Contacts of the helix formed by residues 352 - 366 (chain D) in PDB entry 3IAD
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 THR 352 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350D VAL 5.4 0.2 - - - +
351D PHE* 1.3 77.3 - - - +
353D ASP* 1.3 64.3 + - - +
354D LEU* 3.8 9.0 + - - +
355D GLU* 2.8 41.3 + - - +
356D ILE* 2.9 22.7 + - - +
472D ARG* 4.9 7.9 - - - +
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Residues in contact with ASP 353 (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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297D LEU* 4.4 7.4 - - + +
300D THR* 3.7 20.7 + - + +
301D PHE* 3.7 21.6 - - + -
351D PHE 5.2 1.0 - - - +
352D THR* 1.3 74.6 - - - +
354D LEU* 1.3 57.9 + - - +
356D ILE* 3.1 16.9 + - - +
357D LEU* 2.8 30.1 + - - +
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Residues in contact with LEU 354 (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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301D PHE* 3.6 28.5 - - + -
352D THR* 3.2 9.0 + - - +
353D ASP* 1.3 78.4 - - - +
355D GLU* 1.3 58.0 + - + +
357D LEU* 3.4 3.9 + - + +
358D ALA* 3.1 27.7 + - - +
418D LEU* 4.1 20.0 - - + -
422D GLN* 3.8 39.0 - - + +
425D SER* 3.8 22.7 - - - +
426D LEU* 4.3 12.6 - - + +
429D MET* 4.2 8.7 - - + -
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Residues in contact with GLU 355 (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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351D PHE* 3.5 15.7 - - + -
352D THR* 2.8 41.4 + - - +
354D LEU* 1.3 75.5 - - + +
356D ILE* 1.3 61.1 + - - +
358D ALA* 3.5 1.6 + - - +
359D ALA* 3.1 28.4 + - - +
429D MET* 3.6 32.1 - - + +
469D TYR* 5.5 3.8 - - - -
472D ARG* 2.5 49.2 + - - +
476D LEU* 4.1 13.6 - - + +
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Residues in contact with ILE 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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295D ARG* 3.8 31.9 - - - +
297D LEU* 4.7 8.1 - - + -
342D LEU* 4.1 21.5 - - + -
351D PHE* 4.2 23.1 - - + +
352D THR 2.9 18.9 + - - +
353D ASP* 3.1 17.5 + - - +
355D GLU* 1.3 75.2 - - - +
357D LEU* 1.3 65.1 + - - +
359D ALA* 3.4 2.0 + - - +
360D ILE* 3.0 45.8 + - + +
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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
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292D PHE* 3.6 36.1 - - + -
297D LEU* 4.3 11.9 - - + -
301D PHE* 3.9 35.4 - - + -
303D ILE* 4.8 4.7 - - + -
353D ASP 2.8 16.3 + - - +
354D LEU* 3.5 5.8 - - + +
356D ILE* 1.3 79.0 - - - +
358D ALA* 1.3 56.1 + - - +
360D ILE* 3.9 3.7 - - - +
361D PHE* 2.8 33.3 + - + +
415D PHE* 3.7 25.8 - - + -
418D LEU* 4.5 6.1 - - + -
426D LEU* 3.6 21.5 - - + -
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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 LEU 3.1 17.5 + - - +
355D GLU 3.9 4.0 - - - +
356D ILE 3.2 0.4 - - - -
357D LEU* 1.3 73.6 - - - +
359D ALA* 1.3 55.7 + - - +
361D PHE* 4.4 0.4 - - - -
362D ALA* 2.7 37.4 + - - +
426D LEU* 4.0 9.4 - - + +
429D MET* 4.0 28.9 - - + -
430D VAL* 3.9 24.7 - - + +
433D ILE* 4.4 3.4 - - + -
476D LEU* 6.0 0.2 - - + -
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Residues in contact with ALA 359 (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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338D THR* 4.3 9.9 - - + -
342D LEU* 4.2 14.8 - - + -
355D GLU 3.1 17.4 + - - +
356D ILE 3.4 4.0 + - - +
358D ALA* 1.3 76.1 - - - +
360D ILE* 1.3 62.1 + - - +
362D ALA* 3.5 2.6 - - - +
363D SER* 3.1 27.1 + - - -
433D ILE* 3.8 15.6 - - + +
476D LEU* 3.9 23.3 - - + -
479D MET* 5.4 0.4 - - - -
480D VAL* 4.1 5.5 - - + +
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Residues in contact with ILE 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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288D MET* 3.8 13.7 - - - -
291D ILE* 3.8 24.7 - - + -
292D PHE* 3.7 25.6 - - + -
295D ARG* 3.8 13.0 - - - +
297D LEU* 4.1 9.4 - - + -
335D VAL* 4.1 11.8 - - + +
338D THR* 4.9 5.4 - - + -
339D HIS* 5.1 6.7 - - + +
342D LEU* 4.1 12.6 - - + -
356D ILE* 3.0 38.3 + - + +
357D LEU 3.9 2.9 - - - +
359D ALA* 1.3 77.9 - - - +
361D PHE* 1.3 63.4 + - - +
363D SER* 3.1 8.9 + - - -
364D ALA* 3.0 19.6 + - - +
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Residues in contact with PHE 361 (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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288D MET* 5.0 7.4 - - + -
292D PHE* 5.5 2.7 - + + -
311D TYR* 3.2 42.6 - + - -
357D LEU* 2.8 26.0 + - + +
358D ALA* 3.9 4.0 - - - +
360D ILE* 1.3 71.7 - - - +
362D ALA* 1.3 66.6 + - - +
364D ALA* 3.1 18.6 + - + +
365D ILE* 3.2 39.0 + - + +
403D GLY 4.2 6.5 - - - -
404D PHE* 4.2 16.4 - + - -
407D LEU* 4.5 5.4 - - + -
414D ILE* 4.0 9.9 - - + -
415D PHE* 3.8 41.3 - + + -
426D LEU* 5.4 0.2 - - + -
430D VAL* 4.0 18.2 - - + -
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Residues in contact with ALA 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 22.1 + - - +
359D ALA 3.5 5.6 - - - +
361D PHE* 1.3 75.0 - - - +
363D SER* 1.3 56.7 + - - +
365D ILE* 3.3 3.5 + - - +
366D HIS* 3.0 33.3 + - - +
430D VAL* 4.3 10.5 - - + -
433D ILE* 3.5 36.8 - - + -
434D VAL* 4.0 14.8 - - + +
480D VAL* 5.2 1.1 - - - -
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Residues in contact with SER 363 (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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319D TYR* 4.5 0.2 + - - -
331D ALA* 4.2 4.9 - - - +
334D VAL* 3.9 8.7 - - - +
335D VAL* 3.5 31.6 - - - +
338D THR* 2.9 24.8 + - - +
359D ALA 3.1 12.4 + - - -
360D ILE* 3.1 9.4 + - - -
362D ALA* 1.3 75.3 - - - +
364D ALA* 1.3 67.2 + - - +
366D HIS* 3.1 24.7 + - - -
480D VAL* 3.8 11.0 - - - +
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Residues in contact with ALA 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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284D LEU* 4.2 5.1 - - + +
288D MET* 3.8 31.4 - - + -
315D LEU* 3.7 22.6 - - + +
319D TYR* 2.7 31.7 + - - -
331D ALA* 4.0 4.9 - - - +
335D VAL* 3.3 10.3 - - + +
360D ILE 3.0 8.5 + - - +
361D PHE* 3.1 12.7 + - + +
363D SER* 1.3 77.7 - - - +
365D ILE* 1.3 54.4 + - + +
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Residues in contact with ILE 365 (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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311D TYR* 3.6 15.7 - - - +
315D LEU* 3.5 30.7 - - + -
319D TYR* 3.4 3.4 - - - -
361D PHE* 3.2 41.3 + - + +
362D ALA* 3.6 6.3 - - - +
364D ALA* 1.3 76.0 - - + +
366D HIS* 1.3 66.4 + - - +
367D ASP 3.0 5.3 + - - -
368D VAL* 3.1 16.5 + - - +
399D HIS* 3.6 9.5 - - - +
400D LEU* 4.2 15.3 - - + +
403D GLY* 4.1 20.2 - - - -
404D PHE* 4.8 1.8 - - + -
430D VAL* 4.0 17.3 - - + -
434D VAL* 4.4 3.8 - - + -
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Residues in contact with HIS 366 (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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319D TYR* 3.6 1.6 + - - -
330D HIS* 3.3 16.6 - + - -
331D ALA* 4.9 2.9 - - - -
334D VAL* 3.4 27.1 - - + +
362D ALA 3.0 18.4 + - - +
363D SER* 3.1 19.5 + - - +
364D ALA 3.4 2.6 - - - -
365D ILE* 1.3 78.5 - - - +
367D ASP* 1.3 77.1 + - + +
399D HIS* 2.9 22.5 - - - +
434D VAL* 4.3 14.7 - - + +
437D THR* 4.5 25.0 + - + -
480D VAL* 5.2 2.2 - - + -
484D ASP* 3.2 13.1 + - - -
620D ZN 2.0 37.9 - - - -
621D MG 4.5 1.8 - - - -
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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