Contacts of the helix formed by residues 7 - 18 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A MET* 5.5 1.7 - - + +
4A ASN* 3.0 25.3 + - + +
5A PHE 3.4 1.5 - - - -
6A LEU* 1.3 73.1 - - - +
8A GLU* 1.3 63.6 + - - +
9A THR 3.3 2.7 - - - -
10A ALA* 3.3 17.3 + - + +
11A HIS* 3.3 11.5 + - - +
38B SER* 3.8 17.9 - - - +
39B TYR 4.4 5.4 - - - +
40B ASP* 4.5 4.9 - - + +
6K LEU* 3.8 20.7 - - + +
5L PHE* 5.5 0.5 - - - -
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Residues in contact with GLU 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PHE 4.6 2.0 - - - +
6A LEU* 2.9 22.8 + - - +
7A ALA* 1.3 73.0 - - - +
9A THR* 1.3 59.5 + - - +
11A HIS* 3.3 8.3 + - - +
12A LYS* 2.9 35.2 + - - +
11L HIS* 3.6 31.2 - - + +
15L ALA* 5.0 5.7 - - - +
39L TYR* 3.7 7.3 + - - -
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Residues in contact with THR 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ALA 3.3 1.2 - - - -
8A GLU* 1.3 78.2 - - - +
10A ALA* 1.3 63.4 + - - +
12A LYS* 3.3 11.4 + - + +
13A VAL* 3.1 30.5 + - + +
37B ARG* 3.6 40.8 + - + +
38B SER* 4.0 5.6 - - - -
46B VAL* 4.9 0.7 - - + -
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Residues in contact with ALA 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A MET* 3.6 22.6 - - + +
7A ALA* 3.3 12.4 + - + +
9A THR* 1.3 75.3 - - - +
11A HIS* 1.3 66.2 + - - +
13A VAL* 3.2 12.1 + - - +
14A LEU* 3.4 16.6 + - - +
38B SER* 3.5 18.6 + - - +
44B ASN* 6.0 3.6 - - + +
45B LEU 5.6 2.0 - - - +
46B VAL* 3.5 23.9 - - + +
66B VAL* 5.0 2.2 - - + +
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Residues in contact with HIS 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A MET* 4.2 2.4 - - - +
5A PHE 5.4 4.3 - - - +
7A ALA 3.3 9.3 + - - +
8A GLU* 3.6 11.7 - - - +
9A THR 3.3 0.6 - - - -
10A ALA* 1.3 78.4 - - - +
12A LYS* 1.3 57.3 + - - +
14A LEU* 3.3 4.6 + - - +
15A ALA* 2.8 30.4 + - + +
39A TYR* 2.9 34.5 + + - -
5L PHE* 3.3 61.9 + + + -
6L LEU* 4.3 5.7 - - + +
8L GLU* 4.7 17.3 - - - +
11L HIS* 5.7 6.7 - + - -
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Residues in contact with LYS 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A GLU* 2.9 20.3 + - - +
9A THR* 3.6 11.9 - - + +
10A ALA 3.2 0.2 - - - -
11A HIS* 1.3 74.9 - - - +
13A VAL* 1.3 65.6 + - + +
15A ALA* 4.2 7.0 - - + -
16A GLU* 2.9 51.2 + - + +
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Residues in contact with VAL 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A THR* 3.1 20.8 + - + +
10A ALA 3.2 7.4 + - - +
12A LYS* 1.3 76.9 - - + +
14A LEU* 1.3 59.2 + - + +
16A GLU* 3.5 6.6 + - - +
17A SER* 2.7 32.8 + - - +
77A PRO* 4.0 21.3 - - + -
46B VAL* 4.0 22.9 - - + -
64B THR* 4.1 15.9 - - + -
66B VAL* 3.7 24.7 - - + -
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Residues in contact with LEU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A MET* 3.7 35.2 - - + -
10A ALA 3.4 7.4 + - - +
11A HIS* 3.3 7.0 + - - +
12A LYS 3.2 0.4 - - - -
13A VAL* 1.3 76.8 - - + +
15A ALA* 1.3 64.7 + - - +
17A SER* 2.9 16.3 + - - +
18A LEU* 3.2 10.0 + - - +
36A LEU* 3.9 11.8 - - + +
39A TYR* 3.7 45.3 - - + -
40A ASP 4.9 1.8 - - - +
43A MET* 5.2 2.7 - - + -
75A ILE* 4.1 31.6 - - + -
66B VAL* 4.1 24.5 - - + -
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Residues in contact with ALA 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A HIS* 2.8 21.7 + - + +
12A LYS* 3.3 9.4 + - + +
14A LEU* 1.3 78.5 - - - +
16A GLU* 1.3 61.1 + - + +
18A LEU* 3.4 22.3 + - + +
39A TYR* 3.5 20.8 + - - +
8L GLU* 5.5 7.6 - - - +
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Residues in contact with GLU 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LYS* 2.9 46.9 + - + +
13A VAL* 4.0 5.4 - - - +
15A ALA* 1.3 78.1 - - + +
17A SER* 1.3 58.2 + - - +
18A LEU 3.2 1.0 - - - +
20A ASN* 3.0 21.3 + - - -
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Residues in contact with SER 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 2.7 20.4 + - - +
14A LEU* 2.9 11.3 + - - +
16A GLU* 1.3 76.3 - - - +
18A LEU* 1.3 65.7 + - - +
19A ASN 3.4 0.3 + - - -
20A ASN* 3.0 30.0 + - - +
22A VAL* 4.0 13.2 - - - -
36A LEU* 3.6 18.7 - - - +
75A ILE* 6.0 0.4 - - - -
77A PRO* 2.9 30.5 - - - +
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Residues in contact with LEU 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU 3.2 4.6 + - - -
15A ALA* 3.4 18.6 - - + +
16A GLU 3.2 2.2 - - - +
17A SER* 1.3 77.0 - - - +
19A ASN* 1.3 77.2 + - - +
20A ASN* 3.1 12.5 + - - -
36A LEU* 3.7 8.5 - - + +
37A ARG* 3.7 33.2 - - - +
38A SER* 3.8 3.6 - - - +
39A TYR* 3.5 42.2 - - + +
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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