Contacts of the helix formed by residues 303 - 313 (chain B) in PDB entry 1ADO
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 ARG 303 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B GLU* 5.4 0.2 + - - -
41B LYS* 5.5 6.3 - - - +
42B ARG* 3.1 50.7 - - - +
271B SER* 4.6 1.6 - - - +
273B GLY* 5.8 2.9 - - - +
274B GLN 5.5 5.2 - - - +
276B GLU* 4.9 0.2 - - - -
302B GLY* 1.3 71.8 - - - +
304B ALA* 1.3 59.4 + - - +
305B LEU 3.1 0.4 + - - -
306B GLN* 4.5 4.5 - - - +
307B ALA* 3.0 41.6 + - + +
310B LEU* 6.5 0.4 - - - -
354B GLU* 2.8 46.8 + - - +
1053B 13P 2.8 50.4 + - - +
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Residues in contact with ALA 304 (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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271B SER* 3.6 29.3 + - - +
274B GLN 4.6 5.1 + - - +
276B GLU* 3.2 36.0 - - - +
279B ALA* 3.8 13.2 - - + -
301B TYR* 3.6 20.6 - - + -
302B GLY 3.3 1.4 - - - -
303B ARG* 1.3 76.9 - - - +
305B LEU* 1.3 60.4 + - - +
306B GLN 3.6 0.2 - - - -
330B ARG* 4.1 7.1 - - - +
334B ASN* 4.4 4.6 + - - +
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Residues in contact with LEU 305 (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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29B ILE 3.8 16.6 - - - +
30B LEU* 3.9 23.6 - - + -
73B ILE* 4.9 2.9 - - + -
276B GLU* 4.0 4.5 - - - +
299B PHE* 4.0 12.1 - - + -
301B TYR* 3.6 30.5 - - + +
302B GLY 3.2 8.3 + - - +
303B ARG 3.1 0.6 - - - -
304B ALA* 1.3 75.9 - - - +
306B GLN* 1.3 59.7 + - - +
307B ALA 3.9 0.7 - - - -
309B ALA* 4.8 0.7 + - - +
327B TYR* 3.4 37.0 - - + +
330B ARG* 3.8 6.6 - - + +
331B ALA* 3.7 30.7 - - + +
334B ASN* 3.5 25.4 - - - +
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Residues in contact with GLN 306 (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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30B LEU* 4.4 9.9 - - + +
31B ALA 3.2 21.0 + - - -
32B ALA* 4.2 3.5 - - - +
34B GLU* 3.2 28.1 + - - +
39B ILE* 5.3 0.2 - - - +
58B TYR* 2.7 41.1 + - - +
59B ARG* 5.7 0.3 + - - -
62B LEU* 3.7 21.0 - - + +
302B GLY 3.2 19.9 + - - +
303B ARG* 3.2 4.1 + - - +
305B LEU* 1.3 81.9 - - - +
307B ALA* 1.3 66.3 + - - +
308B SER 3.4 2.5 - - - -
309B ALA* 3.3 7.9 + - - +
310B LEU* 2.9 27.4 + - + +
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Residues in contact with ALA 307 (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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276B GLU* 3.3 21.6 + - + +
303B ARG* 3.0 25.1 + - + +
306B GLN* 1.3 77.0 - - - +
308B SER* 1.3 62.4 + - - +
310B LEU* 3.6 8.5 + - - +
311B LYS* 3.4 23.2 + - - +
351B ALA* 6.3 1.1 - - - -
353B SER* 6.2 4.0 - - - -
354B GLU* 5.1 12.1 - - + +
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Residues in contact with SER 308 (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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276B GLU* 2.6 32.3 + - - -
307B ALA* 1.3 73.0 - - - +
309B ALA* 1.3 64.4 + - - +
311B LYS* 3.4 12.8 - - - +
312B ALA* 2.9 28.1 + - - +
326B GLU* 3.5 33.0 + - - -
330B ARG* 5.2 1.9 - - - -
350B ALA* 3.0 19.3 + - - +
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Residues in contact with ALA 309 (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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58B TYR* 5.1 3.1 - - + +
61B LEU* 4.5 4.0 - - + +
62B LEU* 4.4 15.3 - - + -
276B GLU* 4.9 0.2 + - - -
305B LEU 5.4 0.4 + - - -
306B GLN* 3.3 12.0 + - - +
308B SER* 1.3 77.3 - - - +
310B LEU* 1.3 58.0 + - - +
313B TRP* 3.0 31.2 + - - +
323B ALA* 3.2 33.6 - - - +
326B GLU* 3.8 4.2 - - - +
327B TYR* 4.0 19.5 - - + +
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Residues in contact with LEU 310 (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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42B ARG* 3.6 44.4 - - + +
43B LEU* 5.1 2.2 - - + -
45B SER* 4.5 3.6 - - - +
46B ILE* 3.7 34.5 - - + +
58B TYR* 3.7 35.8 + - + +
303B ARG* 6.5 0.4 - - - -
306B GLN* 2.9 18.9 + - + +
307B ALA* 3.6 7.6 - - - +
309B ALA* 1.3 77.7 - - - +
311B LYS* 1.3 58.2 + - - +
313B TRP* 3.3 12.1 + - + +
314B GLY 3.1 21.5 + - - -
354B GLU* 5.4 7.2 - - - +
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Residues in contact with LYS 311 (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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46B ILE* 4.0 14.6 - - + +
307B ALA 3.4 12.9 + - - +
308B SER* 3.4 17.9 - - - +
310B LEU* 1.3 76.4 - - - +
312B ALA* 1.3 69.6 + - + +
314B GLY* 3.3 11.8 + - - -
353B SER* 2.9 36.8 + - - -
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Residues in contact with ALA 312 (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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308B SER 2.9 19.5 + - - +
311B LYS* 1.3 78.7 - - + +
313B TRP* 1.3 62.2 + - - +
319B ASN* 3.2 24.5 + - - +
322B ALA* 4.3 8.5 - - + +
323B ALA* 3.9 22.0 - - - +
326B GLU* 4.0 15.5 - - + +
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Residues in contact with TRP 313 (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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43B LEU* 3.9 19.3 - - + -
46B ILE* 3.6 29.8 - - + -
48B THR* 4.5 8.7 - - + -
54B ASN* 4.0 14.8 - - + -
57B PHE* 3.6 37.7 - + + -
58B TYR* 4.0 35.4 - + + -
61B LEU* 3.8 18.6 - - + -
309B ALA 3.0 20.0 + - - +
310B LEU* 3.4 6.5 - - + +
312B ALA* 1.3 77.5 - - - +
314B GLY* 1.3 61.4 + - - +
315B GLY* 3.1 28.8 + - - -
316B LYS 3.1 24.2 + - - -
319B ASN* 3.2 21.2 + - - +
320B LEU 4.9 5.4 - - - -
323B ALA* 3.7 12.5 - - + +
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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