Contacts of the helix formed by residues 10 - 22 (chain P) in PDB entry 1ZQ3
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 THR 10 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8P THR* 4.5 5.2 - - + +
9P PHE* 1.4 81.5 - - - +
11P SER* 1.3 63.8 + - - +
12P SER* 3.3 19.2 + - - -
13P GLN* 3.1 15.8 + - + +
14P ILE* 3.1 28.1 + - - +
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Residues in contact with SER 11 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10P THR* 1.3 71.5 - - - +
12P SER* 1.4 50.2 + - - +
14P ILE* 3.6 11.1 - - - +
15P ALA* 2.7 35.1 + - - +
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Residues in contact with SER 12 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10P THR* 3.2 11.1 + - - -
11P SER* 1.4 73.5 - - - +
13P GLN* 1.4 71.0 + - - +
15P ALA* 3.3 7.5 + - - +
16P GLU* 3.1 30.8 + - - +
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Residues in contact with GLN 13 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8P THR 5.3 2.5 - - - +
9P PHE* 4.2 19.5 - - + -
10P THR* 3.1 26.2 + - + +
12P SER* 1.4 84.2 - - - +
14P ILE* 1.3 60.7 + - - +
15P ALA 3.3 0.2 + - - -
16P GLU* 3.4 1.7 + - - +
17P LEU* 2.8 40.2 + - + +
39P LEU* 2.8 49.7 + - + +
40P ALA 4.9 0.2 - - - -
41P LEU* 3.8 24.2 - - + +
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Residues in contact with ILE 14 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9P PHE* 4.4 23.8 - - + -
10P THR 3.1 18.5 + - - +
11P SER* 3.9 10.5 - - - +
13P GLN* 1.3 75.5 - - - +
15P ALA* 1.3 61.5 + - - +
17P LEU* 4.4 4.9 - - - -
18P GLU* 3.1 48.5 + - + +
49P TRP* 4.8 11.7 - - - +
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Residues in contact with ALA 15 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11P SER 2.7 21.3 + - - +
12P SER* 3.4 11.0 - - - +
13P GLN 3.2 0.2 - - - -
14P ILE* 1.3 73.4 - - - +
16P GLU* 1.3 65.3 + - - +
18P GLU* 4.3 2.5 - - - +
19P GLN* 3.1 32.8 + - - +
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Residues in contact with GLU 16 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P SER 3.1 15.8 + - - +
13P GLN* 3.5 1.8 - - - +
15P ALA* 1.3 77.9 - - - +
17P LEU* 1.3 58.5 + - - +
19P GLN* 3.2 1.8 + - - -
20P HIS* 2.8 60.7 + - - -
35P LEU* 3.7 4.4 - - + +
38P LYS* 3.5 22.0 - - - +
39P LEU* 3.5 40.2 - - + +
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Residues in contact with LEU 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9P PHE* 3.8 24.5 - - + -
13P GLN* 2.8 24.6 + - + +
14P ILE* 4.2 2.2 - - - +
16P GLU* 1.3 75.1 - - - +
18P GLU* 1.3 51.6 - - - +
21P PHE* 2.9 36.9 + - - +
35P LEU* 3.7 11.5 - - + +
39P LEU* 3.5 35.9 - - + -
45P GLN 6.0 0.2 - - - -
46P VAL* 3.6 24.7 - - + -
49P TRP* 3.1 53.9 - - + -
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Residues in contact with GLU 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14P ILE* 3.1 37.2 + - + +
15P ALA* 4.3 3.2 - - - +
17P LEU* 1.3 75.7 - - - +
19P GLN* 1.3 66.6 + - + +
21P PHE* 3.4 6.7 - - + +
22P LEU* 3.1 29.4 + - + +
49P TRP* 3.6 13.7 - - + -
53P ARG* 2.8 38.4 + - - +
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Residues in contact with GLN 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15P ALA* 3.1 20.1 + - - +
16P GLU* 3.2 4.9 + - - +
18P GLU* 1.3 80.0 - - + +
20P HIS* 1.3 69.9 + - + +
22P LEU* 3.4 42.5 + - - +
23P GLN* 4.1 10.6 + - - +
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Residues in contact with HIS 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P GLU* 2.8 54.0 + - - -
19P GLN* 1.3 75.0 + - + +
21P PHE* 1.3 63.7 + - - +
22P LEU 3.3 0.9 - - - -
23P GLN* 3.1 26.1 + - - +
24P GLY 3.5 4.6 + - - +
31P ARG* 6.1 0.3 - - - +
34P ASP* 4.5 7.4 + - - +
35P LEU* 3.2 35.7 - - + -
38P LYS* 3.0 36.5 + - + +
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Residues in contact with PHE 21 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17P LEU 2.9 23.8 + - - +
18P GLU* 3.4 11.7 - - - +
20P HIS* 1.3 70.7 - - - +
22P LEU* 1.3 82.5 + - + +
24P GLY 2.9 29.6 + - - -
25P ARG* 3.1 49.5 + - + -
35P LEU* 4.2 1.4 - - - +
49P TRP* 3.7 14.4 - + + -
50P PHE* 3.5 27.8 - + + -
53P ARG* 3.5 44.4 - - - -
54P ARG* 5.7 2.7 - - - -
57P HIS* 5.6 1.1 - + - -
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Residues in contact with LEU 22 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18P GLU* 3.1 23.9 + - + +
19P GLN* 3.4 31.6 - - - +
20P HIS 3.3 1.0 - - - -
21P PHE* 1.3 91.3 - - + +
23P GLN* 1.4 72.7 + - - +
25P ARG* 2.9 32.6 + - + +
53P ARG* 5.7 1.8 - - - +
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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