Contacts of the helix formed by residues 326 - 343 (chain D) in PDB entry 1OKW
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 326 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322D GLN* 3.4 21.2 + - - +
324D PRO 4.3 2.9 - - - +
325D ALA* 1.3 75.7 - - - +
327D CYS* 1.3 68.0 + - - +
328D LYS* 3.0 23.6 + - - +
329D VAL* 3.0 23.8 + - + +
330D GLU* 3.1 16.2 + - - +
367D VAL* 4.1 4.0 - - - +
368D THR* 3.3 31.7 - - - +
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Residues in contact with CYS 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D ALA 4.2 0.6 + - - -
326D ASN* 1.3 73.0 + - - +
328D LYS* 1.3 60.2 + - + +
330D GLU* 3.5 12.0 + - - +
331D SER* 3.0 31.4 + - - -
419D HIS* 3.6 33.2 - - + +
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Residues in contact with LYS 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326D ASN* 3.1 10.8 + - - +
327D CYS* 1.3 78.2 - - + +
329D VAL* 1.3 61.4 + - - +
330D GLU 3.1 0.9 - - - -
331D SER* 3.8 0.3 - - - -
332D LEU* 2.7 34.8 + - - +
367D VAL* 4.0 21.8 - - + -
419D HIS* 4.3 17.7 - - + +
421D VAL* 4.2 20.4 - - + +
424D LEU* 4.8 12.3 - - + -
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Residues in contact with VAL 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322D GLN* 3.6 14.1 - - - +
326D ASN* 3.0 34.9 + - + +
328D LYS* 1.3 77.6 - - - +
330D GLU* 1.3 57.5 + - - +
333D ALA* 2.9 26.0 + - - +
360D PHE* 4.0 14.8 - - + -
363D ALA* 3.4 10.7 - - + +
364D LEU* 3.6 40.6 - - + +
367D VAL* 3.9 25.3 - - + +
368D THR* 4.5 3.4 - - + -
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Residues in contact with GLU 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319D PHE* 3.4 45.2 - - + +
322D GLN* 3.0 25.7 - - - +
325D ALA* 4.0 9.7 - - - +
326D ASN 3.1 18.5 + - - +
327D CYS* 3.6 12.2 + - - +
328D LYS 3.1 0.2 - - - -
329D VAL* 1.3 75.7 - - - +
331D SER* 1.3 66.9 + - - +
333D ALA 3.3 1.6 + - - -
334D MET* 3.1 28.8 + - - +
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Residues in contact with SER 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327D CYS 3.0 15.3 + - - -
328D LYS 3.8 0.2 - - - -
330D GLU* 1.3 76.8 - - - +
332D LEU* 1.3 65.3 + - - -
334D MET* 3.3 8.3 + - - +
335D PHE* 3.0 20.6 + - - +
413D TYR* 4.0 6.6 - - - -
417D LYS 4.6 0.7 + - - -
418D TYR* 3.4 41.3 + - - +
419D HIS* 3.4 16.0 - - - -
421D VAL* 3.7 14.8 - - - -
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Residues in contact with LEU 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D LYS 2.7 23.6 + - - +
329D VAL* 4.0 3.1 - - - +
331D SER* 1.3 72.9 - - - +
333D ALA* 1.3 59.9 + - - +
335D PHE* 2.9 36.2 - - + +
336D LEU* 3.0 11.8 + - + +
362D LEU 4.8 0.2 - - - +
363D ALA* 3.9 16.6 - - + -
366D THR* 3.8 22.9 - - + -
367D VAL* 3.7 24.0 - - + -
398D TYR* 3.4 27.6 - - + +
421D VAL* 3.8 29.8 - - + +
424D LEU* 4.8 4.9 - - + -
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Residues in contact with ALA 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315D LEU* 3.3 21.6 - - + +
319D PHE* 4.3 8.3 - - + -
329D VAL 2.9 19.5 + - - +
330D GLU 3.3 2.4 + - - +
332D LEU* 1.3 73.1 - - - +
334D MET* 1.3 66.0 + - - +
336D LEU* 3.5 5.1 + - - +
337D GLY 3.0 16.8 + - - -
359D ALA* 3.5 27.2 - - - +
360D PHE* 4.2 7.6 - - + -
363D ALA* 3.5 9.5 - - + +
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Residues in contact with MET 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D ASN* 3.1 34.3 - - + +
233D HIS* 5.6 3.6 - - + -
312D ASN* 3.3 28.5 - - - +
315D LEU* 3.7 19.9 - - - +
316D THR* 5.8 2.2 - - - -
319D PHE* 4.5 12.3 - - + -
330D GLU 3.1 16.8 + - - +
331D SER* 3.4 9.9 - - - +
333D ALA* 1.3 74.0 - - - +
335D PHE* 1.3 56.4 + - - +
337D GLY* 2.8 21.3 + - - -
338D GLU* 2.8 17.0 + - - +
413D TYR* 3.7 13.7 - - + +
418D TYR* 5.4 5.2 - - + -
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Residues in contact with PHE 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D SER 3.0 12.9 + - - +
332D LEU* 2.9 24.2 - - + +
334D MET* 1.3 76.1 - - - +
336D LEU* 1.3 74.8 + - + +
338D GLU* 3.3 3.8 + - - +
339D LEU* 3.1 51.1 + - + +
398D TYR* 4.4 15.7 - + - -
401D ALA* 5.2 2.0 - - + -
409D ILE* 3.5 19.7 - - + -
410D ARG* 3.9 24.2 - - + -
413D TYR* 3.3 46.1 - + + -
421D VAL* 4.4 3.6 - - + -
422D SER* 3.8 19.7 - - - -
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Residues in contact with LEU 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332D LEU* 3.0 14.7 + - + +
333D ALA 3.7 7.0 - - - +
334D MET 3.3 0.2 - - - -
335D PHE* 1.3 91.6 - - + +
337D GLY* 1.3 62.6 + - - +
339D LEU* 3.1 19.6 + - + +
340D SER* 3.2 11.8 + - - -
359D ALA* 3.9 13.2 - - + +
362D LEU* 3.5 43.7 - - + -
363D ALA* 4.5 5.6 - - - +
394D LEU* 3.9 25.7 - - + +
398D TYR* 3.8 40.8 - - + -
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Residues in contact with GLY 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233D HIS* 4.3 8.9 + - - -
311D VAL* 4.1 21.4 - - - +
315D LEU* 5.0 0.2 - - - -
333D ALA 3.0 10.3 + - - -
334D MET* 2.8 10.5 + - - -
336D LEU* 1.3 76.5 - - - +
338D GLU* 1.3 56.7 - - - -
340D SER* 2.4 32.3 + - - -
341D LEU* 3.6 5.7 + - - +
355D ILE* 4.8 2.0 - - - -
359D ALA* 4.3 5.8 - - - +
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Residues in contact with GLU 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D VAL* 4.7 0.3 - - - +
229D ASN* 2.8 27.0 + - - +
232D LEU* 4.0 12.4 - - + +
233D HIS* 3.9 16.4 - - + -
334D MET* 2.8 18.4 + - + +
335D PHE 3.3 6.7 + - - +
337D GLY* 1.3 67.7 - - - +
339D LEU* 1.3 67.3 + - - +
340D SER 3.0 1.8 - - - -
341D LEU* 3.0 29.3 + - + +
342D ILE 3.9 0.7 + - - -
409D ILE* 3.3 34.3 - - + +
412D LYS* 2.4 35.9 + - - -
413D TYR* 2.8 15.8 + - + +
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Residues in contact with LEU 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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335D PHE* 3.1 43.5 + - + +
336D LEU* 3.1 16.1 + - + +
338D GLU* 1.3 78.2 - - - +
340D SER* 1.3 62.0 + - - +
341D LEU 3.3 0.9 + - - -
342D ILE* 3.3 19.3 + - + +
343D ASP* 4.2 9.7 - - - +
394D LEU* 5.7 1.3 - - + -
397D THR* 4.3 24.5 - - + +
398D TYR* 5.1 2.5 - - - -
401D ALA* 4.1 20.9 - - + -
409D ILE* 3.3 38.4 - - + -
410D ARG* 5.1 4.7 - - + +
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Residues in contact with SER 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311D VAL* 4.5 4.5 - - - +
336D LEU 3.2 8.6 + - - -
337D GLY 2.4 23.6 + - - -
338D GLU 3.0 0.2 - - - -
339D LEU* 1.3 80.3 - - - +
341D LEU* 1.3 63.3 + - - +
342D ILE 3.2 0.9 + - - -
343D ASP 3.7 3.8 + - - +
347D TYR* 3.5 50.1 - - - +
355D ILE* 3.7 31.4 - - - +
394D LEU* 4.7 3.1 - - - +
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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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211D ARG* 2.9 34.4 + - - +
215D VAL* 4.3 16.5 - - + +
219D VAL* 6.0 0.2 - - + -
232D LEU* 3.8 29.2 - - + -
233D HIS* 3.7 37.7 - - + +
236D VAL* 4.1 28.9 - - + -
311D VAL* 5.6 3.4 - - + -
337D GLY 3.9 7.0 - - - +
338D GLU* 3.0 24.0 + - - +
340D SER* 1.3 85.6 + - - +
342D ILE* 1.3 55.8 + - - +
343D ASP 3.3 0.7 + - - -
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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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208D ASN 4.8 0.9 - - - +
211D ARG* 3.2 11.5 + - - +
212D ALA* 3.6 36.7 + - + +
215D VAL* 4.1 11.9 - - + -
216D ASP* 3.6 42.8 - - + +
219D VAL* 5.1 0.2 - - + -
338D GLU 4.1 0.4 - - - +
339D LEU* 3.6 12.3 - - + +
340D SER 3.2 1.0 - - - -
341D LEU* 1.3 75.3 - - - +
343D ASP* 1.3 68.4 + - - +
344D ALA 3.8 0.5 + - - -
404D HIS* 3.9 14.1 - - + +
406D GLN* 4.2 7.4 - - + -
409D ILE* 3.6 32.1 - - + -
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Residues in contact with ASP 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D ARG* 4.0 0.7 - - - -
212D ALA* 4.7 2.9 - - - +
339D LEU 4.2 10.1 + - - +
340D SER 3.7 5.2 + - - -
341D LEU 3.3 2.0 - - - -
342D ILE* 1.3 83.5 - - - +
344D ALA* 1.3 55.2 + - - +
345D ASP* 2.6 36.4 + - - +
346D PRO* 3.5 7.4 - - + +
347D TYR* 3.3 31.4 + - + +
397D THR* 4.4 14.9 + - - +
404D HIS* 3.1 35.0 + - - -
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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
------------------------------------------------------------
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