Contacts of the helix formed by residues 6 - 18 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7N ILE* 1.3 81.5 + - + +
8N GLN 3.4 2.2 - - - +
9N ASP* 3.4 13.9 + - - +
10N LYS* 2.8 38.1 + - + +
39S TYR 5.6 0.2 + - - -
40S ASP* 3.7 20.8 + - - +
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Residues in contact with ILE 7 (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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6N ASN* 1.3 99.3 - - - +
8N GLN* 1.3 62.7 + - - +
10N LYS* 3.5 25.3 - - + +
11N ALA* 3.1 23.2 + - + +
38S GLU* 4.2 30.5 - - + +
39S TYR 3.8 29.2 - - - +
40S ASP* 3.2 14.3 + - + +
43S VAL* 4.3 12.6 - - + -
45S SER* 4.9 5.2 - - - -
54S LEU* 4.6 8.9 - - + +
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Residues in contact with GLN 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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6N ASN 3.4 0.2 - - - -
7N ILE* 1.3 76.0 - - - +
9N ASP* 1.3 66.3 + - - +
11N ALA* 3.3 2.8 + - - +
12N LEU* 2.9 42.7 + - + +
57N LYS* 2.5 34.8 + - - +
40S ASP* 2.9 15.2 + - - +
42S TYR* 4.0 30.1 - - - +
43S VAL* 3.8 21.7 - - + +
54S LEU* 4.6 7.6 - - + +
56S TYR* 2.6 31.2 + - + +
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Residues in contact with ASP 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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6N ASN* 3.4 14.0 + - - +
7N ILE 3.4 0.4 - - - -
8N GLN* 1.3 80.3 + - - +
10N LYS* 1.3 60.0 - - - +
12N LEU* 4.3 8.4 - - - +
13N GLU* 2.8 37.0 + - - +
39N TYR* 3.7 24.6 + - - +
40N ASP 5.5 0.7 - - - +
57N LYS* 4.8 6.8 + - - -
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Residues in contact with LYS 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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6N ASN* 2.8 23.4 + - + +
7N ILE* 3.5 22.0 - - + +
9N ASP* 1.3 77.3 - - - +
11N ALA* 1.3 56.1 + - - +
13N GLU* 3.5 4.9 + - - +
14N ASN* 3.1 26.7 + - - +
38S GLU* 3.5 24.4 + - - -
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Residues in contact with ALA 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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7N ILE* 3.1 15.6 + - + +
8N GLN 3.8 0.2 - - - +
10N LYS* 1.3 78.4 - - - +
12N LEU* 1.3 64.9 + - - +
14N ASN* 3.1 8.7 + - - +
15N PHE* 3.0 37.6 + - + -
54S LEU* 3.8 28.7 - - + -
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Residues in contact with LEU 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 GLN* 2.9 47.1 + - + +
9N ASP* 4.1 1.3 - - - +
11N ALA* 1.3 72.8 - - - +
13N GLU* 1.3 66.5 + - - +
15N PHE* 3.3 10.5 + - + +
16N LYS* 3.1 24.3 + - - +
36N ILE* 3.8 27.1 - - + +
39N TYR* 3.6 45.7 - - + -
44N VAL* 4.9 2.2 - - + -
57N LYS* 3.8 13.7 - - - +
63N TYR* 3.8 26.9 - - + +
54S LEU* 5.0 2.5 - - + -
56S TYR* 4.5 0.7 - - - +
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Residues in contact with GLU 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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9N ASP 2.8 24.2 + - - +
10N LYS* 3.7 5.4 - - - +
12N LEU* 1.3 71.9 - - - +
14N ASN* 1.3 56.2 + - - +
16N LYS* 3.8 16.6 - - - -
17N ALA* 2.8 42.8 + - + +
39N TYR* 2.8 28.1 + - - +
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Residues in contact with ASN 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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21J GLU* 2.7 39.7 + - - +
10N LYS 3.1 14.9 + - - +
11N ALA* 3.1 12.7 + - - +
13N GLU* 1.3 74.3 - - - +
15N PHE* 1.3 70.6 + - + +
17N ALA* 4.5 4.2 - - - +
18N ASN* 2.9 52.5 + - - +
20N THR* 4.6 1.4 + - - -
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Residues in contact with PHE 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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11N ALA* 3.0 34.3 + - + -
12N LEU* 3.3 9.8 + - + +
14N ASN* 1.3 84.0 - - + +
16N LYS* 1.3 59.2 + - - +
19N GLN* 2.9 23.0 + - - -
20N THR* 3.1 24.6 + - + +
22N VAL* 3.5 33.2 - - + -
36N ILE* 3.9 28.9 + - + +
63N TYR* 4.0 29.4 - + + -
65N VAL* 3.8 27.1 - - + -
54S LEU* 4.9 6.1 - - + -
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Residues in contact with LYS 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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50J GLY* 4.0 7.0 - - - -
12N LEU 3.1 17.5 + - - +
13N GLU* 3.9 24.4 + - - +
15N PHE* 1.3 77.1 - - - +
17N ALA* 1.3 66.7 + - - +
19N GLN* 3.4 15.6 + - - +
36N ILE* 3.5 22.3 - - + +
37N GLU* 3.1 30.1 + - - +
38N GLU* 3.8 17.7 + - - +
39N TYR* 4.2 12.1 - - + -
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Residues in contact with ALA 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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48J SER* 3.5 4.3 + - - -
49J GLN* 3.3 24.1 + - + +
50J GLY* 2.7 28.6 + - - +
13N GLU* 2.8 31.6 + - + +
14N ASN* 3.9 4.9 - - - +
16N LYS* 1.3 77.9 - - - +
18N ASN* 1.3 68.0 + - - +
19N GLN* 3.5 1.7 + - - -
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Residues in contact with ASN 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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21J GLU* 2.6 33.2 + - - +
33J LYS 4.3 3.3 - - - +
34J GLY* 3.8 12.6 - - - -
35J VAL* 3.8 27.4 - - + +
47J ASN* 3.1 28.6 + - - +
48J SER* 4.7 0.9 - - - -
49J GLN 4.8 0.3 + - - -
14N ASN* 2.9 36.0 + - - +
17N ALA* 1.3 84.4 - - - +
19N GLN* 1.3 67.3 + - - +
20N THR* 3.1 12.7 + - - +
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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