Contacts of the helix formed by residues 335 - 348 (chain D) in PDB entry 6Q2N
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 ASN 335 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263D PHE* 5.1 3.6 - - - -
267D CYS* 2.3 31.8 + - - +
269D PRO* 3.2 24.5 - - + +
331D PHE* 3.9 20.9 + - + +
332D PHE 5.0 2.0 + - - +
333D LYS 3.8 4.4 + - - -
334D ASP* 1.3 77.2 + - - +
336D THR* 1.3 65.4 + - - +
337D CYS* 2.6 23.0 + - - +
338D LEU* 3.2 35.9 - - + +
339D LYS* 3.2 23.6 + - - +
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Residues in contact with THR 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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269D PRO* 4.4 9.0 - - - +
276D SER* 3.2 23.8 - - - +
334D ASP* 4.1 6.8 + - - -
335D ASN* 1.3 74.9 + - - +
337D CYS* 1.3 59.0 + - - +
339D LYS* 3.4 9.7 + - + +
340D ASN* 2.8 44.2 + - - +
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Residues in contact with CYS 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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266D ASN 4.9 2.2 - - - -
267D CYS* 3.4 27.6 - - - +
268D GLN 4.1 7.2 - - - +
269D PRO* 4.3 0.9 - - - +
276D SER* 3.2 17.0 + - - +
277D CYS* 2.0 61.4 - - - -
282D TYR* 4.8 1.6 - - - -
285D CYS* 4.9 4.7 - - - -
335D ASN* 2.6 19.4 + - - +
336D THR* 1.3 70.0 - - - +
338D LEU* 1.3 58.9 + - - +
340D ASN 3.3 0.5 + - - -
341D ALA* 2.9 25.9 + - - +
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Residues in contact with LEU 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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213D PHE* 5.7 1.3 - - + -
263D PHE* 3.6 25.4 - - + -
267D CYS* 4.0 5.4 - - + +
285D CYS* 3.7 24.2 - - - +
286D LEU* 5.6 4.9 - - + -
289D TYR* 4.4 27.6 - - + -
307D LEU 6.0 2.0 - - - +
309D VAL* 4.9 12.8 - - + -
331D PHE 5.8 0.2 - - - +
332D PHE 5.1 4.5 - - - +
335D ASN* 3.2 27.3 - - + +
337D CYS* 1.3 78.6 - - - +
339D LYS* 1.3 58.3 + - - +
341D ALA* 3.2 5.7 + - + -
342D ILE* 2.9 52.3 + - + +
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Residues in contact with LYS 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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306D SER* 5.9 4.3 - - - -
307D LEU* 3.6 40.8 - - + +
334D ASP* 4.8 11.3 + - - +
335D ASN 3.2 21.9 + - - +
336D THR* 4.0 8.7 - - - +
338D LEU* 1.3 73.4 - - - +
340D ASN* 1.3 60.9 + - - +
342D ILE* 3.3 8.6 + - - +
343D GLN* 2.9 51.6 + - - +
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Residues in contact with ASN 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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275D SER* 2.5 41.6 + - - +
276D SER* 2.7 16.2 + - - -
277D CYS* 4.3 0.2 - - - -
282D TYR* 3.7 13.4 + - - +
336D THR* 2.8 25.7 + - - +
337D CYS 3.6 3.8 - - - +
339D LYS* 1.3 77.7 - - - +
341D ALA* 1.3 55.2 + - - +
343D GLN* 3.5 16.2 + - - +
344D ALA* 2.9 30.5 + - - +
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Residues in contact with ALA 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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282D TYR* 3.7 32.6 - - + +
285D CYS* 4.1 18.8 - - + -
286D LEU* 4.9 11.1 - - + +
337D CYS 2.9 14.3 + - - +
338D LEU* 3.2 11.6 + - + +
340D ASN* 1.3 79.3 - - - +
342D ILE* 1.3 56.7 + - - +
344D ALA* 3.7 2.2 - - - +
345D PHE* 2.9 31.5 + - - +
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Residues in contact with ILE 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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213D PHE* 4.2 34.9 - - + +
215D SER* 5.4 5.6 - - - -
225D ARG* 6.3 1.1 - - - -
286D LEU* 5.8 1.3 - - + -
289D TYR* 6.0 2.0 - - + -
301D TYR* 4.7 16.6 - - + +
307D LEU* 3.8 49.8 - - + +
309D VAL* 5.8 2.5 - - + -
338D LEU* 2.9 41.2 + - + +
339D LYS* 3.3 5.1 + - - +
341D ALA* 1.3 78.4 - - - +
343D GLN* 1.3 58.4 + - - +
345D PHE* 3.3 5.7 + - - +
346D GLY* 2.9 26.7 + - - -
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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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215D SER* 6.2 1.6 - - - -
307D LEU* 4.4 13.7 - - + +
339D LYS* 2.9 45.9 + - - +
340D ASN* 3.9 17.0 - - - +
342D ILE* 1.3 75.1 - - - +
344D ALA* 1.3 57.2 + - - +
346D GLY* 3.3 2.3 + - - -
347D ASN* 2.7 43.5 + - - +
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Residues in contact with ALA 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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282D TYR* 3.7 28.7 - - + +
340D ASN 2.9 18.8 + - - +
341D ALA 3.7 2.2 - - - +
342D ILE 3.3 0.2 - - - -
343D GLN* 1.3 78.9 - - - +
345D PHE* 1.3 60.3 + - - +
347D ASN* 3.4 14.1 + - - +
348D GLY 3.5 0.7 + - - -
349D SER* 2.9 32.2 + - - +
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Residues in contact with PHE 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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205D ALA* 5.2 3.6 - - + -
206D LYS* 5.3 8.1 - - + -
209D TYR* 3.3 49.8 - + + -
210D GLY* 3.8 8.3 - - - -
213D PHE* 3.9 17.5 - + + -
286D LEU* 3.5 34.5 - - + -
341D ALA 2.9 17.6 + - - +
342D ILE* 3.9 4.9 - - - +
344D ALA* 1.3 76.6 - - - +
346D GLY* 1.3 60.2 + - - +
348D GLY* 3.5 11.8 + - - -
349D SER* 3.6 18.9 + - - +
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Residues in contact with GLY 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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153D ASN* 4.7 2.1 + - - -
213D PHE 4.4 8.0 + - - -
215D SER* 3.0 38.9 + - - -
342D ILE 2.9 16.6 + - - -
343D GLN* 3.6 3.1 - - - -
344D ALA 3.2 0.4 - - - -
345D PHE* 1.3 76.5 - - - +
347D ASN* 1.3 63.5 + - - +
348D GLY 3.4 0.2 - - - -
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Residues in contact with ASN 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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343D GLN* 2.7 32.1 + - - +
344D ALA* 3.4 8.3 + - - +
345D PHE 3.3 0.4 - - - -
346D GLY* 1.3 80.2 - - - +
348D GLY* 1.3 57.7 + - - +
349D SER 5.2 0.2 - - - +
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Residues in contact with GLY 348 (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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344D ALA 3.5 0.8 + - - -
345D PHE 3.5 6.8 + - - -
346D GLY 3.4 3.0 - - - -
347D ASN* 1.3 79.4 - - - +
349D SER* 1.3 66.5 + - - +
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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