Contacts of the helix formed by residues 6 - 19 (chain G) in PDB entry 3QSU
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 ASN 6 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40F ASP* 4.0 8.9 - - - +
42F TYR* 6.1 4.0 - - - -
7G ILE* 1.3 69.8 + - - +
8G GLN* 3.4 13.1 + - - +
9G ASP* 3.0 45.7 + - + +
10G LYS* 3.2 48.4 + - + +
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Residues in contact with ILE 7 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F GLU* 3.3 46.7 - - + +
39F TYR 3.9 24.0 - - - +
40F ASP* 3.1 18.3 + - + +
43F VAL* 4.1 4.5 - - + -
45F SER* 4.7 2.5 - - - -
54F LEU* 3.7 24.7 - - + -
6G ASN* 1.3 76.1 - - - +
8G GLN* 1.3 65.6 + - - +
10G LYS* 3.3 9.2 + - + +
11G ALA* 2.9 23.8 + - + +
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Residues in contact with GLN 8 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F ASP* 3.4 6.0 + - - +
42F TYR* 4.1 22.4 - - - +
43F VAL* 3.9 19.0 - - + +
54F LEU* 4.1 15.3 - - + -
56F TYR* 2.4 40.2 + - + +
6G ASN* 3.3 7.9 + - - +
7G ILE* 1.3 80.1 - - - +
9G ASP* 1.3 64.0 + - - +
11G ALA* 3.1 2.8 + - - +
12G LEU* 3.0 39.6 + - + +
57G LYS* 3.0 27.9 + - - +
63G TYR* 5.3 0.2 - - + -
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Residues in contact with ASP 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G ASN* 3.0 33.8 + - + +
8G GLN* 1.3 90.4 + - - +
10G LYS* 1.3 58.4 + - + +
12G LEU* 3.5 10.1 + - - +
13G GLU* 2.9 30.5 + - - +
39G TYR* 3.6 19.7 + - + +
57G LYS* 4.4 5.9 + - - -
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Residues in contact with LYS 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G ASN* 3.2 38.5 + - + +
7G ILE* 3.8 8.3 - - + +
9G ASP* 1.3 73.9 - - + +
11G ALA* 1.3 66.8 + - - +
13G GLU* 3.4 5.9 + - - +
14G ASN* 3.0 24.1 + - - +
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Residues in contact with ALA 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F GLN* 4.9 7.4 - - - +
54F LEU* 3.6 27.1 - - + -
7G ILE* 2.9 18.8 + - + +
8G GLN 3.4 4.3 - - - +
10G LYS* 1.3 77.5 - - - +
12G LEU* 1.3 57.7 + - - +
14G ASN* 3.2 8.5 + - - +
15G PHE* 2.9 45.0 + - + -
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Residues in contact with LEU 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F LEU* 5.4 0.9 - - + -
8G GLN* 3.0 44.6 + - + +
9G ASP* 4.0 5.6 - - - +
11G ALA* 1.3 76.8 - - + +
13G GLU* 1.3 57.2 + - - +
15G PHE* 3.3 11.8 + - + +
16G LYS* 2.8 30.3 + - - +
36G ILE* 4.0 15.1 - - + +
39G TYR* 3.8 38.6 - - + -
44G VAL* 4.8 2.7 - - + -
57G LYS* 4.2 10.1 - - - +
63G TYR* 3.5 44.6 - - + +
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Residues in contact with GLU 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G ASP 2.9 19.1 + - - +
10G LYS* 3.8 7.4 - - - +
12G LEU* 1.3 74.3 - - - +
14G ASN* 1.3 59.6 - - - +
16G LYS* 4.2 14.7 + - - +
17G ALA* 2.8 42.9 + - + +
39G TYR* 2.8 29.3 + - - +
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Residues in contact with ASN 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G LYS 3.0 13.5 + - - +
11G ALA* 3.2 12.6 - - - +
13G GLU* 1.3 74.1 - - - +
15G PHE* 1.3 71.7 + - + +
17G ALA* 4.6 0.9 - - - -
18G ASN* 2.9 49.9 + - - +
20G THR* 4.1 8.7 + - - -
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Residues in contact with PHE 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F GLN* 4.2 21.3 - - + -
54F LEU* 5.3 2.2 - - + -
11G ALA* 2.9 34.6 + - + -
12G LEU* 3.6 14.4 - - + +
14G ASN* 1.3 83.6 - - + +
16G LYS* 1.3 57.1 + - - +
19G GLN* 2.9 24.3 + - - -
20G THR* 3.0 28.9 + - + +
22G VAL* 4.2 13.7 - - + -
36G ILE* 4.1 29.9 + - + +
63G TYR* 4.2 26.9 - + + -
65G VAL* 3.2 33.0 - - + -
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Residues in contact with LYS 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G LEU 2.8 17.5 + - - +
13G GLU* 3.8 16.1 + - - +
15G PHE* 1.3 75.7 - - - +
17G ALA* 1.3 67.1 + - - +
19G GLN* 3.3 15.9 + - - +
36G ILE* 3.5 30.7 - - + +
37G GLU* 3.6 16.2 - - - +
38G GLU* 3.7 23.0 - - - +
39G TYR* 4.1 21.6 - - + +
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Residues in contact with ALA 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G GLU* 2.8 32.9 + - + +
14G ASN* 4.0 2.7 - - - +
16G LYS* 1.3 76.5 - - - +
18G ASN* 1.3 70.3 + - - +
19G GLN* 3.6 3.5 + - - +
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Residues in contact with ASN 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G ASN* 2.9 51.0 + - - +
17G ALA* 1.3 82.8 - - - +
19G GLN* 1.3 72.0 + - - +
20G THR* 3.1 11.4 + - - +
16M LYS* 5.1 3.8 + - - -
38M GLU* 5.7 0.9 - - - +
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Residues in contact with GLN 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G PHE 2.9 9.5 + - - -
16G LYS 3.3 13.5 + - - +
17G ALA 3.4 3.2 - - - +
18G ASN* 1.3 79.4 - - - +
20G THR* 1.3 66.5 + - - +
21G GLU* 3.4 2.3 + - - +
35G VAL* 3.5 33.0 - - + +
13M GLU* 2.8 28.8 + - - +
16M LYS* 3.2 36.7 + - - -
17M ALA* 3.8 20.8 - - - +
37M GLU 5.6 0.5 - - - +
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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