Contacts of the helix formed by residues 316 - 335 (chain D) in PDB entry 3OLJ
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 316 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245D TRP* 6.2 0.2 - - - -
310D VAL* 4.5 0.2 - - - -
314D GLY 4.1 0.8 + - - -
315D MET* 1.3 70.7 - - - +
317D CYS* 1.3 64.8 + - - +
318D THR* 2.9 26.0 + - - -
319D LEU* 3.2 35.4 + - + +
320D MET* 3.0 23.7 + - - +
347D PHE* 4.8 3.9 - - + -
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Residues in contact with CYS 317 (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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304D LEU 4.1 8.5 - - - -
305D THR* 3.8 23.9 - - + +
309D PRO* 4.6 4.9 - - - -
310D VAL* 3.6 28.0 - - - -
311D LYS* 3.7 39.9 - - - +
315D MET 3.4 1.2 + - - -
316D ASN* 1.3 71.7 + - - +
318D THR* 1.3 56.5 + - - +
320D MET* 3.3 2.8 + - - +
321D LYS* 3.0 32.3 + - - +
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Residues in contact with THR 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D ASN* 2.9 11.8 + - - -
317D CYS* 1.3 77.9 - - - +
319D LEU* 1.3 68.3 + - + +
321D LYS* 3.3 15.7 + - + +
322D GLN* 3.3 18.7 + - - +
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Residues in contact with LEU 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D ASN* 3.2 34.9 + - + +
318D THR* 1.3 77.6 - - + +
320D MET* 1.3 60.5 + - - +
322D GLN* 3.1 21.9 + - - +
323D TYR* 2.9 24.3 + - - +
346D PRO* 3.2 27.8 - - + +
347D PHE* 3.9 21.8 - - + -
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Residues in contact with MET 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D GLY* 3.6 23.8 - - - +
241D ALA* 3.9 9.2 - - + -
304D LEU* 3.7 37.2 - - + -
305D THR* 5.7 0.9 - - + -
310D VAL* 4.0 18.8 - - + -
315D MET* 3.6 36.3 - - + -
316D ASN 3.0 13.6 + - - +
317D CYS 3.5 8.7 - - - +
318D THR 3.3 0.2 - - - -
319D LEU* 1.3 73.4 - - - +
321D LYS* 1.3 64.2 + - - +
323D TYR* 3.2 12.9 + - - -
324D ILE* 3.2 27.2 + - - +
347D PHE* 3.8 16.7 - - + -
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Residues in contact with LYS 321 (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 GLN* 2.9 55.1 + - + +
305D THR* 3.7 33.7 + - + +
317D CYS 3.0 14.7 + - - +
318D THR* 3.5 14.8 - - + +
320D MET* 1.3 76.8 - - - +
322D GLN* 1.3 62.0 + - - +
324D ILE* 3.5 2.0 + - - +
325D GLU* 3.4 12.7 + - - +
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Residues in contact with GLN 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318D THR* 3.3 9.1 + - - +
319D LEU* 3.1 27.1 + - - +
321D LYS* 1.3 76.2 - - - +
323D TYR* 1.3 65.6 + - - +
325D GLU* 3.2 9.3 + - - -
326D PHE* 3.0 19.9 + - - +
343D VAL* 3.6 22.6 - - + +
344D GLU* 3.0 41.5 + - - +
346D PRO* 3.8 17.0 - - + +
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Residues in contact with TYR 323 (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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237D SER* 3.6 26.7 + - - -
241D ALA* 3.7 15.9 - - + -
319D LEU 2.9 7.7 + - - +
320D MET* 3.2 6.9 + - - +
322D GLN* 1.3 76.5 - - - +
324D ILE* 1.3 68.8 + - + +
326D PHE* 3.2 13.1 + + - +
327D VAL* 2.9 53.5 + - + +
330D ARG* 4.7 5.8 + - - -
345D ASN* 3.3 27.8 - - - -
346D PRO* 3.7 8.9 - - + +
347D PHE* 3.5 29.4 - + + -
350D MET* 3.2 41.0 - - + +
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Residues in contact with ILE 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D ILE* 3.8 19.4 - - + +
237D SER* 3.4 20.0 - - - +
238D GLY* 3.8 9.4 - - - +
297D VAL* 4.0 16.8 - - + +
300D GLU* 3.7 21.3 - - + -
301D GLN* 4.2 11.2 - - + -
304D LEU* 3.5 31.6 - - + -
320D MET* 3.2 21.2 + - - +
321D LYS 3.8 6.7 - - - +
322D GLN 3.3 0.2 - - - -
323D TYR* 1.3 78.3 - - + +
325D GLU* 1.3 57.3 + - - +
327D VAL* 3.4 7.8 + - - +
328D ALA* 3.0 26.9 + - - +
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Residues in contact with GLU 325 (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 VAL* 3.9 7.0 - - + -
298D ARG* 3.0 23.9 + - - -
301D GLN* 3.1 22.3 + - - +
321D LYS* 3.4 5.8 + - - +
322D GLN* 3.2 10.5 + - - +
324D ILE* 1.3 74.7 - - - +
326D PHE* 1.3 59.4 + - - +
328D ALA* 3.4 0.6 + - - -
329D ASP* 3.0 33.3 + - - +
341D PHE* 3.6 47.3 - - + +
343D VAL* 3.7 21.1 - - + +
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Residues in contact with PHE 326 (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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322D GLN 3.0 12.6 + - - +
323D TYR* 3.4 18.8 - + - +
325D GLU* 1.3 75.9 - - - +
327D VAL* 1.3 64.7 + - - +
329D ASP* 3.3 8.6 + - + +
330D ARG* 3.1 61.3 + - + +
343D VAL* 3.8 17.3 - - - +
344D GLU* 3.7 13.7 - - - +
345D ASN* 3.6 52.3 - - + -
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Residues in contact with VAL 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233D GLY* 3.2 30.1 - - - +
234D ILE* 4.4 6.3 - - + -
237D SER* 4.0 11.7 - - - +
323D TYR* 2.9 53.0 + - + +
324D ILE* 3.5 9.9 - - - +
325D GLU 3.3 0.2 - - - -
326D PHE* 1.3 77.0 - - + +
328D ALA* 1.3 57.9 + - - +
330D ARG* 3.2 25.6 + - - +
331D LEU* 3.0 27.5 + - + +
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Residues in contact with ALA 328 (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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234D ILE* 3.9 12.8 - - + -
293D ILE* 3.8 14.2 - - + +
297D VAL* 3.4 33.2 - - + -
324D ILE 3.0 10.7 + - - +
325D GLU 3.7 4.3 - - - +
327D VAL* 1.3 73.8 - - - +
329D ASP* 1.3 59.3 + - - +
331D LEU* 3.2 4.7 + - - +
332D MET* 2.8 34.2 + - - +
340D VAL* 5.1 0.4 - - + -
341D PHE* 4.0 8.3 - - + -
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Residues in contact with ASP 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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325D GLU 3.0 15.8 + - - +
326D PHE* 3.3 11.6 + - + +
328D ALA* 1.3 75.7 - - - +
330D ARG* 1.3 56.5 + - - +
332D MET* 3.2 8.4 + - - +
333D LEU* 3.0 33.9 + - - +
339D LYS* 3.8 19.5 - - + +
340D VAL* 2.9 32.6 + - - +
341D PHE* 2.9 12.7 + - - +
342D ARG* 2.8 29.0 + - - -
343D VAL 3.6 10.7 + - - +
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Residues in contact with ARG 330 (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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323D TYR* 4.7 5.9 + - - -
326D PHE* 3.1 48.3 + - + +
327D VAL* 3.2 32.3 + - - +
329D ASP* 1.3 72.2 - - - +
331D LEU* 1.3 60.5 + - - +
333D LEU* 3.5 13.1 + - + +
334D GLU* 2.9 34.0 + - + +
345D ASN* 5.7 0.4 - - - +
350D MET 5.8 3.0 + - - -
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Residues in contact with LEU 331 (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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229D ALA* 4.0 37.9 - - + +
230D ALA* 4.3 0.2 - - - -
233D GLY* 5.5 2.5 - - - -
234D ILE* 4.2 14.4 - - + -
270D CYS* 5.0 8.3 - - + -
274D CYS* 3.7 25.1 - - - -
293D ILE* 3.7 28.7 - - + -
327D VAL* 3.0 14.5 + - + +
328D ALA* 3.5 9.4 - - - +
330D ARG* 1.3 75.2 - - - +
332D MET* 1.3 58.3 + - - +
334D GLU* 3.2 8.7 + - - +
335D LEU* 2.9 38.5 + - + +
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Residues in contact with MET 332 (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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286D GLU* 4.6 1.6 - - + -
289D VAL* 3.6 30.5 - - + -
290D ARG* 3.7 30.5 - - + +
293D ILE* 3.8 23.1 - - + -
328D ALA 2.8 17.8 + - - +
329D ASP* 3.4 10.3 - - - +
331D LEU* 1.3 76.6 - - - +
333D LEU* 1.3 60.1 + - - +
335D LEU* 3.2 12.4 + - - +
336D GLY 3.2 0.2 + - - -
337D PHE* 2.9 51.2 + - + +
338D SER 3.7 19.3 - - - +
339D LYS* 4.7 0.2 - - - -
340D VAL* 4.2 18.4 - - + -
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Residues in contact with LEU 333 (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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278D LYS* 5.3 0.9 + - - -
329D ASP 3.0 17.3 + - - +
330D ARG* 3.7 12.8 - - + +
332D MET* 1.3 76.3 - - - +
334D GLU* 1.3 57.6 + - - +
336D GLY* 2.9 21.0 + - - -
337D PHE 3.6 17.9 + - - +
338D SER* 4.7 1.1 - - - -
339D LYS* 3.8 42.2 - - + +
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Residues in contact with GLU 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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270D CYS* 5.0 2.3 - - - +
271D ASP* 2.6 41.0 + - - +
274D CYS* 3.8 31.4 - - + +
278D LYS* 3.6 15.2 + - - +
330D ARG* 2.9 23.1 + - + +
331D LEU* 3.2 11.3 + - - +
333D LEU* 1.3 75.9 - - - +
335D LEU* 1.3 59.0 + - - +
336D GLY 3.4 0.7 + - - -
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Residues in contact with LEU 335 (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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225D VAL* 6.1 0.4 - - + -
226D VAL* 4.0 28.9 - - + -
229D ALA* 5.6 3.4 - - + -
273D ALA 4.8 1.3 - - - +
274D CYS* 3.7 23.3 - - - +
277D PHE* 3.5 54.3 - - + -
278D LYS* 3.5 11.6 - - - +
283D LYS* 5.4 0.3 + - - -
289D VAL* 4.2 17.3 - - + -
293D ILE* 5.0 0.7 - - + -
331D LEU* 2.9 36.3 + - + +
332D MET* 3.2 10.0 + - - +
334D GLU* 1.3 74.5 - - - +
336D GLY* 1.3 60.4 + - - +
337D PHE* 3.5 13.2 - - + -
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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