Contacts of the helix formed by residues 15 - 23 (chain A) in PDB entry 3BQT
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 VAL 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A GLY 3.2 0.4 - - - -
14A LYS* 1.3 77.9 - - + +
16A LEU* 1.3 64.9 + - - +
17A GLU 3.4 0.4 - - - -
18A GLN* 3.2 24.0 - - + +
19A ASP* 3.3 9.9 + - + +
43A ILE* 5.8 0.3 - - - +
67B TRP* 3.8 39.5 - - + -
68B HIS* 3.9 18.8 - - + +
75B LYS* 5.1 4.9 - - - +
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Residues in contact with LEU 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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11A ASN 4.2 0.4 - - - +
12A ILE* 3.6 32.3 - - + -
13A GLY* 3.4 13.1 + - - +
15A VAL* 1.3 76.9 - - - +
17A GLU* 1.3 58.3 + - - +
18A GLN 2.9 5.0 + - - -
19A ASP* 3.2 4.4 + - - +
20A LEU* 2.8 37.2 + - + +
43A ILE* 5.6 7.4 - - + +
54A GLU* 3.4 40.6 - - + +
57A ALA* 4.0 21.8 - - + -
58A LEU* 4.3 17.5 - - + -
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Residues in contact with GLU 17 (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 ASN 5.6 0.3 + - - -
6A LEU* 4.1 12.8 + - + +
7A SER* 2.7 33.5 + - - -
12A ILE* 3.2 25.6 - - + +
13A GLY 3.3 17.2 + - - +
14A LYS* 3.5 17.4 - - - +
16A LEU* 1.3 79.0 - - - +
18A GLN* 1.3 72.1 + - - +
20A LEU* 3.7 7.2 - - - -
21A ILE* 3.1 32.4 + - + +
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Residues in contact with GLN 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 LYS* 3.5 16.4 + - - +
15A VAL* 3.2 25.5 - - + +
16A LEU 2.9 0.8 - - - -
17A GLU* 1.3 92.7 + - - +
19A ASP* 1.3 59.5 + - - +
21A ILE* 3.4 11.4 + - - +
22A LYS* 3.1 33.7 + - + +
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Residues in contact with ASP 19 (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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15A VAL* 3.3 6.3 + - + +
16A LEU* 3.2 5.2 + - - +
18A GLN* 1.3 76.4 - - - +
20A LEU* 1.3 67.7 + - - +
21A ILE 3.1 1.3 - - - -
22A LYS* 3.2 24.2 + - - +
23A ALA* 2.8 15.4 + - - +
43A ILE* 3.0 42.2 - - + +
46A ASN* 2.9 27.1 + - - +
47A ASP* 3.1 23.2 - - - +
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Residues in contact with LEU 20 (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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6A LEU* 4.2 5.8 - - + -
12A ILE* 4.2 20.6 - - + -
16A LEU* 2.8 29.5 + - + +
17A GLU* 3.9 6.3 - - - +
18A GLN 3.3 0.2 - - - -
19A ASP* 1.3 74.3 - - - +
21A ILE* 1.3 64.7 + - - +
23A ALA* 2.9 12.1 + - - +
24A GLY 3.3 0.3 + - - -
25A ILE* 3.1 56.3 + - + +
31A LEU* 4.3 11.2 - - + -
39A ALA* 4.0 14.4 - - + -
43A ILE* 4.3 13.0 - - + +
58A LEU* 3.7 33.2 - - + -
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Residues in contact with ILE 21 (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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6A LEU* 4.3 15.7 - - + -
17A GLU* 3.1 21.2 + - + +
18A GLN* 3.4 16.2 - - - +
20A LEU* 1.3 79.2 - - - +
22A LYS* 1.3 68.0 + - + +
24A GLY* 2.7 16.5 + - - -
25A ILE 3.7 8.3 - - - +
26A LYS* 3.8 28.4 + - + +
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Residues in contact with LYS 22 (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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18A GLN* 3.2 21.8 - - + +
19A ASP* 3.0 39.4 + - - +
21A ILE* 1.3 79.2 - - + +
23A ALA* 1.3 58.6 + - - +
24A GLY* 3.0 6.1 + - - -
46A ASN* 4.0 19.3 + - - +
47A ASP* 4.4 5.8 + - - -
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Residues in contact with ALA 23 (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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19A ASP* 2.8 13.7 + - - +
20A LEU* 2.9 10.3 + - - +
22A LYS* 1.3 74.4 - - - +
24A GLY* 1.3 52.3 + - - +
25A ILE* 3.4 8.7 - - + -
42A ARG* 2.7 61.6 + - + -
43A ILE* 3.9 14.6 - - + +
46A ASN* 4.2 5.6 - - - +
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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