Contacts of the helix formed by residues 7 - 18 (chain F) in PDB entry 1U1T
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 LEU 7 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38E SER* 3.4 29.4 - - - +
39E PHE* 3.7 26.0 - - - +
40E ASP* 2.9 14.9 + - + +
43E VAL* 3.9 15.9 - - + -
45E LEU* 3.8 21.1 - - + +
53E MET* 5.7 1.8 - - + -
6F SER* 1.3 78.5 - - - +
8F GLN* 1.3 66.1 + - - +
9F ASP 3.4 1.6 - - - -
10F PRO* 3.1 4.8 - - - +
11F TYR* 3.0 32.5 + - + +
70F LEU* 3.4 32.3 - - + -
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Residues in contact with GLN 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E ASP* 2.9 13.9 + - - +
42E PHE* 4.2 14.5 - - - +
43E VAL* 4.0 12.3 - - + +
53E MET* 3.9 21.5 - - - -
55E TYR* 2.6 35.7 + - - -
5F HIS* 3.5 23.3 + - + +
7F LEU* 1.3 78.0 - - - +
9F ASP* 1.3 59.7 + - - +
11F TYR* 3.6 0.5 - - - +
12F LEU* 2.9 41.1 + - + +
56F LYS* 2.8 29.4 + - - +
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Residues in contact with ASP 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F HIS* 2.8 41.6 + - - +
8F GLN* 1.3 77.4 - - - +
10F PRO* 1.3 65.8 - - + +
13F ASN* 2.9 33.9 + - - +
39F PHE* 3.7 26.1 - - + -
56F LYS* 5.0 4.0 + - - -
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Residues in contact with PRO 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F HIS 3.3 9.9 - - - +
6F SER* 3.3 17.7 - - - +
7F LEU 3.1 12.3 - - - +
9F ASP* 1.3 95.0 - - + +
11F TYR* 1.3 56.4 + - - +
13F ASN* 3.7 5.0 - - + +
14F THR* 2.9 34.8 + - - -
70F LEU* 3.8 16.4 - - + -
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Residues in contact with TYR 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E LEU* 3.8 20.6 - - + -
51E SER* 3.1 14.4 + - - -
53E MET* 3.4 42.5 + - + -
7F LEU* 3.0 24.1 + - + +
8F GLN* 3.6 3.4 - - - +
10F PRO* 1.3 78.5 - - - +
12F LEU* 1.3 65.0 + - + +
14F THR* 3.2 4.5 + - - -
15F LEU* 3.2 44.1 + - + +
62F VAL* 3.7 10.9 + - + -
64F PRO* 3.0 31.7 - - + +
68F VAL* 4.1 20.2 - - + -
70F LEU* 3.7 28.9 - - + +
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Residues in contact with LEU 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E MET* 4.0 18.8 - - + -
55E TYR* 3.9 7.9 - - - +
8F GLN* 2.9 44.7 + - + +
11F TYR* 1.3 78.9 - - + +
13F ASN* 1.3 57.7 + - - +
15F LEU* 3.2 13.9 + - + +
16F ARG* 2.9 28.8 + - - +
36F ILE* 3.8 26.2 - - + +
39F PHE* 3.8 30.0 - - + -
44F ILE* 4.1 19.1 - - + -
56F LYS* 4.1 7.4 - - - +
62F VAL* 4.5 6.1 - - + -
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Residues in contact with ASN 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ASP 2.9 20.7 + - - +
10F PRO* 3.7 5.8 - - + +
12F LEU* 1.3 77.1 - - - +
14F THR* 1.3 57.9 + - - +
16F ARG* 3.0 27.3 + - - +
17F LYS* 2.9 67.7 + - - +
39F PHE* 3.7 17.0 - - + -
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Residues in contact with THR 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F PRO* 2.9 24.0 + - - +
11F TYR* 3.6 5.2 - - - -
12F LEU 3.2 0.2 - - - -
13F ASN* 1.3 74.1 - - - +
15F LEU* 1.3 64.7 + - - +
17F LYS* 3.4 5.6 + - - -
18F GLU* 3.0 46.1 + - + +
68F VAL* 4.6 17.7 - - + -
69F ARG 4.0 19.8 + - - +
70F LEU* 3.7 14.3 - - + +
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Residues in contact with LEU 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F TYR* 3.2 44.6 + - + +
12F LEU* 3.2 8.3 + - + +
14F THR* 1.3 76.3 - - - +
16F ARG* 1.3 61.8 + - - +
19F ARG* 3.1 17.0 + - - -
20F VAL* 3.2 24.6 + - + +
22F VAL* 4.1 10.3 - - + -
36F ILE* 3.9 27.4 + - + +
62F VAL* 4.1 12.3 - - + -
64F PRO* 3.9 19.1 - - + -
68F VAL* 3.6 33.9 - - + -
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Residues in contact with ARG 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F LEU 2.9 17.3 + - - +
13F ASN* 3.0 31.8 + - - +
14F THR 3.2 0.2 - - - -
15F LEU* 1.3 76.9 - - - +
17F LYS* 1.3 100.0 + - - +
19F ARG* 3.0 20.1 + - - +
36F ILE* 3.4 34.2 - - + +
37F GLU 3.3 21.9 + - - +
38F SER* 4.2 10.1 - - - +
39F PHE* 4.6 6.7 - - + -
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Residues in contact with LYS 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F ASN* 2.9 45.5 + - - +
14F THR* 4.0 5.2 - - - +
16F ARG* 1.3 102.2 - - - +
18F GLU* 1.3 72.5 + - - +
19F ARG* 3.1 8.4 + - - +
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Residues in contact with GLU 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F THR* 3.0 32.4 + - + +
17F LYS* 1.3 85.6 - - - +
19F ARG* 1.3 70.7 + - - +
20F VAL* 3.0 22.2 + - + +
66F ARG* 4.2 16.1 + - - +
68F VAL* 5.8 1.1 - - + -
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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