Contacts of the helix formed by residues 12 - 22 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10E VAL* 3.7 21.0 - - + +
11E GLY* 1.3 81.5 - - - +
13E GLU* 1.3 67.8 + - - +
14E LEU 3.3 2.7 - - - -
15E ASP* 3.1 15.6 + - - +
16E TYR* 3.0 40.9 + - + -
245E ALA* 3.6 17.8 + - - +
248E GLU* 4.9 6.5 + - - +
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Residues in contact with GLU 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E VAL* 4.1 8.6 - - - +
10E VAL* 2.6 35.1 + - - +
11E GLY* 2.8 22.4 + - - -
12E THR* 1.3 77.3 + - - +
14E LEU* 1.3 64.3 + - - +
16E TYR* 3.2 3.0 + - - +
17E MSE 3.0 30.5 + - + +
241E ALA 5.0 0.2 - - - +
242E TYR* 3.6 49.8 - - + +
245E ALA* 3.7 19.3 - - + -
246E GLN* 3.3 17.9 + - - +
21F MSE 5.0 2.7 - - - -
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Residues in contact with LEU 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E GLY 5.2 2.2 - - - +
12E THR* 3.3 0.8 - - - +
13E GLU* 1.3 79.0 - - - +
15E ASP* 1.3 71.0 + - - +
17E MSE 3.7 22.5 + - + +
18E GLN* 3.3 50.1 + - - +
14F LEU* 3.7 23.6 - - + -
17F MSE 5.4 0.9 - - + -
18F GLN* 3.9 21.5 - - + +
21F MSE 3.7 22.3 - - + -
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Residues in contact with ASP 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E GLY 3.6 19.9 - - - +
12E THR* 3.1 13.5 + - - +
14E LEU* 1.3 87.1 + - - +
16E TYR* 1.3 67.0 + - + +
18E GLN* 3.5 19.7 + - - +
19E SER* 3.5 10.6 + - - -
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Residues in contact with TYR 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E THR* 3.0 44.7 + - + +
13E GLU 3.2 2.9 + - - +
15E ASP* 1.3 79.4 - - + +
17E MSE 1.3 61.8 + - - +
18E GLN 3.3 0.2 - - - -
19E SER* 3.5 5.5 + - - -
20E ALA 3.3 13.2 + - - -
32E PHE* 3.5 19.6 - + - -
241E ALA* 3.3 32.6 - - + +
244E TRP* 3.3 34.3 + + - -
245E ALA* 3.6 17.7 - - + -
248E GLU* 2.5 35.5 + - - -
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Residues in contact with MSE 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E GLU 3.0 13.1 + - - +
14E LEU* 3.7 31.2 - - + +
15E ASP 3.3 0.2 - - - -
16E TYR* 1.3 76.6 - - - +
18E GLN* 1.3 59.1 + - - +
19E SER 3.2 0.4 - - - -
20E ALA* 3.4 2.5 + - - +
21E MSE 3.1 39.8 + - + +
238E LEU* 3.9 32.1 - - + +
241E ALA* 4.1 4.7 - - - -
242E TYR* 3.6 31.2 - - + +
17F MSE 4.8 9.4 - - + +
21F MSE 3.6 30.1 - - + -
238F LEU* 3.6 22.4 - - + -
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Residues in contact with GLN 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E LEU* 3.3 38.0 + - - +
15E ASP* 3.7 12.9 - - - +
16E TYR 3.3 0.4 - - - -
17E MSE 1.3 76.4 - - - +
19E SER* 1.3 58.7 + - - +
21E MSE 3.4 19.3 + - + +
22E GLY* 2.9 26.2 + - - -
14F LEU* 3.6 25.2 - - + +
18F GLN* 5.3 0.2 - - - +
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Residues in contact with SER 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ASP 3.5 8.5 + - - -
16E TYR* 3.5 12.7 + - - -
17E MSE 3.2 0.6 - - - -
18E GLN* 1.3 80.1 - - - +
20E ALA* 1.3 61.7 + - - +
22E GLY* 3.5 2.7 + - - +
23E SER* 3.4 20.8 + - - -
32E PHE* 3.9 17.3 - - - -
35E ARG* 5.4 0.9 + - - -
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Residues in contact with ALA 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E TYR 3.3 6.8 + - - +
17E MSE 3.7 8.5 - - - +
18E GLN 3.3 0.2 - - - -
19E SER* 1.3 80.5 - - - +
21E MSE 1.3 58.6 + - - +
23E SER* 2.8 21.9 + - - -
24E GLY 4.0 1.7 + - - -
25E LYS 3.4 14.9 + - - +
26E LEU* 4.3 3.0 - - + +
32E PHE* 3.6 28.9 - - + -
237E ASP* 4.2 16.8 - - - +
238E LEU* 4.8 5.8 - - + -
241E ALA* 3.9 9.6 - - + -
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Residues in contact with MSE 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E MSE 3.1 24.7 + - + +
18E GLN* 3.4 17.9 + - + +
19E SER 3.3 0.2 - - - -
20E ALA* 1.3 75.9 - - - +
22E GLY* 1.3 59.1 + - - +
23E SER 3.2 3.6 + - - -
24E GLY* 3.6 10.0 + - - -
26E LEU* 3.7 30.6 - - + +
238E LEU* 4.0 6.1 - - + -
13F GLU* 5.1 3.1 - - - -
14F LEU* 3.7 29.8 - - + -
17F MSE 3.6 24.0 - - + -
242F TYR* 3.6 21.8 - - + +
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Residues in contact with GLY 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E GLN 2.9 17.4 + - - -
19E SER* 3.5 4.5 + - - -
20E ALA 3.3 0.4 - - - -
21E MSE 1.3 76.8 - - - +
23E SER* 1.3 60.1 + - - +
24E GLY 3.4 0.7 - - - -
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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