Contacts of the helix formed by residues 7 - 18 (chain N) in PDB entry 1TH7
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 7 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E LEU* 3.8 20.0 - - + +
38H SER* 3.9 16.8 - - - +
39H TYR 4.2 6.5 - - - +
40H ASP* 4.4 5.6 - - + +
3N MET* 6.2 0.7 - - + -
4N ASN* 3.0 25.0 + - + +
5N PHE 3.2 1.8 - - - -
6N LEU* 1.3 73.5 - - - +
8N GLU* 1.3 62.6 + - - +
9N THR 3.3 3.1 - - - -
10N ALA* 3.2 17.4 + - + +
11N HIS* 3.4 9.8 + - - +
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Residues in contact with GLU 8 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5N PHE 4.6 4.9 - - - +
6N LEU* 2.9 11.4 + - - +
7N ALA* 1.3 74.0 - - - +
9N THR* 1.3 58.3 + - - +
11N HIS* 3.3 7.5 + - + +
12N LYS* 2.8 69.0 + - + +
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Residues in contact with THR 9 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H ARG* 3.6 40.4 + - + +
38H SER* 3.8 7.6 - - - -
46H VAL* 4.7 7.0 - - + -
7N ALA 3.2 1.2 + - - -
8N GLU* 1.3 79.1 - - - +
10N ALA* 1.3 62.9 + - - +
12N LYS* 3.2 10.0 + - + +
13N VAL* 3.0 26.7 + - + +
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Residues in contact with ALA 10 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H SER* 3.5 18.3 + - - +
44H ASN* 5.9 5.2 - - + +
45H LEU 5.6 1.8 - - - +
46H VAL* 3.5 22.9 - - + -
66H VAL* 4.9 2.8 - - + +
3N MET* 3.6 22.1 - - + +
7N ALA* 3.2 12.8 + - + +
9N THR* 1.3 78.8 - - - +
11N HIS* 1.3 62.8 + - - +
13N VAL* 3.3 11.7 + - - +
14N LEU* 3.4 17.5 + - - +
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Residues in contact with HIS 11 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F PHE* 3.5 58.9 - + + -
6F LEU* 4.4 4.7 - - + +
8F GLU* 5.1 11.5 + - + -
11F HIS* 5.9 1.8 - + - -
3N MET* 4.2 6.4 - - - +
5N PHE* 5.1 6.7 + - - +
7N ALA 3.4 8.5 + - - +
8N GLU* 3.3 10.7 + - - +
9N THR 3.3 0.6 - - - -
10N ALA* 1.3 78.9 - - - +
12N LYS* 1.3 58.4 + - + +
14N LEU* 3.3 3.6 + - - -
15N ALA* 2.9 28.5 + - + +
39N TYR* 3.1 33.1 + + - -
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Residues in contact with LYS 12 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8N GLU* 2.8 58.8 + - + +
9N THR* 3.2 9.6 + - + +
11N HIS* 1.3 75.2 - - + +
13N VAL* 1.3 60.9 + - + +
15N ALA* 4.2 6.3 - - - -
16N GLU* 2.9 46.6 + - + +
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Residues in contact with VAL 13 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46H VAL* 4.1 23.1 - - + -
64H THR* 4.3 14.6 - - + -
66H VAL* 3.6 24.7 - - + -
9N THR* 3.0 23.2 + - + +
10N ALA 3.6 7.4 - - - +
11N HIS 3.2 0.2 - - - -
12N LYS* 1.3 77.6 - - + +
14N LEU* 1.3 55.5 + - + +
16N GLU* 3.5 11.5 + - - +
17N SER* 2.6 36.3 + - - +
77N PRO* 4.0 21.3 - - + -
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Residues in contact with LEU 14 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66H VAL* 4.2 18.8 - - + -
3N MET* 3.7 35.0 - - + -
10N ALA 3.4 8.2 + - - +
11N HIS* 3.3 7.2 + - - +
13N VAL* 1.3 75.4 - - + +
15N ALA* 1.3 66.5 + - - +
17N SER* 3.1 6.2 + - - +
18N LEU* 3.0 18.9 + - - -
36N LEU* 4.0 11.8 - - + +
39N TYR* 3.6 46.1 - - + -
40N ASP 4.9 2.0 - - - +
43N MET* 5.2 2.5 - - + -
45N LEU* 5.7 0.2 - - + -
75N ILE* 4.1 35.7 - - + -
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Residues in contact with ALA 15 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F GLU* 5.5 4.9 - - - +
11N HIS* 2.9 20.3 + - + +
12N LYS* 3.8 8.5 - - + +
14N LEU* 1.3 76.9 - - - +
16N GLU* 1.3 63.2 + - + +
18N LEU* 3.4 19.6 + - - +
39N TYR* 3.6 18.6 + - - +
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Residues in contact with GLU 16 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N LYS* 2.9 36.3 + - + +
13N VAL* 3.9 9.8 - - - +
15N ALA* 1.3 78.2 - - + +
17N SER* 1.3 58.8 + - - +
18N LEU 3.5 1.2 + - - +
20N ASN* 3.1 22.0 + - - -
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Residues in contact with SER 17 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13N VAL* 2.6 22.2 + - - +
14N LEU* 3.1 10.1 + - - +
16N GLU* 1.3 77.7 - - - +
18N LEU* 1.3 63.0 + - - +
19N ASN 3.3 0.3 + - - -
20N ASN* 3.0 30.7 + - - +
22N VAL* 4.0 14.6 - - - -
36N LEU* 3.7 16.6 - - - +
75N ILE* 6.0 0.4 - - - -
77N PRO* 3.0 29.8 - - - +
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Residues in contact with LEU 18 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14N LEU 3.0 10.3 + - - +
15N ALA* 3.4 16.1 - - - +
16N GLU 3.2 2.3 - - - +
17N SER* 1.3 77.7 - - - +
19N ASN* 1.3 85.6 + - - +
20N ASN* 3.5 9.0 + - - -
36N LEU* 3.7 10.8 - - + +
37N ARG* 3.5 34.8 - - - +
38N SER* 3.7 8.5 - - - +
39N TYR* 4.2 20.0 - - + -
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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