Contacts of the helix formed by residues 315 - 334 (chain D) in PDB entry 3OX4
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 GLY 315 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301D LYS* 3.9 0.8 - - - +
313D ASN 3.8 0.2 + - - -
314D LEU* 1.3 77.8 - - - +
316D ASP* 1.3 56.0 + - - -
317D LYS* 3.3 2.9 - - - -
318D GLU* 3.0 18.5 + - - -
319D GLY* 2.6 32.6 + - - -
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Residues in contact with ASP 316 (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 ALA* 3.8 9.4 - - + +
298D GLY* 3.5 34.5 - - - +
301D LYS* 4.1 20.5 + - - -
315D GLY* 1.3 69.9 - - - -
317D LYS* 1.3 54.7 + - - +
319D GLY 4.4 0.2 - - - +
320D ALA* 2.8 37.8 + - - +
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Residues in contact with LYS 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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297D ALA* 4.3 9.6 - - + +
315D GLY* 3.3 0.8 - - - -
316D ASP* 1.3 78.5 - - - +
318D GLU* 1.3 61.1 + - + +
320D ALA* 3.8 2.2 - - - +
321D GLU* 3.0 46.6 + - + +
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Residues in contact with GLU 318 (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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314D LEU* 3.8 30.9 - - + +
315D GLY* 3.0 24.7 + - - +
317D LYS* 1.3 79.2 - - + +
319D GLY* 1.3 64.9 + - - +
321D GLU* 3.4 6.7 + - - +
322D ALA* 3.0 24.3 + - - +
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Residues in contact with GLY 319 (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 LYS* 3.5 28.5 - - - -
311D ILE* 3.7 14.2 - - - +
314D LEU* 4.1 1.7 - - - +
315D GLY 2.6 17.1 + - - -
318D GLU* 1.3 72.4 - - - +
320D ALA* 1.3 56.3 + - - +
322D ALA* 3.2 3.9 + - - +
323D THR* 2.9 34.7 + - - -
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Residues in contact with ALA 320 (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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293D ALA* 4.6 7.9 - - + -
297D ALA* 3.6 29.6 - - + +
300D LEU* 4.0 22.2 - - + +
301D LYS* 4.2 2.4 - - - +
316D ASP 2.8 21.7 + - - +
317D LYS* 3.8 4.3 - - - +
319D GLY* 1.3 72.6 - - - +
321D GLU* 1.3 57.9 - - - +
323D THR* 3.3 3.8 + - - -
324D ILE* 2.9 35.9 + - - +
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Residues in contact with GLU 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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290D ALA* 5.5 3.8 - - - +
293D ALA* 4.4 18.4 - - - +
317D LYS* 3.0 34.6 + - + +
318D GLU* 3.8 6.1 - - - +
319D GLY 3.3 0.2 - - - -
320D ALA* 1.3 76.4 - - - +
322D ALA* 1.3 62.9 + - - +
324D ILE* 3.4 15.1 + - - +
325D GLN* 3.0 23.1 + - - +
328D ARG* 4.8 8.1 + - - -
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Residues in contact with ALA 322 (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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309D LEU* 3.9 5.6 - - + +
311D ILE* 3.8 26.2 - - + -
314D LEU* 4.7 4.0 - - + -
318D GLU 3.0 17.2 + - - +
319D GLY 3.5 4.5 - - - +
321D GLU* 1.3 77.0 - - - +
323D THR* 1.3 57.1 + - - +
325D GLN* 3.1 8.4 + - - +
326D ALA* 2.9 28.8 + - - +
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Residues in contact with THR 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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200D PHE* 3.6 31.4 - - + -
300D LEU* 3.3 22.5 + - + +
304D GLY* 3.3 28.5 - - - -
307D MET* 4.5 5.2 - - - -
309D LEU* 3.7 10.3 - - - +
311D ILE* 3.4 4.9 - - - +
319D GLY 2.9 14.2 + - - -
320D ALA* 3.6 8.7 - - - -
322D ALA* 1.3 75.2 - - - +
324D ILE* 1.3 64.4 + - + +
326D ALA* 3.1 5.2 + - - +
327D VAL* 2.9 21.3 + - - +
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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
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286D PRO* 3.8 21.5 - - + +
289D LEU* 3.7 21.5 - - + +
290D ALA* 3.6 33.4 - - + +
293D ALA* 4.5 5.2 - - + -
300D LEU* 4.5 5.4 - - + -
320D ALA 2.9 24.8 + - - +
321D GLU* 3.8 19.7 - - - +
323D THR* 1.3 76.6 - - + +
325D GLN* 1.3 63.2 + - - +
327D VAL* 3.2 10.3 + - - +
328D ARG* 3.1 50.9 + - - +
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Residues in contact with GLN 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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321D GLU 3.0 13.6 + - - +
322D ALA* 3.1 11.9 + - - +
324D ILE* 1.3 76.0 - - - +
326D ALA* 1.3 58.7 + - - +
328D ARG* 3.0 37.0 + - - +
329D ASP* 2.9 65.5 + - - +
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Residues in contact with ALA 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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307D MET* 5.1 10.8 - - + +
309D LEU* 3.6 36.8 - - + -
322D ALA 2.9 6.4 + - - +
323D THR* 3.3 9.4 - - - +
325D GLN* 1.3 77.4 - - - +
327D VAL* 1.3 56.1 + - - +
329D ASP* 3.8 9.0 - - - +
330D LEU* 2.9 31.6 + - - +
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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
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193D MET* 4.2 10.8 - - + +
196D LEU* 4.7 5.4 - - + -
200D PHE* 3.7 34.3 - - + -
285D LEU* 3.6 26.0 - - + -
286D PRO* 3.8 19.5 - - + -
289D LEU* 4.1 9.0 - - + -
307D MET* 4.9 5.2 - - - -
323D THR* 2.9 18.3 + - + +
324D ILE* 3.4 9.2 - - - +
325D GLN 3.2 0.2 - - - -
326D ALA* 1.3 77.1 - - - +
328D ARG* 1.3 63.5 + - - +
330D LEU* 3.4 8.0 + - - +
331D ALA* 2.9 22.4 + - + +
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Residues in contact with ARG 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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286D PRO* 3.9 26.8 + - + +
287D HIS* 6.1 2.6 - - - -
290D ALA* 5.1 7.5 - - - +
321D GLU* 4.8 7.5 + - - -
324D ILE* 3.1 39.9 + - - +
325D GLN* 3.0 53.5 + - - +
327D VAL* 1.3 77.4 - - - +
329D ASP* 1.3 58.9 + - - +
331D ALA* 3.2 8.2 + - - +
332D ALA* 2.9 28.8 + - - +
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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 GLN* 2.9 53.4 + - - +
326D ALA* 3.8 7.8 - - - +
328D ARG* 1.3 71.5 - - - +
330D LEU* 1.3 68.4 + - - +
332D ALA* 3.1 7.8 + - - +
333D SER* 2.9 25.4 + - - -
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Residues in contact with LEU 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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193D MET* 4.4 11.4 - - - -
196D LEU* 4.0 26.9 - - + -
223D ILE* 4.8 6.3 - - + +
224D ALA* 5.1 11.2 - - - +
227D LEU* 4.5 10.1 - - + -
228D LYS* 4.6 23.1 - - + +
307D MET* 4.4 14.4 - - + -
326D ALA 2.9 18.1 + - - +
327D VAL* 3.6 4.3 - - - +
329D ASP* 1.3 74.6 - - - +
331D ALA* 1.3 63.6 + - - +
333D SER* 2.6 30.0 + - - +
334D ILE* 3.3 19.4 - - + +
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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
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193D MET* 4.1 14.1 - - + -
282D ALA 5.3 3.6 - - - +
286D PRO* 5.9 2.5 - - + -
327D VAL* 2.9 18.1 + - + +
328D ARG* 3.4 7.4 - - - +
329D ASP 3.2 0.2 - - - -
330D LEU* 1.3 77.1 - - - +
332D ALA* 1.3 62.5 + - - +
334D ILE* 3.2 17.4 + - - +
336D ILE* 3.2 45.7 + - + -
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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
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328D ARG 2.9 13.5 + - - +
329D ASP* 3.5 10.8 - - - +
331D ALA* 1.3 76.8 - - - +
333D SER* 1.3 59.2 + - - +
334D ILE 3.0 5.5 + - - -
335D GLY* 3.1 13.2 + - - +
336D ILE 5.1 4.9 - - - +
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Residues in contact with SER 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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185D LYS* 4.3 4.7 + - - -
228D LYS* 2.7 49.1 + - - +
329D ASP 2.9 12.2 + - - -
330D LEU* 2.6 28.2 + - - +
332D ALA* 1.3 75.9 - - - +
334D ILE* 1.3 58.9 + - - +
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Residues in contact with ILE 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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185D LYS* 3.7 23.4 - - - +
186D GLY* 5.8 1.0 - - - -
189D ALA* 3.7 33.9 - - + +
193D MET* 3.8 19.1 - - + -
227D LEU* 3.7 28.5 - - + -
228D LYS* 4.0 18.2 - - + +
231D CYS* 3.5 26.5 - - + -
330D LEU* 3.3 13.0 - - + +
331D ALA* 3.3 13.9 - - - +
333D SER* 1.3 88.4 - - - +
335D GLY* 1.3 60.2 + - - +
336D ILE* 4.1 3.1 - - + -
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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