Contacts of the helix formed by residues 12 - 23 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C VAL* 4.0 13.8 - - + +
11C GLY* 1.3 79.8 - - - +
13C GLU* 1.3 64.4 + - - +
14C LEU 3.3 2.5 - - - -
15C ASP* 3.1 21.7 + - - +
16C TYR* 3.1 32.1 - - + +
245C ALA* 3.5 23.9 + - - +
248C GLU* 4.3 5.0 + - - +
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Residues in contact with GLU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C VAL* 3.8 7.0 - - - +
10C VAL* 2.9 34.0 + - - +
11C GLY* 2.9 26.6 + - - -
12C THR* 1.3 77.8 + - - +
14C LEU* 1.3 62.6 + - - +
15C ASP 3.3 0.3 + - - -
16C TYR* 3.4 3.5 + - - +
17C MSE 3.2 28.7 + - + +
241C ALA 4.7 0.3 - - - +
242C TYR* 3.5 53.6 - - + +
245C ALA* 3.8 19.2 - - + +
246C GLN* 3.4 15.9 + - - +
21D MSE 5.3 2.7 - - - -
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Residues in contact with LEU 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C GLY 4.9 4.4 + - - +
12C THR 3.3 0.6 - - - -
13C GLU* 1.3 79.7 - - - +
15C ASP* 1.3 67.6 + - - +
17C MSE 3.5 12.4 + - + +
18C GLN* 3.2 41.5 + - - +
14D LEU* 3.6 28.3 - - + -
18D GLN* 3.6 22.2 - - + +
21D MSE 3.7 28.6 - - + -
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Residues in contact with ASP 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C GLY 3.9 6.2 - - - +
12C THR* 3.1 26.4 + - - +
14C LEU* 1.3 81.6 + - - +
16C TYR* 1.3 67.9 + - + +
18C GLN* 3.3 11.7 + - - +
19C SER* 3.1 19.6 + - - -
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Residues in contact with TYR 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C THR* 3.1 38.9 + - + +
13C GLU 3.4 3.8 + - - +
15C ASP* 1.3 78.6 - - + +
17C MSE 1.3 61.5 + - - +
19C SER* 3.3 8.5 + - - -
20C ALA 3.0 20.4 + - - -
32C PHE* 3.5 16.2 - + + -
241C ALA* 3.3 29.7 - - - +
244C TRP* 3.3 33.4 + + - -
245C ALA* 3.6 15.0 - - + -
248C GLU* 2.6 40.6 + - - -
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Residues in contact with MSE 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C GLU 3.2 12.6 + - - +
14C LEU* 3.7 25.4 - - + +
16C TYR* 1.3 75.4 - - - +
18C GLN* 1.3 59.3 + - - +
19C SER 3.1 0.2 - - - -
20C ALA* 3.2 3.3 + - - +
21C MSE 2.8 39.9 + - + +
238C LEU* 4.0 30.2 - - + +
241C ALA* 3.8 9.6 - - + -
242C TYR* 3.7 16.2 - - + +
17D MSE 4.9 9.6 - - + +
21D MSE 3.6 36.6 - - + -
238D LEU* 3.7 32.8 - - + -
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Residues in contact with GLN 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LEU* 3.2 34.5 + - - +
15C ASP* 3.6 11.8 - - - +
17C MSE 1.3 76.7 - - - +
19C SER* 1.3 57.5 + - - +
21C MSE 3.6 20.7 - - + +
22C GLY* 2.9 25.3 + - - -
14D LEU* 3.6 26.7 - - + +
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Residues in contact with SER 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ASP 3.1 12.9 + - - -
16C TYR* 3.3 13.2 - - - -
17C MSE 3.1 0.4 - - - -
18C GLN* 1.3 77.6 - - - +
20C ALA* 1.3 61.7 + - - +
22C GLY* 3.5 1.7 + - - -
23C SER* 3.2 23.6 + - - -
32C PHE* 3.4 20.3 - - - -
35C ARG* 5.2 1.4 + - - -
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Residues in contact with ALA 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C TYR 3.0 13.2 + - - +
17C MSE 3.6 7.9 - - - +
19C SER* 1.3 77.9 - - - +
21C MSE 1.3 60.5 + - - +
23C SER* 2.7 22.7 + - - -
25C LYS 3.1 18.1 + - - +
26C LEU* 4.2 3.1 - - + +
32C PHE* 3.6 21.3 - - + -
237C ASP* 4.2 13.7 - - - +
238C LEU* 4.7 8.7 - - + -
241C ALA* 3.8 11.4 - - + -
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Residues in contact with MSE 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C MSE 2.8 41.9 + - + +
18C GLN* 3.6 17.3 - - + +
20C ALA* 1.3 77.9 - - - +
22C GLY* 1.3 59.8 + - - +
23C SER 3.4 0.7 + - - -
24C GLY* 3.4 12.3 + - - -
26C LEU* 3.9 30.2 - - + +
238C LEU* 4.4 4.3 - - + -
13D GLU* 5.2 1.6 - - - -
14D LEU* 3.7 32.5 - - + -
17D MSE 3.5 26.9 - - + -
242D TYR* 4.1 13.9 - - + +
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Residues in contact with GLY 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C GLN 2.9 17.9 + - - -
19C SER* 3.5 3.1 + - - -
20C ALA 3.3 0.2 - - - -
21C MSE 1.3 73.6 - - - +
23C SER* 1.3 58.5 + - - +
24C GLY 3.2 4.0 + - - -
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Residues in contact with SER 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C SER 3.2 12.8 + - - -
20C ALA* 2.7 25.8 + - - -
22C GLY* 1.3 78.5 - - - +
24C GLY* 1.3 62.6 + - - +
25C LYS* 3.5 15.6 + - - +
32C PHE* 5.7 1.4 - - - -
237C ASP* 5.0 2.4 + - - -
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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