Contacts of the helix formed by residues 337 - 347 (chain D) in PDB entry 3LUE
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 TYR 337 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D LYS* 3.9 21.5 - - + -
26D ALA* 5.6 4.0 - - + -
27D PRO* 4.0 31.0 - - + -
30D VAL* 3.4 23.3 - - + +
334D GLU* 2.8 3.9 + - + +
336D LYS* 1.3 118.8 + - + +
338D SER* 1.3 61.7 + - - -
339D VAL 3.4 2.5 - - - -
340D TRP* 3.1 15.7 + - + +
341D ILE* 3.1 33.3 + - + +
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Residues in contact with SER 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D LEU 3.9 2.3 - - - +
141D SER* 3.6 31.3 + - - -
144D ALA* 4.1 6.6 - - - +
300D SER* 5.0 1.2 - - - -
332D PRO* 5.2 5.7 - - - +
334D GLU* 3.7 12.2 + - - +
335D ARG* 4.0 18.0 + - - -
336D LYS 3.7 1.6 - - - -
337D TYR* 1.3 72.9 - - - +
339D VAL* 1.3 67.3 + - - +
340D TRP 3.1 0.7 + - - -
341D ILE* 3.1 4.4 + - - +
342D GLY* 3.0 22.2 + - - -
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Residues in contact with VAL 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ASP* 3.4 34.3 - - - +
106D THR* 4.0 9.2 - - + -
137D GLN* 3.4 46.2 - - + +
140D LEU* 3.3 22.9 - - + +
141D SER* 3.2 22.4 - - - +
154D ASP* 4.4 2.0 - - - +
301D GLY* 5.0 12.8 - - - +
335D ARG 5.4 1.3 + - - +
336D LYS 5.4 0.2 + - - -
337D TYR 3.3 1.0 + - - -
338D SER* 1.3 74.4 - - - +
340D TRP* 1.3 64.4 + - - +
342D GLY 3.5 0.2 + - - -
343D GLY 3.4 3.3 + - - -
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Residues in contact with TRP 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 3.2 35.1 + - + +
11D ASP* 4.1 12.1 + - + +
18D LYS* 3.3 43.5 - - + -
19D ALA 3.7 0.6 - - - -
20D GLY* 3.4 33.8 - - - +
21D PHE 3.8 10.5 - - - -
24D ASP* 3.2 29.8 - - + -
25D ASP 3.8 1.6 - - - -
26D ALA* 3.4 25.1 - - - -
27D PRO* 3.4 27.8 - - + -
337D TYR* 3.1 10.3 + - - +
339D VAL* 1.3 79.3 - - - +
341D ILE* 1.3 62.0 + - + +
343D GLY* 3.3 1.2 + - - -
344D SER* 3.0 37.3 + - - -
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Residues in contact with ILE 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ASP 4.4 6.1 - - - +
25D ASP 3.2 27.6 - - - +
26D ALA* 4.8 1.3 - - + -
27D PRO* 5.1 0.7 - - + -
144D ALA* 4.0 7.6 - - + -
337D TYR* 3.1 42.8 + - + +
338D SER* 4.3 2.9 - - - +
340D TRP* 1.3 86.7 - - + +
342D GLY* 1.3 60.9 + - - +
344D SER* 4.0 2.2 - - - -
345D ILE* 3.2 22.1 + - + +
99M MET* 4.3 7.9 - - + -
101M PHE* 3.8 29.4 - - + -
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Residues in contact with GLY 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D LEU* 3.1 32.9 - - - +
143D TYR* 4.6 6.2 - - - +
144D ALA* 3.4 13.5 - - - +
338D SER 3.0 10.3 + - - -
341D ILE* 1.3 80.2 - - - +
343D GLY* 1.3 55.7 + - - +
345D ILE* 3.8 3.8 - - - +
346D LEU* 3.2 27.5 + - - +
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Residues in contact with GLY 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 3.8 14.8 - - - -
104D LEU* 4.1 6.8 - - - +
140D LEU* 3.6 22.0 - - - +
339D VAL 3.4 6.3 + - - -
340D TRP 3.3 5.6 + - - -
342D GLY* 1.3 72.9 - - - +
344D SER* 1.3 59.0 + - - +
345D ILE 3.2 0.2 + - - -
346D LEU* 3.3 3.8 + - - -
347D ALA* 2.8 33.1 + - - +
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Residues in contact with SER 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 3.4 15.0 - - - +
21D PHE 3.8 0.3 + - - -
22D ALA* 3.7 5.3 - - - +
23D GLY* 3.1 11.8 + - - -
24D ASP 2.7 41.7 + - - -
340D TRP* 3.0 32.6 + - - -
341D ILE* 3.9 6.4 - - - +
343D GLY* 1.3 73.6 - - - +
345D ILE* 1.3 49.3 + - - +
348D SER* 2.8 24.3 + - - -
101M PHE* 5.5 1.6 - - - -
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Residues in contact with ILE 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D TYR* 4.0 22.2 - - + +
144D ALA* 4.0 22.7 - - - +
341D ILE 3.2 14.5 + - - +
342D GLY 3.8 4.3 - - - +
343D GLY 3.2 0.8 - - - -
344D SER* 1.3 72.2 - - - +
346D LEU* 1.3 69.3 + - - +
348D SER* 2.6 19.7 + - - -
349D LEU* 3.2 21.1 - - + +
101M PHE* 1.9 96.7 - - + +
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Residues in contact with LEU 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B GLN* 5.0 9.0 - - + -
104D LEU* 3.5 22.2 - - + -
133D TYR* 5.1 4.0 - - + -
135D ALA* 5.3 5.4 - - + -
140D LEU* 5.7 4.5 - - + -
143D TYR* 4.7 22.4 - - + -
342D GLY 3.2 17.2 + - - +
343D GLY* 3.6 4.5 - - - +
345D ILE* 1.3 81.8 - - + +
347D ALA* 1.3 56.0 + - - +
348D SER 2.8 7.8 + - - -
349D LEU* 3.0 28.7 + - + +
351D THR* 6.0 1.3 - - + -
352D PHE* 3.3 52.9 - - + +
355D MET* 4.8 6.7 - - - -
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Residues in contact with ALA 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ALA* 5.8 0.3 - - - -
7D ALA* 3.9 22.2 + - + +
9D VAL* 4.8 2.5 - - + -
22D ALA* 3.6 21.9 - - + +
104D LEU* 4.4 13.5 - - + -
343D GLY 2.8 19.6 + - - +
346D LEU* 1.3 71.0 - - - +
348D SER* 1.3 56.1 + - - +
349D LEU 4.7 0.7 - - - +
352D PHE* 3.7 17.7 - - + +
356D TRP* 4.1 14.1 - - + -
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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