Contacts of the helix formed by residues 12 - 23 (chain A) in PDB entry 1BW5
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 GLU 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ASN* 1.3 85.8 + - - +
13A LYS* 1.3 61.9 + - - +
15A LEU* 4.3 3.1 - - - -
16A HIS* 2.7 51.8 + - + +
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Residues in contact with LYS 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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11A ASN* 2.8 19.1 + - - +
12A GLU* 1.3 80.0 - - - +
14A GLN* 1.3 83.7 + - + +
16A HIS* 3.6 5.7 + - - +
17A THR* 3.1 14.4 + - - -
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Residues in contact with GLN 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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8A THR* 5.9 0.2 - - - +
9A VAL* 3.4 36.6 + - - +
10A LEU* 3.8 17.9 - - + -
11A ASN* 2.7 26.1 + - - +
13A LYS* 1.3 84.8 - - + +
15A LEU* 1.3 69.0 + - - +
17A THR* 3.0 24.4 + - - -
18A LEU* 3.2 14.0 + - + +
40A THR* 4.0 32.0 + - - +
42A LEU* 4.3 9.4 - - + +
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Residues in contact with LEU 15 (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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10A LEU* 3.7 26.5 - - + +
11A ASN* 2.8 29.8 + - - +
12A GLU* 4.3 4.3 - - - -
14A GLN* 1.3 73.8 - - - +
16A HIS* 1.3 56.4 + - - +
17A THR 3.0 0.3 + - - -
18A LEU* 3.2 4.1 + - - +
19A ARG* 2.6 53.5 + - + +
50A TRP* 4.6 23.3 - - + +
54A LYS* 5.1 9.2 - - - +
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Residues in contact with HIS 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 GLU* 2.7 47.9 + - + +
13A LYS* 3.7 4.5 - - - +
15A LEU* 1.3 80.3 - - - +
17A THR* 1.3 66.9 + - - +
19A ARG* 3.1 31.4 + - + +
20A THR* 3.2 10.0 + - - +
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Residues in contact with THR 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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13A LYS 3.1 16.3 + - - -
14A GLN* 3.0 11.2 + - - -
16A HIS* 1.3 80.2 - - - +
18A LEU* 1.3 67.2 + - + +
20A THR* 2.9 23.7 - - + +
21A CYS* 3.4 3.8 + - - +
36A LEU* 4.7 12.3 - - + +
39A MET* 3.8 48.3 + - + +
40A THR* 5.1 5.9 - - - +
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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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10A LEU* 4.8 9.4 - - + -
14A GLN* 3.8 17.0 - - + +
15A LEU* 3.2 6.6 + - - +
17A THR* 1.3 77.3 - - + +
19A ARG* 1.3 66.3 + - - +
21A CYS* 2.8 24.8 + - - +
22A TYR 3.3 4.2 + - - -
36A LEU* 4.0 22.9 - - + -
40A THR* 6.0 4.9 - - - +
46A VAL* 6.2 3.6 - - + -
47A ILE* 4.3 18.6 - - + -
50A TRP* 3.3 64.7 - - + +
51A PHE* 4.6 13.0 - - + -
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Residues in contact with ARG 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 LEU* 2.6 42.8 + - + +
16A HIS* 3.1 23.1 + - + +
18A LEU* 1.3 73.0 - - - +
20A THR* 1.3 66.7 + - - +
21A CYS 3.0 1.2 + - - -
22A TYR* 3.4 12.9 + - - +
23A ALA* 3.6 9.5 + - - +
50A TRP* 4.8 4.2 - - + -
54A LYS* 6.1 2.5 - - - +
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Residues in contact with THR 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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16A HIS 3.2 7.0 + - - +
17A THR* 2.9 27.8 - - + +
19A ARG* 1.3 81.1 - - - +
21A CYS* 1.3 65.0 + - + +
23A ALA* 3.5 18.0 - - - +
24A ALA* 3.6 7.3 + - - +
39A MET* 6.5 0.9 - - - -
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Residues in contact with CYS 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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17A THR 4.0 2.0 - - - +
18A LEU* 2.8 24.9 + - - +
20A THR* 1.3 84.2 - - + +
22A TYR* 1.3 56.9 + - - +
24A ALA* 2.8 29.7 + - - +
25A ASN 3.2 7.2 + - - +
28A PRO* 5.5 3.1 - - - -
32A MET* 5.1 15.2 - - - +
36A LEU* 3.8 35.7 - - - -
51A PHE* 4.5 14.8 - - + -
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Residues in contact with TYR 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 LEU 3.3 5.7 + - - +
19A ARG* 3.4 8.0 + - - +
21A CYS* 1.3 78.6 - - - +
23A ALA* 1.3 66.3 + - - +
24A ALA 2.8 1.7 + - - -
25A ASN 3.2 19.5 + - - -
26A PRO* 4.1 32.6 - - + +
50A TRP* 4.5 16.2 - + + -
51A PHE* 4.2 22.3 - + + -
54A LYS* 4.9 9.9 - - + -
55A ARG* 3.7 28.8 + - - -
58A ASP* 4.5 13.2 + - - +
62A SER* 3.1 34.1 + - - -
64A MET* 5.5 0.3 - - - +
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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 ARG 3.6 8.2 + - - +
20A THR* 3.5 16.4 + - - +
21A CYS 3.1 0.2 + - - -
22A TYR* 1.3 81.4 - - - +
24A ALA* 1.3 59.1 + - - +
64A MET* 3.3 46.4 - - + +
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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