRP* 3.5 43.0 - - + +
69C PRO 4.4 3.8 - - - +
70C PRO* 3.9 28.9 - - + +
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Residues in contact with ALA 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLN* 3.9 27.6 + - - +
15C TRP* 3.7 25.4 - - + +
60C ALA 2.9 19.8 + - - +
61C TRP* 3.1 18.4 + - + +
63C VAL* 1.3 78.2 - - - +
65C ARG* 1.3 60.6 + - - +
66C GLY 3.1 0.7 + - - -
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Residues in contact with ARG 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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8C GLN* 4.4 7.9 + - - +
58C PHE 5.0 0.4 + - - -
61C TRP* 2.9 62.8 + - + +
62C ALA* 3.0 29.7 + - - +
64C ALA* 1.3 77.8 - - - +
66C GLY* 1.3 62.7 + - - +
67C ARG* 3.4 46.1 + - + +
91C TRP* 4.5 10.3 + - - +
94C ASN* 3.0 39.5 + - - +
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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