Contacts of the helix formed by residues 335 - 348 (chain D) in PDB entry 5DO7
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 GLU 335 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331D SER 3.3 7.0 + - - +
332D ARG* 2.8 24.1 + - - +
334D GLN* 1.3 67.1 - - - +
336D LEU* 1.3 54.6 + - + +
337D ALA* 2.8 9.1 - - - +
338D THR* 1.9 89.3 + - - +
339D ARG* 5.0 0.2 - - - +
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Residues in contact with LEU 336 (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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290D THR* 4.6 8.9 + - - +
292D ILE* 4.9 8.1 - - + +
320D PHE 4.3 1.3 - - - +
321D TYR* 3.6 49.6 - - + +
323D ASP* 6.3 0.2 - - - -
332D ARG 4.1 2.9 - - - +
333D GLU* 2.8 47.7 + - + +
334D GLN* 5.0 0.2 - - - -
335D GLU* 1.3 74.1 - - + +
337D ALA* 1.3 58.6 + - - +
338D THR 3.2 0.2 - - - -
339D ARG* 3.5 41.4 + - + +
340D GLU* 3.0 21.3 + - - +
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Residues in contact with ALA 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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89D GLN* 4.0 24.9 - - - +
290D THR* 4.5 7.9 + - + +
334D GLN 2.8 18.1 + - - +
335D GLU* 2.8 5.6 - - - +
336D LEU* 1.3 75.5 - - - +
338D THR* 1.3 56.4 + - - +
340D GLU* 2.7 35.0 - - - +
341D LYS* 2.8 10.0 + - - +
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Residues in contact with THR 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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335D GLU* 1.9 79.4 + - - +
337D ALA* 1.3 68.5 - - - +
339D ARG* 1.3 57.1 + - - +
341D LYS* 2.8 27.5 + - + +
342D ALA* 2.9 12.1 + - - +
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Residues in contact with ARG 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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292D ILE* 4.3 13.1 - - + +
303D TYR* 5.0 1.0 + - - -
307D ILE* 3.6 26.2 - - - +
320D PHE* 3.9 27.1 + - - -
321D TYR* 2.8 68.0 + - + -
333D GLU* 5.8 0.4 + - - -
335D GLU 3.7 1.0 + - - +
336D LEU* 3.5 39.5 + - + +
337D ALA 3.3 0.6 - - - -
338D THR* 1.3 73.7 - - - +
340D GLU* 1.3 68.7 + - - +
342D ALA* 3.2 16.6 + - - +
343D GLN* 3.5 7.8 + - - +
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Residues in contact with GLU 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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89D GLN* 4.9 8.3 + - - +
90D ASN* 3.9 26.3 + - - +
290D THR* 4.2 10.5 - - + -
291D PRO* 3.6 43.3 - - + +
292D ILE* 4.7 3.3 - - - +
336D LEU 3.0 11.3 + - - +
337D ALA* 2.7 24.4 + - - +
339D ARG* 1.3 78.1 - - - +
341D LYS* 1.3 82.7 + - - +
343D GLN* 3.4 6.2 + - - +
344D SER* 3.2 25.3 + - - -
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Residues in contact with LYS 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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337D ALA 2.8 9.2 + - - +
338D THR* 2.8 21.4 + - + +
340D GLU* 1.3 86.6 - - - +
342D ALA* 1.3 66.5 + - - +
344D SER* 2.6 32.3 + - - +
345D LEU* 3.1 5.8 + - + +
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Residues in contact with ALA 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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303D TYR* 4.4 4.7 - - - +
338D THR 2.9 11.0 + - - +
339D ARG* 3.2 12.9 + - - +
341D LYS* 1.3 76.6 - - - +
343D GLN* 1.3 59.1 + - - +
345D LEU* 3.1 6.8 + - - +
346D ALA* 2.8 24.4 + - - +
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Residues in contact with GLN 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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291D PRO* 5.7 2.4 - - - +
292D ILE 4.1 10.8 - - - +
293D TYR* 2.7 51.4 - - + -
294D LEU* 4.0 14.4 - - - +
303D TYR* 2.9 22.9 + - + +
339D ARG 3.5 1.9 + - - +
340D GLU 3.4 9.0 + - - +
341D LYS 3.2 0.2 - - - -
342D ALA* 1.3 75.8 - - - +
344D SER* 1.3 88.7 + - - +
345D LEU 2.8 2.7 - - - -
346D ALA* 2.4 6.7 + - - +
347D ALA* 2.4 41.7 + - - +
352D LYS 5.0 5.3 + - - -
353D VAL 5.6 0.4 - - - +
354D ARG 5.1 0.2 + - - -
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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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340D GLU* 3.2 20.0 + - - -
341D LYS* 2.6 36.1 + - - +
343D GLN* 1.3 93.1 + - - +
345D LEU* 1.3 57.8 + - - +
347D ALA* 3.0 18.4 - - - +
348D LEU* 3.2 7.3 + - - -
352D LYS* 5.9 0.7 + - - -
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Residues in contact with LEU 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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341D LYS* 3.1 6.1 + - + +
342D ALA* 3.5 7.9 - - - +
343D GLN 2.5 3.2 + - - -
344D SER* 1.3 77.3 + - - +
346D ALA* 1.3 64.6 + - - +
347D ALA 2.9 5.5 + - - -
348D LEU* 3.2 18.6 + - + +
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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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293D TYR* 6.1 0.4 - - - -
303D TYR* 4.3 19.1 - - + +
342D ALA 2.8 13.3 + - - +
343D GLN* 2.4 22.6 + - + +
345D LEU* 1.3 72.5 - - - +
347D ALA* 1.3 58.7 + - - +
348D LEU* 4.9 0.9 - - - +
349D PHE* 4.8 9.2 - - - -
355D ASP* 4.0 19.4 - - - +
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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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293D TYR* 5.7 0.7 - - - -
343D GLN* 2.4 47.6 + - - +
344D SER* 3.0 17.3 - - - +
345D LEU 2.9 1.0 - - - -
346D ALA* 1.3 67.3 - - - +
348D LEU* 1.3 48.0 - - - +
349D PHE* 2.3 41.4 + - - +
352D LYS* 4.8 21.3 + - + -
353D VAL 5.1 7.4 - - - +
354D ARG 5.7 2.9 - - - -
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Residues in contact with LEU 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344D SER 3.2 9.7 + - - -
345D LEU* 3.2 13.8 + - + +
346D ALA 4.9 0.9 - - - +
347D ALA* 1.3 72.5 - - - +
349D PHE* 1.3 92.3 + - + +
350D LEU* 4.5 0.2 - - - -
352D LYS* 3.7 17.8 + - - +
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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