Contacts of the helix formed by residues 336 - 346 (chain D) in PDB entry 6G2T
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 336 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15D MET* 5.0 7.0 - - + +
17D LYS* 4.3 21.1 - - + +
26D PRO* 4.2 24.7 - - + -
29D VAL* 3.7 33.3 - - + +
304D MET* 6.4 1.6 - - + -
333D GLU* 3.1 38.7 + - + +
335D LYS* 1.3 97.9 + - + +
337D SER* 1.3 63.3 + - - +
338D VAL 3.3 2.7 - - - -
339D TRP* 3.3 6.8 + - + +
340D ILE* 3.0 25.9 + - + +
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Residues in contact with SER 337 (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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139D LEU 3.7 2.3 - - - +
140D SER* 4.1 16.8 - - - -
143D ALA* 3.3 26.4 - - - +
144D SER* 5.6 1.3 + - - -
298D LEU 5.6 0.2 + - - -
299D SER* 4.9 2.2 - - - -
331D PRO* 5.4 5.0 - - - +
333D GLU 3.3 5.6 + - - -
334D ARG* 3.2 31.5 + - - -
335D LYS 3.3 0.2 - - - -
336D TYR* 1.3 78.8 - - - +
338D VAL* 1.3 57.7 + - - +
340D ILE* 3.2 5.1 + - - +
341D GLY 2.8 25.8 + - - -
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Residues in contact with VAL 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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10D ASP* 3.1 28.5 - - + +
105D THR* 3.8 20.6 - - - +
136D GLN* 3.7 27.6 - - + +
139D LEU* 3.3 13.5 - - + +
140D SER* 4.1 17.0 - - - +
153D ASP* 3.9 18.6 - - - +
299D SER* 4.8 4.9 - - - +
300D GLY* 5.5 3.8 - - - +
334D ARG 4.6 0.4 + - - +
335D LYS 4.4 6.8 + - - +
336D TYR 3.3 0.8 - - - -
337D SER* 1.3 76.5 - - - +
339D TRP* 1.3 62.2 + - - +
341D GLY 3.3 1.2 + - - -
342D GLY 3.0 16.6 + - - -
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Residues in contact with TRP 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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8D VAL* 3.0 39.5 + - + +
10D ASP* 3.7 12.9 + - + -
17D LYS* 3.7 38.1 - - + -
18D ALA 3.7 0.6 - - - -
19D GLY* 3.5 26.7 - - - +
20D PHE 3.8 12.6 - - - -
23D ASP 3.1 28.9 - - - -
24D ASP 3.5 6.3 - - - -
25D ALA 3.5 24.7 - - - -
26D PRO* 3.6 31.9 - - + -
336D TYR* 3.3 9.1 + - - +
338D VAL* 1.3 79.0 - - - +
340D ILE* 1.3 66.4 + - + +
342D GLY* 3.0 3.3 + - - -
343D SER* 2.9 34.7 + - - -
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Residues in contact with ILE 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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24D ASP* 3.5 22.4 - - - +
25D ALA* 5.6 0.2 - - - -
143D ALA* 3.6 22.2 - - + +
333D GLU* 3.2 34.1 - - + +
336D TYR* 3.0 25.1 + - + +
337D SER* 3.5 12.1 - - - +
339D TRP* 1.3 78.9 - - + +
341D GLY* 1.3 65.2 + - - +
343D SER* 2.7 25.4 + - - +
344D ILE* 3.0 12.8 + - + +
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Residues in contact with GLY 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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139D LEU* 3.0 32.5 - - - -
142D TYR* 3.8 5.0 - - - +
143D ALA* 4.1 2.2 - - - +
337D SER 2.8 11.5 + - - -
338D VAL 3.7 0.9 - - - -
340D ILE* 1.3 77.5 - - - +
342D GLY* 1.3 57.4 + - - +
344D ILE* 3.0 12.7 - - - +
345D LEU* 2.8 31.5 + - - +
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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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8D VAL* 3.4 14.9 - - - +
103D LEU* 3.3 19.7 - - - +
139D LEU* 3.4 22.2 - - - +
338D VAL 3.0 10.9 + - - -
339D TRP 3.0 5.1 + - - -
341D GLY* 1.3 77.5 - - - +
343D SER* 1.3 59.1 + - - +
345D LEU* 3.4 1.1 + - - -
346D ALA 3.1 18.2 + - - -
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Residues in contact with SER 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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8D VAL* 3.8 10.4 - - - +
21D ALA* 3.9 6.6 - - - +
22D GLY* 3.5 20.1 + - - -
23D ASP 3.4 24.4 + - - -
24D ASP* 5.4 0.3 - - - -
339D TRP* 2.9 25.9 + - - -
340D ILE* 2.7 25.0 + - - +
342D GLY* 1.3 73.1 - - - +
344D ILE* 1.3 63.7 + - - +
346D ALA 3.6 0.5 + - - -
347D SER* 3.3 21.8 + - - -
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Residues in contact with ILE 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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142D TYR* 3.6 42.2 - - + +
143D ALA* 5.4 0.4 - - - -
340D ILE* 3.0 14.5 + - + +
341D GLY* 3.0 22.9 - - - +
343D SER* 1.3 79.1 + - - +
345D LEU* 1.3 63.7 + - - +
347D SER* 2.7 24.2 + - - +
348D LEU* 2.9 29.9 - - + +
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Residues in contact with LEU 345 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B VAL* 3.4 37.0 - - + -
103D LEU* 4.1 15.0 - - + -
132D TYR* 4.7 1.1 - - + -
134D ALA* 4.2 21.1 - - + -
138D VAL* 6.2 0.9 - - + -
139D LEU* 4.4 11.0 - - + -
142D TYR* 4.2 22.7 - - + -
341D GLY 2.8 18.7 + - - +
342D GLY 3.6 4.9 - - - +
343D SER 3.3 0.2 - - - -
344D ILE* 1.3 80.4 - - + +
346D ALA* 1.3 58.9 + - - +
347D SER 3.4 0.7 + - - -
348D LEU* 3.6 9.1 + - + +
351D PHE* 3.1 51.8 - - + +
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Residues in contact with ALA 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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6D ALA* 4.1 8.2 - - + +
8D VAL* 4.4 3.8 - - + -
21D ALA* 3.8 24.1 - - + +
103D LEU* 4.6 2.0 - - + +
342D GLY 3.1 15.9 + - - +
343D SER 4.0 0.2 - - - -
345D LEU* 1.3 75.4 - - - +
347D SER* 1.3 58.8 + - - +
348D LEU 3.3 4.7 + - - +
351D PHE* 3.7 12.3 - - + -
352D GLN* 4.4 17.5 + - - +
355D TRP* 3.7 27.3 - - + -
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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