Contacts of the helix formed by residues 12 - 24 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B VAL* 3.6 19.0 - - + +
11B GLY* 1.3 84.0 - - - +
13B GLU* 1.3 64.5 + - - +
14B LEU 3.2 2.7 - - - -
15B ASP* 3.2 22.0 + - - +
16B TYR* 3.1 31.9 - - + -
245B ALA* 3.4 25.9 + - - +
248B GLU* 4.4 8.2 + - - +
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Residues in contact with GLU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A MSE 5.2 2.7 - - - -
8B PRO 3.7 0.3 - - - +
9B VAL* 3.6 6.4 - - - +
10B VAL* 2.7 34.4 + - - +
11B GLY* 2.9 20.1 + - - -
12B THR* 1.3 79.0 + - - +
14B LEU* 1.3 62.4 + - - +
16B TYR* 3.5 1.9 + - - +
17B MSE 3.1 31.7 + - + +
241B ALA 4.8 1.1 - - - +
242B TYR* 3.6 59.9 - - + +
245B ALA* 3.7 12.1 - - + -
246B GLN* 3.2 15.8 + - + -
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Residues in contact with LEU 14 (chain B).
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* 3.7 28.0 - - + -
18A GLN* 4.2 20.6 - - + +
21A MSE 3.7 27.8 - - + -
11B GLY 5.2 3.7 - - - +
12B THR* 3.2 1.7 - - - +
13B GLU* 1.3 80.6 + - - +
15B ASP* 1.3 65.6 + - - +
17B MSE 3.6 11.9 + - + +
18B GLN* 3.3 39.3 + - - +
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Residues in contact with ASP 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLY 4.5 5.0 - - - +
12B THR* 3.2 20.0 + - - +
14B LEU* 1.3 82.5 - - - +
16B TYR* 1.3 66.3 + - + +
18B GLN* 3.4 22.4 + - - +
19B SER* 3.6 9.2 + - - -
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Residues in contact with TYR 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B THR* 3.1 36.7 + - - +
13B GLU 4.1 1.3 - - - +
15B ASP* 1.3 79.2 - - + +
17B MSE 1.3 63.8 + - - +
19B SER* 3.2 20.6 + - - -
20B ALA 3.4 3.1 + - - -
32B PHE* 3.7 13.4 - + - -
241B ALA* 3.4 32.1 - - + +
244B TRP* 3.4 36.2 + + - -
245B ALA* 3.6 15.0 - - + -
248B GLU* 2.9 41.3 + - - -
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Residues in contact with MSE 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A MSE 5.2 4.3 - - + +
21A MSE 3.5 38.8 - - + -
238A LEU* 3.7 20.6 - - - -
13B GLU 3.1 28.0 + - - +
14B LEU* 3.6 16.2 - - + +
15B ASP 3.3 0.4 - - - -
16B TYR* 1.3 76.9 - - - +
18B GLN* 1.3 58.5 + - - +
19B SER 3.2 0.2 - - - -
20B ALA* 3.4 5.3 + - - +
21B MSE 3.2 37.4 + - + +
238B LEU* 3.8 35.8 - - + +
241B ALA* 3.9 9.6 - - + -
242B TYR* 3.6 25.1 - - + +
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Residues in contact with GLN 18 (chain B).
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* 3.7 29.0 - - + +
14B LEU* 3.3 29.9 + - - +
15B ASP* 3.4 16.6 + - - +
16B TYR 3.2 0.8 - - - -
17B MSE 1.3 75.3 - - - +
19B SER* 1.3 60.6 + - - +
21B MSE 3.6 22.4 - - + +
22B GLY* 2.9 23.6 + - - -
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Residues in contact with SER 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ASP 3.6 6.6 + - - -
16B TYR* 3.2 15.4 + - - -
17B MSE 3.2 0.4 - - - -
18B GLN* 1.3 77.7 - - - +
20B ALA* 1.3 58.3 + - - +
22B GLY* 3.9 1.6 - - - -
23B SER* 3.0 29.5 + - - -
32B PHE* 3.3 21.8 - - - -
35B ARG* 5.0 0.9 + - - -
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Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B TYR 3.4 5.1 + - - +
17B MSE 3.4 8.3 + - - +
18B GLN 3.3 0.2 - - - -
19B SER* 1.3 77.8 - - - +
21B MSE 1.3 61.8 + - - +
23B SER* 2.6 22.4 + - - -
24B GLY 3.5 4.7 + - - -
25B LYS 3.5 9.2 - - - +
26B LEU* 3.5 14.8 - - + +
32B PHE* 3.8 18.8 - - + -
237B ASP* 4.0 26.9 - - - +
238B LEU* 4.8 3.4 - - + -
241B ALA* 4.3 4.0 - - + -
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Residues in contact with MSE 21 (chain B).
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* 5.1 5.2 - - - -
14A LEU* 3.7 22.4 - - + -
17A MSE 3.7 23.8 - - + +
242A TYR* 4.1 20.9 - - + +
17B MSE 3.2 24.4 + - + +
18B GLN* 3.6 28.7 - - + +
20B ALA* 1.3 75.4 - - - +
22B GLY* 1.3 63.3 + - - +
24B GLY* 3.4 12.1 + - - -
26B LEU* 3.8 19.2 - - + +
238B LEU* 4.5 6.5 - - + -
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Residues in contact with GLY 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLN 2.9 18.8 + - - -
19B SER* 3.5 2.7 + - - -
20B ALA 3.3 0.2 - - - -
21B MSE 1.3 77.5 - - - +
23B SER* 1.3 62.8 + - - +
24B GLY* 3.4 0.7 + - - -
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Residues in contact with SER 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B SER 3.0 13.3 + - - -
20B ALA* 2.6 27.2 + - - -
22B GLY* 1.3 76.3 - - - +
24B GLY* 1.3 60.4 + - - +
25B LYS* 3.6 14.9 + - - +
32B PHE* 5.7 1.1 - - - -
237B ASP* 5.0 1.7 + - - -
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Residues in contact with GLY 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PRO* 3.3 36.0 - - - +
179A GLU* 4.2 1.9 - - - +
20B ALA 3.5 0.6 + - - -
21B MSE 3.4 11.5 + - - -
22B GLY 3.2 4.4 - - - -
23B SER* 1.3 81.4 + - - +
25B LYS* 1.3 59.7 + - - +
26B LEU* 5.2 1.1 - - - -
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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