Contacts of the helix formed by residues 336 - 347 (chain D) in PDB entry 4AVP
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 GLN 336 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334D SER 5.3 2.0 - - - +
335D LEU* 1.3 76.6 - - - +
337D LEU* 1.3 64.7 + - - +
338D TRP* 3.2 25.3 + - + -
339D GLN* 2.9 22.9 + - - +
340D PHE* 3.0 20.3 + - - +
375D TRP* 3.8 2.0 - - - -
395D TYR* 5.9 3.0 - - - -
396D TYR* 3.4 23.3 + - - +
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Residues in contact with LEU 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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336D GLN* 1.3 69.8 - - - +
338D TRP* 1.4 58.5 + - - +
340D PHE* 3.2 5.3 + - + +
341D LEU* 3.0 45.0 + - + +
375D TRP* 3.5 49.4 - - + +
389D LEU* 3.7 24.9 - - + +
392D SER* 3.7 29.8 - - - -
393D LEU* 3.8 24.5 - - + +
396D TYR* 3.0 20.6 + - + +
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Residues in contact with TRP 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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421C LEU* 4.4 6.1 - - + -
424C MET* 4.6 4.9 - - + -
425C ALA* 3.6 39.9 - - + -
336D GLN* 3.2 27.5 + - + -
337D LEU* 1.4 74.8 - - - +
339D GLN* 1.3 78.4 + - + +
341D LEU* 3.4 3.7 + - - +
342D VAL* 3.1 34.9 + - + +
396D TYR* 3.2 43.4 + + + -
401D ILE* 4.5 14.2 - - + +
402D MET* 3.7 21.3 - - + -
414D PHE* 3.8 17.3 - + + -
423D SER 5.5 0.6 + - - -
424D MET* 3.8 56.0 + - + +
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Residues in contact with GLN 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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425C ALA* 3.0 26.6 + - + +
426C PHE* 3.3 18.2 - - + -
334D SER 4.4 2.6 - - - +
335D LEU* 3.7 23.7 - - + +
336D GLN* 2.9 39.6 + - + +
338D TRP* 1.3 107.6 - - + +
340D PHE* 1.3 60.3 + - - +
342D VAL* 3.2 4.9 + - - +
343D ALA 2.9 24.4 + - - -
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Residues in contact with PHE 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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335D LEU* 4.1 14.3 - - + +
336D GLN 3.0 7.2 + - - +
337D LEU* 3.5 15.7 - - + +
339D GLN* 1.3 76.7 - - - +
341D LEU* 1.4 62.5 + - + +
343D ALA* 3.2 6.2 + - + +
344D LEU* 2.9 66.0 + - + +
371D VAL 4.3 3.4 - - - -
374D ARG* 3.5 27.6 - - + -
375D TRP* 3.5 44.9 - + + -
378D GLN* 3.6 40.4 - - + -
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Residues in contact with LEU 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 LEU* 3.0 35.6 + - + +
338D TRP 3.8 4.3 - - - +
339D GLN 3.3 0.2 - - - -
340D PHE* 1.4 78.8 - - + +
342D VAL* 1.3 56.6 + - - +
344D LEU* 3.2 6.6 + - + +
345D LEU* 2.8 42.5 + - + +
354D ILE* 3.7 24.9 - - + -
363D PHE* 4.2 13.5 - - + -
365D LEU* 4.8 3.6 - - + -
371D VAL* 3.8 20.6 - - + -
389D LEU* 5.5 1.6 - - + -
393D LEU* 3.7 30.3 - - + -
402D MET* 4.1 14.8 - - + -
414D PHE* 4.7 4.0 - - + -
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Residues in contact with VAL 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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418C PRO 4.9 1.6 - - - +
421C LEU* 3.4 35.0 - - + +
422C PHE* 3.7 41.3 - - + +
425C ALA* 4.3 4.9 - - + -
426C PHE* 4.4 0.7 - - + -
338D TRP* 3.1 25.4 + - + +
339D GLN* 3.2 9.4 + - - +
341D LEU* 1.3 75.0 - - - +
343D ALA* 1.3 57.2 + - - +
345D LEU* 3.3 8.4 + - - +
346D ASP* 3.0 27.8 + - + +
356D TRP* 5.1 5.0 - - + -
414D PHE* 3.5 11.4 - - + -
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Residues in contact with ALA 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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422C PHE* 4.4 9.9 - - + -
426C PHE* 3.7 21.7 - - + -
335D LEU* 5.0 5.2 - - + -
339D GLN 2.9 13.5 + - - +
340D PHE* 3.6 12.1 - - + +
342D VAL* 1.3 75.3 - - - +
344D LEU* 1.4 62.1 + - + +
346D ASP* 3.4 10.2 + - - +
347D ASP* 3.6 12.6 + - - +
350D ASN* 4.6 0.2 + - - -
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Residues in contact with LEU 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 PHE* 2.9 58.3 + - + +
341D LEU* 3.2 7.2 + - + +
343D ALA* 1.4 74.7 - - + +
345D LEU* 1.4 60.7 + - - +
346D ASP 3.4 0.2 + - - -
347D ASP 3.2 12.1 + - - +
350D ASN* 3.2 42.5 + - - +
353D PHE* 4.0 21.8 - - + -
354D ILE* 3.7 25.4 - - + +
371D VAL* 4.6 8.1 - - + -
374D ARG* 5.0 8.1 - - + +
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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 LEU* 2.8 26.2 + - + +
342D VAL* 3.6 4.0 - - - +
344D LEU* 1.4 75.6 - - - +
346D ASP* 1.3 61.6 + - - +
347D ASP 3.5 3.5 + - - +
348D PRO* 5.6 0.2 - - - +
351D SER* 5.2 4.2 + - - -
354D ILE* 3.7 23.1 - - + +
355D ALA* 3.4 39.9 - - - -
356D TRP* 3.4 57.1 + - + +
363D PHE* 3.7 30.5 - - + -
414D PHE* 4.3 4.9 - - + -
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Residues in contact with ASP 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C PRO* 4.8 5.7 - - - +
419C GLU* 5.6 1.6 - - - -
422C PHE* 3.4 50.7 - - + +
342D VAL* 3.0 16.7 + - + +
343D ALA 3.7 3.8 - - - +
344D LEU 3.3 0.4 - - - -
345D LEU* 1.3 75.8 - - - +
347D ASP* 1.3 57.7 + - + +
348D PRO* 3.5 10.6 - - - +
356D TRP* 4.3 5.2 + - - +
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Residues in contact with ASP 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 ALA 3.6 7.5 + - - +
344D LEU 3.2 10.6 + - - +
345D LEU 3.3 3.4 - - - +
346D ASP* 1.3 76.0 - - - +
348D PRO* 1.4 65.5 - - - +
349D SER* 3.0 34.1 + - - -
350D ASN* 3.0 29.6 + - - +
351D SER* 4.0 2.6 + - - -
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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