Contacts of the helix formed by residues 350 - 364 (chain D) in PDB entry 4AY6
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 PHE 350 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314D PRO 5.2 0.4 - - - -
317D ALA* 3.9 33.9 - - + -
318D ASP* 3.4 22.9 - - - -
321D ASN* 3.9 33.9 - - + -
343D ALA* 4.6 3.8 - - + -
344D LEU* 3.8 8.3 - - + -
347D PHE* 3.2 26.9 + + + +
348D PRO 3.0 4.9 + - - -
349D GLU* 1.3 73.9 - - - +
351D ALA* 1.3 70.3 + - - +
352D ALA* 3.6 24.9 - - + -
353D ALA* 3.6 13.7 - - + -
354D HIS* 3.0 26.9 + - - -
380D ILE* 4.7 0.4 - - - -
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Residues in contact with ALA 351 (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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349D GLU 3.5 5.5 + - - -
350D PHE* 1.3 74.1 - - - +
352D ALA* 1.3 65.8 + - - +
354D HIS* 3.0 17.0 + - - +
355D SER* 3.1 11.6 + - - -
377D ALA* 4.1 9.7 - - - +
380D ILE* 3.9 22.4 - - + +
381D SER* 3.9 26.7 - - - +
384D PHE* 4.7 9.4 - - + -
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Residues in contact with ALA 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321D ASN* 4.6 3.8 - - - +
350D PHE* 3.6 21.1 - - + -
351D ALA* 1.3 77.6 - - - +
353D ALA* 1.3 53.9 + - - +
355D SER* 3.3 8.2 + - - -
356D ASN* 2.8 47.9 + - - +
384D PHE* 4.6 9.2 - - + -
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Residues in contact with ALA 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321D ASN* 3.6 18.6 - - - +
340D TYR* 4.4 5.5 - - + +
343D ALA* 4.6 8.5 - - + -
344D LEU* 3.2 27.8 - - + -
350D PHE* 3.6 26.4 + - + -
351D ALA 3.2 0.6 - - - -
352D ALA* 1.3 73.8 - - - +
354D HIS* 1.3 61.5 + - - +
356D ASN* 3.1 2.1 + - - +
357D LEU* 2.8 33.3 + - - +
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Residues in contact with HIS 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344D LEU* 3.3 27.4 - - + +
348D PRO* 3.0 22.8 + - - +
350D PHE 3.0 23.4 + - - +
351D ALA 3.0 8.4 + - - +
353D ALA* 1.3 79.3 - - - +
355D SER* 1.3 55.8 + - - +
357D LEU* 4.0 1.1 - - - -
358D ALA* 3.1 28.9 + - - +
373D HIS* 3.0 48.5 + + - +
376D GLU* 3.5 35.3 + - + +
377D ALA* 4.1 8.1 - - + +
380D ILE* 4.2 7.0 - - + -
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Residues in contact with SER 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351D ALA 3.1 6.9 + - - -
352D ALA* 3.6 8.1 - - - -
354D HIS* 1.3 75.8 - - - +
356D ASN* 1.3 67.4 + - - +
358D ALA* 3.4 14.1 + - - +
359D SER* 3.4 12.6 + - - -
374D TYR* 3.9 15.6 - - - -
377D ALA* 4.1 9.8 - - - +
384D PHE* 3.5 37.3 - - - -
386D ASP* 4.9 4.7 + - - -
387D ALA* 4.3 6.3 - - - +
390D ASN* 5.1 1.9 + - - -
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Residues in contact with ASN 356 (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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321D ASN* 3.4 27.1 + - - +
325D ASN* 3.8 8.8 + - - +
328D ARG* 4.0 10.0 + - - +
340D TYR* 3.3 29.2 - - + +
352D ALA* 2.8 28.9 + - - +
353D ALA 3.1 1.1 + - - +
355D SER* 1.3 76.2 + - - +
357D LEU* 1.3 64.9 + - - +
359D SER* 3.0 21.2 + - - -
360D VAL* 3.5 10.9 + - - +
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Residues in contact with LEU 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D VAL* 4.0 33.9 - - + -
340D TYR* 3.9 25.7 - - + -
341D ARG* 4.0 22.9 - - + +
344D LEU* 4.1 11.7 - - + -
353D ALA 2.8 17.3 + - - +
354D HIS 4.1 2.0 - - - +
356D ASN* 1.3 76.4 - - - +
358D ALA* 1.3 62.2 + - - +
360D VAL* 3.3 6.7 - - - +
361D LEU* 3.2 29.8 + - + +
373D HIS* 3.6 39.7 - - + +
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Residues in contact with ALA 358 (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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354D HIS 3.1 20.7 + - - +
355D SER 3.5 7.0 - - - +
356D ASN 3.2 0.4 - - - -
357D LEU* 1.3 78.2 - - - +
359D SER* 1.3 50.7 + - - +
361D LEU* 3.1 3.1 + - - -
362D GLN* 2.7 30.7 + - - +
370D ALA* 3.2 38.3 - - - +
373D HIS* 3.9 7.4 - - + +
374D TYR* 3.6 22.9 - - + -
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Residues in contact with SER 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D ARG* 3.2 26.1 + - - -
355D SER 3.4 7.7 + - - -
356D ASN* 3.0 14.4 + - - -
358D ALA* 1.3 76.0 - - - +
360D VAL* 1.3 60.3 + - - +
362D GLN* 3.6 7.6 - - - +
363D GLN* 3.0 24.9 + - - +
374D TYR* 3.2 20.9 - - - -
390D ASN* 5.7 3.1 - - - -
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Residues in contact with VAL 360 (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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328D ARG* 3.5 34.3 - - + +
333D ILE* 4.1 26.2 - - + -
336D ALA* 5.2 4.0 - - + -
337D VAL* 3.7 26.9 - - + -
340D TYR* 4.4 11.0 - - + -
356D ASN 3.5 9.4 - - - +
357D LEU* 3.3 21.3 - - - +
359D SER* 1.3 76.8 + - - +
361D LEU* 1.3 59.8 + - - +
362D GLN 3.1 0.2 - - - -
363D GLN* 3.2 5.4 + - - +
364D GLN* 2.8 34.2 + - - +
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Residues in contact with LEU 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D VAL* 5.7 2.9 - - + -
341D ARG* 4.1 14.1 - - - +
357D LEU* 3.2 37.6 + - + +
358D ALA 3.1 8.4 + - - +
360D VAL* 1.3 77.6 - - + +
362D GLN* 1.3 58.7 + - - +
364D GLN* 3.5 12.4 + - - +
365D GLY 3.2 2.3 + - - -
366D LYS* 2.8 62.7 + - + +
369D GLU* 4.1 15.3 - - + +
370D ALA* 3.5 22.9 - - + +
373D HIS* 3.9 20.6 - - + -
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Residues in contact with GLN 362 (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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358D ALA 2.7 18.7 + - - +
359D SER* 3.7 7.8 - - - +
360D VAL 3.1 0.4 - - - -
361D LEU* 1.3 72.5 - - - +
363D GLN* 1.3 62.2 + - - +
365D GLY* 2.8 20.4 + - - -
367D LEU* 3.8 18.5 - - + +
370D ALA* 3.5 10.3 - - + +
374D TYR* 3.4 16.7 + - - +
390D ASN* 4.0 5.7 - - - +
393D ASN* 3.8 22.2 + - - +
394D THR* 3.2 29.5 + - - +
397D GLU* 3.6 21.4 + - - +
524D LYS* 4.7 4.7 + - - -
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Residues in contact with GLN 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D ARG* 3.4 27.1 + - - -
333D ILE* 3.3 32.9 - - - +
359D SER 3.0 12.3 + - - +
360D VAL* 3.2 9.3 + - - +
362D GLN* 1.3 76.0 - - - +
364D GLN* 1.3 63.8 + - + +
365D GLY 3.2 1.0 + - - -
491D ARG* 5.6 3.3 + - - -
520D LEU* 5.0 7.9 - - + +
523D ASP* 4.8 19.1 + - + +
524D LYS* 3.7 20.1 + - - +
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Residues in contact with GLN 364 (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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333D ILE* 3.4 31.2 - - + +
334D GLU* 5.0 5.7 + - - +
337D VAL* 4.1 17.7 - - - +
360D VAL 2.8 19.8 + - - +
361D LEU* 3.9 15.4 - - - +
362D GLN 3.2 0.4 - - - -
363D GLN* 1.3 78.0 - - + +
365D GLY* 1.3 60.4 + - - +
366D LYS* 3.4 25.9 + - + +
523D ASP* 4.5 10.1 - - + +
524D LYS* 3.8 13.7 - - - +
527D VAL* 3.6 45.3 - - + +
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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