Contacts of the helix formed by residues 12 - 23 (chain A) in PDB entry 4PIW
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 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A VAL* 3.9 20.6 - - + +
11A GLY* 1.3 83.0 - - - +
13A GLU* 1.3 64.4 + - - +
14A LEU 3.3 2.7 - - - -
15A ASP* 3.4 21.2 + - - +
16A TYR* 3.1 30.6 - - - -
245A ALA* 3.7 14.6 + - - +
248A GLU* 4.2 8.3 + - - +
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Residues in contact with GLU 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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9A VAL* 3.7 7.2 - - - +
10A VAL* 2.8 35.7 + - - +
11A GLY* 2.9 20.6 + - - -
12A THR* 1.3 77.9 + - - +
14A LEU* 1.3 63.3 + - - +
15A ASP 3.4 0.2 + - - -
16A TYR* 3.4 3.8 + - - +
17A MSE 3.1 30.2 + - + +
241A ALA 4.8 0.2 - - - +
242A TYR* 3.5 53.4 - - + +
245A ALA* 3.9 17.4 - - + +
246A GLN* 3.4 15.8 + - - +
21B MSE 5.1 2.9 - - - -
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Residues in contact with LEU 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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11A GLY 5.2 2.4 + - - +
12A THR* 3.3 1.0 - - - +
13A GLU* 1.3 79.0 - - - +
15A ASP* 1.3 65.6 + - - +
17A MSE 3.5 13.9 + - + +
18A GLN* 3.2 47.1 + - + +
14B LEU* 3.7 24.2 - - + -
18B GLN* 3.7 20.6 - - - +
21B MSE 3.7 30.6 - - + -
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Residues in contact with ASP 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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11A GLY 4.0 5.2 - - - +
12A THR* 3.5 28.0 - - - +
13A GLU 3.2 0.4 - - - -
14A LEU* 1.3 82.0 + - - +
16A TYR* 1.3 66.7 + - + +
18A GLN* 3.7 10.5 + - - +
19A SER* 3.4 18.7 + - - -
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Residues in contact with TYR 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 THR* 3.1 32.8 - - - -
13A GLU 3.4 4.7 + - - +
14A LEU 3.3 0.4 - - - -
15A ASP* 1.3 79.9 - - + +
17A MSE 1.3 64.2 + - - +
19A SER* 3.5 4.9 - - - -
20A ALA 3.2 14.7 + - - -
32A PHE* 3.4 19.8 - + + -
241A ALA* 3.3 31.7 - - - +
244A TRP* 3.4 36.5 + + - -
245A ALA* 3.6 14.4 - - + -
248A GLU* 2.9 39.5 + - - -
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Residues in contact with MSE 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 GLU 3.1 10.4 + - - +
14A LEU* 3.7 32.1 - - + +
15A ASP 3.3 0.2 - - - -
16A TYR* 1.3 77.2 - - - +
18A GLN* 1.3 59.8 + - - +
19A SER 3.1 1.6 - - - -
20A ALA* 3.2 3.8 + - - +
21A MSE 2.9 41.9 + - + +
238A LEU* 3.7 38.4 - - + +
241A ALA* 3.9 8.7 - - + -
242A TYR* 3.6 28.5 - - - +
17B MSE 5.2 6.7 - - + +
21B MSE 3.7 30.3 - - + -
238B LEU* 3.8 15.3 - - + -
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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 LEU* 3.2 42.0 + - - +
15A ASP* 3.9 10.0 + - - +
16A TYR 3.4 0.2 - - - -
17A MSE 1.3 75.8 - - - +
19A SER* 1.3 58.1 + - - +
21A MSE 3.6 20.8 - - + +
22A GLY* 2.9 25.8 + - - -
14B LEU* 4.2 21.7 - - + +
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Residues in contact with SER 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 ASP 3.4 11.9 + - - -
16A TYR* 3.5 13.9 - - - -
17A MSE 3.1 0.2 - - - -
18A GLN* 1.3 78.9 - - - +
20A ALA* 1.3 61.4 + - - +
22A GLY* 3.4 1.8 + - - -
23A SER* 3.2 21.7 + - - -
32A PHE* 3.5 18.1 - - - -
35A ARG* 5.1 0.9 + - - -
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Residues in contact with ALA 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 TYR 3.2 5.6 + - - +
17A MSE 3.2 9.0 + - - +
19A SER* 1.3 78.2 - - - +
21A MSE 1.3 62.7 + - + +
23A SER* 2.5 24.8 + - - -
24A GLY 3.7 2.4 + - - -
25A LYS 3.5 13.3 + - - +
26A LEU* 4.3 4.8 - - + +
32A PHE* 3.6 26.9 - - + -
237A ASP* 4.1 15.5 - - - +
238A LEU* 4.9 4.0 - - - -
241A ALA* 3.9 10.3 - - + -
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Residues in contact with MSE 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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14A LEU 5.2 0.2 - - - +
17A MSE 2.9 41.5 + - + +
18A GLN* 3.6 16.4 - - + +
19A SER 3.3 0.2 - - - -
20A ALA* 1.3 76.0 - - - +
22A GLY* 1.3 62.4 + - - +
24A GLY* 3.3 13.3 + - - -
26A LEU* 3.9 27.5 - - + +
238A LEU* 5.2 2.5 - - + -
13B GLU* 5.2 1.6 - - - -
14B LEU* 3.7 25.8 - - + -
17B MSE 3.5 34.1 - - + -
242B TYR* 4.2 12.8 - - + +
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Residues in contact with GLY 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 2.9 17.2 + - - -
19A SER* 3.4 2.7 + - - -
20A ALA 3.3 0.6 - - - -
21A MSE 1.3 76.5 - - - +
23A SER* 1.3 60.8 + - - +
24A GLY* 3.2 1.1 + - - -
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Residues in contact with SER 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 SER 3.2 12.7 + - - -
20A ALA* 2.5 27.4 + - - -
22A GLY* 1.3 76.8 - - - +
24A GLY* 1.3 60.7 + - - +
25A LYS* 3.5 18.8 + - - +
32A PHE* 5.7 1.0 - - - -
237A ASP* 5.0 1.6 + - - -
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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