Contacts of the helix formed by residues 327 - 343 (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 ASN 327 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D TYR* 3.5 15.3 - - - -
320D HIS 3.5 22.4 - - - +
321D ALA* 5.2 2.4 + - - -
323D VAL 3.0 21.6 + - - +
324D ALA 3.0 22.6 + - - -
325D TYR 2.6 11.7 + - - +
326D HIS* 1.3 73.6 - - - +
328D ASN* 1.3 65.6 + - - +
329D ILE* 2.7 41.8 + - - +
330D HIS* 3.2 6.2 + - - +
331D ALA 3.0 21.7 + - - -
498D TRP* 5.4 0.6 - - - -
501D ARG* 3.8 10.7 - - - +
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Residues in contact with ASN 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D ASN* 3.0 40.2 + - - +
283D PRO* 3.5 6.6 - - - +
284D LEU* 4.3 3.4 - - + +
316D GLU* 2.9 43.4 + - + +
319D TYR* 3.5 18.5 - - + +
320D HIS 6.0 0.2 - - - -
321D ALA* 5.7 3.5 - - - -
327D ASN* 1.3 81.3 - - - +
329D ILE* 1.3 58.0 + - - +
331D ALA* 3.2 9.8 + - - +
332D ALA* 2.8 35.7 + - - +
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Residues in contact with ILE 329 (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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272D VAL* 4.3 21.4 - - + +
273D PHE* 3.7 32.3 - - + -
276D ALA* 4.3 21.3 - - + -
281D ASN* 4.8 4.9 - - - +
283D PRO* 4.2 9.0 - - + -
327D ASN* 2.7 24.1 + - - +
328D ASN* 1.3 79.3 + - - +
330D HIS* 1.3 53.5 + - - +
332D ALA* 3.3 3.2 + - - +
333D ASP* 2.9 28.4 + - - +
498D TRP* 3.7 9.4 - - + -
501D ARG* 3.9 29.4 - - - +
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Residues in contact with HIS 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D TYR* 3.2 61.1 + + - +
326D HIS* 4.3 5.6 - + - -
327D ASN* 3.2 8.5 + - - +
329D ILE* 1.3 75.0 - - - +
331D ALA* 1.3 65.7 + - - +
333D ASP* 3.3 4.3 + - - +
334D VAL* 3.0 36.4 + - + +
366D HIS* 3.1 9.5 + + - -
367D ASP* 3.0 19.9 + - + -
484D ASP* 3.1 13.2 + - - -
487D ASN* 5.3 1.7 + - - -
498D TRP* 3.6 16.9 - - + -
620D ZN 2.2 31.7 - - - -
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Residues in contact with ALA 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D LEU* 3.9 16.6 - - + -
319D TYR* 3.5 40.4 - - + +
327D ASN 3.0 10.9 + - - +
328D ASN* 3.3 11.0 - - - +
330D HIS* 1.3 79.9 - - - +
332D ALA* 1.3 63.2 + - - +
334D VAL* 3.4 1.7 + - - +
335D VAL* 3.1 26.9 + - - +
363D SER 4.2 4.6 - - - +
364D ALA 4.0 2.2 - - - +
366D HIS* 4.9 2.5 - - - -
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Residues in contact with ALA 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D VAL* 4.1 4.9 - - + -
283D PRO* 3.7 31.0 - - + +
284D LEU* 3.8 19.2 - - - +
287D ILE* 3.9 14.7 - - + +
328D ASN 2.8 18.5 + - - +
329D ILE 3.5 4.9 - - - +
331D ALA* 1.3 72.6 - - - +
333D ASP* 1.3 63.8 + - - +
335D VAL* 3.4 3.4 + - - +
336D GLN* 2.9 25.0 + - - +
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Residues in contact with ASP 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D VAL* 4.4 16.3 - - + +
329D ILE 2.9 18.7 + - - +
330D HIS* 3.6 7.7 + - - +
331D ALA 3.3 0.2 - - - -
332D ALA* 1.3 75.9 - - - +
334D VAL* 1.3 58.6 + - + +
336D GLN* 3.1 9.2 + - - +
337D SER* 2.8 34.3 + - - -
486D SER* 4.3 3.7 + - - -
487D ASN* 3.5 12.6 + - - -
490D LYS* 2.7 30.2 + - - -
498D TRP* 3.3 37.1 + - + -
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Residues in contact with VAL 334 (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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330D HIS* 3.0 39.4 + - + +
331D ALA 3.9 2.0 - - - +
333D ASP* 1.3 76.7 - - + +
335D VAL* 1.3 63.0 + - - +
337D SER 3.5 0.2 + - - -
338D THR* 2.9 29.8 + - - -
363D SER* 3.9 18.4 - - - +
366D HIS* 3.4 32.8 - - + +
480D VAL* 4.3 9.4 - - + +
483D ALA* 3.7 31.7 - - + +
484D ASP* 3.8 8.7 - - + +
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Residues in contact with VAL 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D LEU* 4.1 7.6 - - + -
287D ILE* 4.6 4.7 - - + -
288D MET* 3.6 23.3 - - + -
291D ILE* 3.7 19.7 - - + -
331D ALA 3.1 18.8 + - - +
332D ALA* 3.6 6.3 - - - +
334D VAL* 1.3 76.3 - - - +
336D GLN* 1.3 58.1 + - - +
338D THR* 3.3 2.9 + - - -
339D HIS* 2.9 27.4 + - - +
360D ILE* 4.1 11.0 - - + +
363D SER* 3.5 10.1 - - - -
364D ALA* 3.3 44.0 - - + +
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Residues in contact with GLN 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D VAL* 2.9 37.3 + - + +
267D LYS 2.8 28.6 + - - +
268D TRP* 4.8 1.4 - - - +
269D GLY 5.1 1.2 + - - -
270D LEU* 3.6 36.1 + - + +
287D ILE* 4.2 9.0 - - + -
291D ILE* 4.1 4.3 - - - -
332D ALA 2.9 17.8 + - - +
333D ASP* 3.7 6.5 - - - +
335D VAL* 1.3 77.5 - - - +
337D SER* 1.3 66.9 + - - +
339D HIS* 3.2 8.7 + - - +
340D VAL* 3.0 36.0 + - - +
490D LYS* 4.4 7.6 + - - -
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Residues in contact with SER 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D TRP* 3.5 28.0 - - - -
333D ASP* 2.8 18.6 + - - -
334D VAL* 3.9 3.4 - - - -
336D GLN* 1.3 78.4 + - - +
338D THR* 1.3 59.0 + - - +
340D VAL* 3.2 1.8 + - - -
341D LEU* 2.9 32.5 + - - +
483D ALA* 4.0 14.8 - - - -
486D SER* 3.9 4.1 + - - -
490D LYS* 2.7 31.4 + - - -
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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
----------------------------------------------------------
334D VAL* 2.9 18.3 + - - +
335D VAL 3.5 3.8 - - - -
337D SER* 1.3 74.5 - - - +
339D HIS* 1.3 59.0 + - - +
341D LEU* 3.1 6.3 + - - +
342D LEU* 2.8 46.2 + - + +
359D ALA* 4.2 16.8 - - + +
360D ILE* 4.7 3.6 - - + +
363D SER* 2.9 26.4 + - - +
479D MET* 4.3 13.7 - - + -
480D VAL* 4.1 11.8 - - + +
483D ALA* 3.4 16.7 - - - +
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Residues in contact with HIS 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D VAL* 3.5 24.1 - - - +
266D ASN* 2.7 25.5 + - - -
291D ILE* 3.6 38.9 - - + +
294D GLU* 3.7 17.6 + - + -
295D ARG* 3.1 49.7 + - + +
335D VAL 2.9 15.3 + - - +
336D GLN 3.3 7.6 - - - +
338D THR* 1.3 77.0 - - - +
340D VAL* 1.3 59.4 + - + +
342D LEU* 4.6 3.8 - - - -
343D SER* 2.8 31.1 + - - -
360D ILE* 5.3 4.2 - - + +
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Residues in contact with VAL 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D VAL 3.9 2.7 - - - +
266D ASN* 3.7 30.1 - - - +
267D LYS 3.9 4.0 - - - +
268D TRP* 3.7 30.5 - - + +
336D GLN* 3.0 36.5 + - - +
337D SER 3.2 6.7 + - - +
339D HIS* 1.3 75.3 - - - +
341D LEU* 1.3 65.6 + - + +
343D SER* 3.0 18.9 + - - -
344D THR* 3.4 9.5 + - - -
561D ILE* 5.8 2.7 - - + -
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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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268D TRP* 3.9 13.0 - - + -
337D SER 2.9 17.4 + - - +
338D THR 3.1 6.3 + - - +
340D VAL* 1.3 78.5 - - + +
342D LEU* 1.3 60.3 + - - +
343D SER 3.4 0.3 + - - -
344D THR* 3.4 26.0 + - - +
347D LEU* 3.8 7.1 - - - +
479D MET* 3.4 44.0 - - + +
482D CYS* 4.1 7.4 - - + -
483D ALA* 4.2 7.6 - - + +
547D TRP* 3.7 34.5 - - + -
550D TRP* 3.8 23.2 - - + +
558D ALA* 6.2 0.2 - - + -
561D ILE* 4.7 7.0 - - + -
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Residues in contact with LEU 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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295D ARG* 3.4 20.3 + - - +
338D THR* 2.8 25.4 + - + +
339D HIS* 3.8 0.4 - - - +
341D LEU* 1.3 73.5 - - - +
343D SER* 1.3 57.6 + - - +
344D THR 3.2 4.3 + - - +
347D LEU* 4.0 18.8 - - - +
348D GLU* 5.7 0.7 - - - -
351D PHE* 4.1 21.7 - - + -
356D ILE* 4.1 40.8 - - + +
359D ALA* 4.2 8.3 - - + -
360D ILE* 4.1 18.4 - - + -
476D LEU* 4.2 10.1 - - + -
479D MET* 3.5 27.8 - - + -
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Residues in contact with SER 343 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266D ASN* 5.4 6.5 + - - -
295D ARG* 3.0 15.5 + - - +
339D HIS* 2.8 25.8 + - - -
340D VAL* 3.0 14.8 + - - -
342D LEU* 1.3 74.4 - - - +
344D THR* 1.3 64.2 + - - +
345D PRO* 3.5 5.0 - - - +
348D GLU* 6.1 0.8 - - - +
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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
------------------------------------------------------------
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