Contacts of the helix formed by residues 318 - 337 (chain D) in PDB entry 1OJ7
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 SER 318 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D GLY* 1.3 77.3 - - - +
319D ASP* 1.3 65.0 + - - +
320D ASP* 3.6 8.2 + - - +
321D GLU* 3.2 35.6 + - - +
322D ARG* 3.0 21.3 + - - +
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Residues in contact with ASP 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 ARG* 2.9 32.7 + - + -
305D LEU* 3.8 23.2 - - + +
318D SER* 1.3 73.7 - - - +
320D ASP* 1.3 60.7 + - - +
322D ARG* 3.3 20.1 + - - +
323D ILE* 3.0 39.3 + - + +
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Residues in contact with ASP 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D ARG* 3.2 30.8 + - - +
318D SER* 3.2 7.6 + - - +
319D ASP* 1.3 82.9 - - - +
321D GLU* 1.3 57.6 + - + +
323D ILE* 4.5 4.9 - - - +
324D ASP* 2.9 40.5 + - - +
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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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316D GLU 5.0 2.0 - - - +
317D GLY* 3.2 13.5 - - - -
318D SER* 3.2 37.1 + - - +
320D ASP* 1.3 76.8 - - + +
322D ARG* 1.3 57.7 - - - +
324D ASP* 3.5 7.3 + - - +
325D ALA* 3.0 29.2 + - - +
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Residues in contact with ARG 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305D LEU* 3.8 36.4 + - + +
308D ALA* 4.0 5.1 - - + +
309D GLU* 4.3 17.2 + - - +
314D ILE* 3.9 31.9 + - + +
315D THR* 3.3 25.7 + - - +
316D GLU 3.2 19.1 - - - +
317D GLY 3.4 13.1 + - - -
318D SER 3.0 23.1 + - - +
319D ASP* 3.6 19.3 + - - +
321D GLU* 1.3 75.0 - - - +
323D ILE* 1.3 60.3 + - - +
325D ALA* 3.3 2.8 + - - +
326D ALA* 2.9 28.8 + - - +
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Residues in contact with ILE 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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297D ARG* 3.7 44.0 - - + +
301D ARG* 4.1 32.8 - - + +
304D LEU* 4.0 27.8 - - + -
305D LEU* 3.9 13.0 - - + -
319D ASP* 3.0 22.9 + - + +
320D ASP* 3.9 7.0 - - - +
322D ARG* 1.3 72.3 - - - +
324D ASP* 1.3 66.2 + - - +
326D ALA* 3.2 7.4 + - - +
327D ILE* 2.9 35.5 + - + +
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Residues in contact with ASP 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D ARG* 2.5 39.8 + - - +
320D ASP* 2.9 25.4 + - - +
321D GLU* 3.7 7.4 - - - +
323D ILE* 1.3 76.7 - - - +
325D ALA* 1.3 56.8 + - - +
327D ILE* 3.4 4.8 + - - +
328D ALA* 2.9 30.1 + - - +
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Residues in contact with ALA 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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314D ILE* 3.8 23.0 - - + +
321D GLU 3.0 18.6 + - - +
322D ARG 3.7 4.5 - - - +
323D ILE 3.2 0.2 - - - -
324D ASP* 1.3 73.8 - - - +
326D ALA* 1.3 60.0 + - - +
328D ALA* 3.6 6.9 - - - +
329D ALA* 2.8 30.1 + - - +
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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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304D LEU* 4.5 5.4 - - + +
307D TYR* 4.0 22.3 - - + -
308D ALA* 3.7 23.3 - - + -
312D TRP* 4.4 1.3 + - + -
314D ILE* 3.7 8.7 - - + +
322D ARG 2.9 17.0 + - - +
323D ILE* 3.2 7.6 + - - +
325D ALA* 1.3 74.7 - - - +
327D ILE* 1.3 61.0 + - + +
329D ALA* 3.3 3.9 + - - +
330D THR* 2.8 34.0 + - - -
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Residues in contact with ILE 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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290D PRO* 3.9 31.3 - - + +
293D TRP* 4.0 24.5 - - + -
294D ASN* 3.8 29.4 - - + +
297D ARG* 3.9 20.9 - - - +
304D LEU* 4.9 3.4 - - + -
323D ILE* 2.9 29.5 + - + +
324D ASP* 3.8 4.5 - - - +
326D ALA* 1.3 74.6 - - - +
328D ALA* 1.3 57.8 + - - +
330D THR* 3.2 8.2 + - - -
331D ARG* 2.9 34.6 + - - +
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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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324D ASP 2.9 18.6 + - - +
325D ALA* 3.6 8.5 - - - +
327D ILE* 1.3 78.0 - - - +
329D ALA* 1.3 56.2 + - - +
331D ARG* 3.4 9.6 + - - +
332D ASN* 2.9 30.8 + - - +
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Residues in contact with ALA 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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312D TRP* 3.6 39.6 - - + -
314D ILE* 4.6 4.3 - - + -
325D ALA 2.8 18.5 + - - +
326D ALA* 3.6 5.6 - - - +
328D ALA* 1.3 75.6 - - - +
330D THR* 1.3 58.6 + - - +
332D ASN* 3.5 7.9 + - - +
333D PHE* 3.0 29.3 + - - +
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Residues in contact with THR 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D PHE* 4.0 8.1 - - + -
289D LEU* 4.2 4.5 - - + -
290D PRO* 5.9 4.0 - - + -
293D TRP* 3.5 17.9 - - + -
307D TYR* 2.6 31.8 + - - +
312D TRP* 3.9 7.8 + - - -
326D ALA 2.8 18.3 + - - -
327D ILE* 3.2 8.3 + - - -
329D ALA* 1.3 73.9 - - - +
331D ARG* 1.3 66.0 + - - +
333D PHE* 3.2 4.3 + - - +
334D PHE* 3.1 50.9 + - + -
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Residues in contact with ARG 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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287D ILE 5.1 0.4 + - - -
290D PRO* 3.4 37.5 + - + +
291D ALA* 4.4 5.1 - - - +
327D ILE* 2.9 21.8 + - - +
328D ALA* 3.6 8.4 - - - +
330D THR* 1.3 77.0 - - - +
332D ASN* 1.3 63.0 + - - +
334D PHE* 3.2 8.0 + - - +
335D GLU* 3.0 30.3 + - + +
341D THR* 3.1 60.7 + - - +
342D HIS* 3.4 24.9 + - - -
385D ALA 5.5 4.8 + - - -
386D ALA* 6.3 1.0 - - - +
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Residues in contact with ASN 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 ALA 2.9 18.1 + - - +
329D ALA* 3.7 7.8 + - - +
331D ARG* 1.3 76.2 - - - +
333D PHE* 1.3 59.7 + - - +
335D GLU* 3.7 6.7 - - - +
336D GLN* 2.9 53.1 + - - +
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Residues in contact with PHE 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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192D VAL* 3.9 8.5 - - + -
196D PHE* 3.7 32.5 - + - -
224D LEU 3.5 20.4 - - - -
225D ILE* 3.7 23.8 - - + -
229D PRO* 3.9 22.4 - - + -
312D TRP* 3.9 20.2 - + + -
329D ALA 3.0 16.9 + - - +
330D THR 3.2 4.9 + - - +
332D ASN* 1.3 80.5 - - - +
334D PHE* 1.3 80.6 + + - +
336D GLN* 3.4 4.9 + - + +
337D LEU* 3.1 51.8 + - + +
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Residues in contact with PHE 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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193D VAL* 3.8 21.3 - - + -
196D PHE* 3.8 29.8 - + + -
197D VAL* 4.2 11.7 - - + -
286D ALA* 3.7 38.1 - - + -
289D LEU* 4.0 18.6 - - + -
290D PRO* 5.1 3.1 - - + -
330D THR* 3.1 33.1 + - + -
331D ARG* 3.6 7.4 - - - +
333D PHE* 1.3 94.1 - + - +
335D GLU* 1.3 59.7 + - - +
337D LEU* 3.2 15.0 + - - +
338D GLY 3.4 0.2 + - - -
339D VAL* 3.0 36.4 + - + +
341D THR* 3.9 6.3 - - + -
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Residues in contact with GLU 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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331D ARG* 3.0 24.9 + - + +
332D ASN* 3.7 8.1 - - - +
334D PHE* 1.3 76.2 - - - +
336D GLN* 1.3 70.2 + - - +
338D GLY* 2.9 20.4 + - - -
339D VAL 3.7 4.9 + - - -
340D PRO* 3.7 21.5 - - - +
341D THR* 3.0 34.1 + - + +
342D HIS* 4.2 5.4 + - - -
345D ASP* 4.0 7.6 - - - +
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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
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229D PRO* 6.1 1.0 - - - +
232D LEU* 4.7 4.3 - - - +
332D ASN* 2.9 42.3 + - - +
333D PHE* 4.0 6.1 - - + +
334D PHE 3.3 0.2 - - - -
335D GLU* 1.3 83.4 + - - +
337D LEU* 1.3 61.5 + - - +
338D GLY 3.2 2.9 + - - -
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Residues in contact with LEU 337 (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 PRO 5.0 0.7 - - - +
189D ALA* 3.3 29.0 - - + +
192D VAL* 3.6 30.3 - - + -
193D VAL* 4.0 17.7 - - + -
228D GLY 3.9 6.5 - - - +
229D PRO* 3.8 35.2 - - + -
232D LEU* 3.4 28.9 - - + +
333D PHE* 3.1 34.5 + - + +
334D PHE* 3.2 8.7 + - - +
336D GLN* 1.3 77.2 - - - +
338D GLY* 1.3 56.4 + - - +
339D VAL* 4.5 1.3 - - + -
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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
------------------------------------------------------------
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