Contacts of the helix formed by residues 6 - 18 (chain C) in PDB entry 1DUX
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 THR 6 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B A 4.3 13.7 - - - +
4B C 3.3 25.4 - - - +
5C VAL* 1.3 79.8 - - - +
7C LEU* 1.3 59.5 + - - +
8C TRP* 3.1 22.1 + - + +
9C GLN* 2.8 44.5 + - - +
10C PHE* 2.9 27.0 + - - +
46C TRP* 3.6 1.8 - - - -
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Residues in contact with LEU 7 (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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4B C 2.9 13.4 + - - +
6C THR* 1.3 71.3 - - - +
8C TRP* 1.3 63.0 + - - +
10C PHE* 3.2 3.2 + - + +
11C LEU* 2.9 47.5 + - + +
46C TRP* 3.4 38.7 - - + +
60C LEU* 4.0 18.8 - - + +
63C ALA* 3.5 28.9 - - + -
64C LEU* 3.5 28.7 - - + -
67C TYR* 3.3 13.9 + - + +
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Residues in contact with TRP 8 (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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4B C 4.1 0.6 + - - -
6C THR* 3.1 22.5 + - + +
7C LEU* 1.3 80.4 - - - +
9C GLN* 1.3 103.8 + - + +
11C LEU* 3.4 8.3 + - - +
12C LEU* 3.1 44.7 + - + +
67C TYR* 3.1 45.9 + + + +
72C ILE* 4.1 27.5 - - + +
73C ILE* 4.4 1.6 - - + -
85C PHE* 3.7 22.0 - + + -
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Residues in contact with GLN 9 (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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5C VAL* 3.8 14.4 - - + -
6C THR* 2.8 48.4 + - - +
8C TRP* 1.3 111.5 - - + +
10C PHE* 1.3 58.5 + - - +
12C LEU* 3.2 7.5 + - - +
13C GLN* 2.9 38.1 + - - +
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Residues in contact with PHE 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C VAL* 4.0 5.1 - - + +
6C THR 2.9 13.4 + - - +
7C LEU* 3.4 8.5 - - + +
9C GLN* 1.3 76.5 - - - +
11C LEU* 1.3 78.1 + - + +
13C GLN* 3.0 12.4 + - - +
14C LEU* 2.9 52.6 + - + +
42C VAL* 3.7 7.2 - - + -
45C LEU* 3.8 8.7 - - + -
46C TRP* 3.5 59.2 - + + -
49C ARG* 3.5 43.7 - - + -
17F GLU* 3.8 10.5 - - - -
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Residues in contact with LEU 11 (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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7C LEU* 2.9 41.0 + - + +
8C TRP* 3.6 7.0 - - - +
10C PHE* 1.3 83.1 - - + +
12C LEU* 1.3 61.9 + - - +
14C LEU* 3.3 5.2 + - + +
15C LEU* 3.0 30.7 + - - +
24C ILE* 4.2 10.1 - - + +
34C PHE* 4.0 27.6 - - + -
36C LEU* 4.6 3.1 - - + -
42C VAL* 3.9 28.0 - - + -
60C LEU* 5.0 2.0 - - + -
64C LEU* 3.8 24.0 - - + -
73C ILE* 4.4 6.7 - - + -
85C PHE* 4.0 9.2 - - + -
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Residues in contact with LEU 12 (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 TRP* 3.1 40.2 + - + +
9C GLN* 3.3 9.9 - - - +
11C LEU* 1.3 76.4 - - - +
13C GLN* 1.3 63.9 + - + +
15C LEU* 3.4 3.8 + - - +
16C ARG* 3.0 38.1 + - - +
26C TRP* 4.1 9.8 - - + -
85C PHE* 3.3 36.8 - - + -
89C PRO* 4.0 32.8 - - + +
90C GLU 5.2 7.6 - - - +
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Residues in contact with GLN 13 (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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5C VAL* 4.4 9.6 - - - +
9C GLN* 2.9 23.8 + - + +
10C PHE* 3.4 9.1 - - - +
12C LEU* 1.3 77.2 - - + +
14C LEU* 1.3 51.9 + - - +
16C ARG* 3.2 26.7 + - - +
17C GLU* 2.7 51.3 + - - +
49C ARG* 2.8 43.5 - - - +
49F ARG* 3.3 27.8 + - - +
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Residues in contact with LEU 14 (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 PHE* 2.9 45.6 + - + +
11C LEU* 3.6 8.5 - - + +
13C GLN* 1.3 75.9 - - - +
15C LEU* 1.3 58.2 + - - +
17C GLU* 4.4 2.9 - - + +
18C GLN* 2.8 61.9 + - + +
23C ILE* 4.3 17.9 - - + -
24C ILE* 4.0 14.6 - - + -
42C VAL* 3.9 23.3 - - + -
45C LEU* 4.7 2.2 - - + -
17F GLU* 4.0 27.1 - - + +
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Residues in contact with LEU 15 (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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11C LEU 3.0 20.8 + - - +
12C LEU* 3.7 5.2 - - - +
14C LEU* 1.3 77.1 - - - +
16C ARG* 1.3 61.3 + - - +
18C GLN* 4.5 7.0 + - - +
24C ILE* 3.7 27.8 - - + +
25C SER* 3.7 12.1 - - - +
26C TRP* 3.7 79.1 + - + +
34C PHE* 4.0 11.0 - - + -
85C PHE* 3.9 17.0 - - + -
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Residues in contact with ARG 16 (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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12C LEU* 3.0 33.2 + - - +
13C GLN* 3.6 29.1 - - - +
15C LEU* 1.3 79.2 - - - +
17C GLU* 1.3 66.7 + - - +
18C GLN 4.3 2.8 - - - +
90C GLU 5.9 5.1 - - - -
44F ARG* 4.5 8.5 + - - +
45F LEU* 4.1 13.1 + - + +
48F LEU* 3.7 56.7 + - + +
49F ARG* 3.8 15.0 - - - +
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Residues in contact with GLU 17 (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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13C GLN* 2.7 26.6 + - - +
14C LEU* 4.4 3.3 - - + +
16C ARG* 1.3 85.9 + - + +
18C GLN* 1.3 66.7 + - - +
19C GLY* 3.5 0.9 + - - -
10F PHE* 3.8 11.5 - - - -
14F LEU* 4.0 17.3 - - + +
17F GLU* 4.4 7.8 - - - +
18F GLN* 2.9 20.8 + - - +
23F ILE* 5.0 1.0 - - - +
45F LEU* 3.5 36.6 - - + +
49F ARG* 2.6 50.4 + - - +
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Residues in contact with GLN 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LEU* 2.8 48.5 + - + +
15C LEU* 4.6 5.7 - - - +
16C ARG 3.7 4.9 - - - +
17C GLU* 1.3 74.3 - - - +
19C GLY* 1.3 63.7 + - - +
20C ASN* 3.2 28.7 + - - +
22C HIS* 5.6 0.3 - - - +
23C ILE* 3.4 30.2 + - + +
24C ILE* 4.1 15.0 - - + +
17F GLU* 2.8 33.8 + - - +
18F GLN* 4.2 7.5 - - - +
19F GLY* 4.6 8.7 + - - -
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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