Contacts of the helix formed by residues 318 - 338 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B GLY* 1.3 76.7 - - - +
319B ASP* 1.3 64.9 + - - +
320B ASP* 3.6 7.4 + - - +
321B GLU* 3.1 34.8 + - - +
322B ARG* 3.0 23.0 + - - +
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Residues in contact with ASP 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ARG* 3.1 28.4 + - - +
305B LEU* 3.7 22.2 - - + +
318B SER* 1.3 74.7 - - - +
320B ASP* 1.3 60.2 + - - +
322B ARG* 3.4 22.8 + - - +
323B ILE* 3.0 39.4 + - + +
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Residues in contact with ASP 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ARG* 3.2 32.0 + - - +
318B SER* 3.3 7.6 + - - +
319B ASP* 1.3 79.3 - - - +
321B GLU* 1.3 54.4 + - + +
323B ILE* 3.3 3.4 + - - +
324B ASP* 2.8 44.8 + - - +
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Residues in contact with GLU 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B GLU 4.9 2.2 - - - +
317B GLY* 3.3 12.8 - - - -
318B SER* 3.1 36.8 + - - +
320B ASP* 1.3 78.8 - - + +
322B ARG* 1.3 56.3 + - - +
324B ASP* 3.4 10.6 + - - +
325B ALA* 3.0 29.3 + - - +
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Residues in contact with ARG 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LEU* 3.8 37.5 + - + +
308B ALA* 4.0 7.0 - - + +
309B GLU* 4.6 13.1 + - - -
314B ILE* 3.9 29.2 + - + +
315B THR* 3.4 26.1 + - - +
316B GLU 3.2 20.6 - - - +
317B GLY 3.3 21.1 + - - -
318B SER 3.0 13.2 + - - +
319B ASP* 3.4 23.5 + - - +
321B GLU* 1.3 74.8 - - - +
323B ILE* 1.3 58.9 + - - +
325B ALA* 3.3 2.9 + - - +
326B ALA* 3.0 28.1 + - - +
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Residues in contact with ILE 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B ARG* 3.6 41.3 - - + +
301B ARG* 4.0 33.9 - - + +
304B LEU* 4.0 29.4 - - + -
305B LEU* 3.9 14.4 - - + +
319B ASP* 3.0 24.0 + - + +
320B ASP* 3.8 6.1 - - - +
322B ARG* 1.3 74.5 - - - +
324B ASP* 1.3 65.1 + - - +
326B ALA* 3.2 6.4 + - - +
327B ILE* 3.0 37.1 + - + +
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Residues in contact with ASP 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ARG* 2.7 39.9 + - - +
320B ASP* 2.8 29.1 + - - +
321B GLU* 3.6 10.8 - - - +
323B ILE* 1.3 72.3 - - - +
325B ALA* 1.3 57.8 + - - +
327B ILE* 3.5 4.8 + - - +
328B ALA* 3.0 28.5 + - - +
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Residues in contact with ALA 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ILE* 3.7 23.9 - - + +
321B GLU 3.0 17.9 + - - +
322B ARG* 3.7 5.4 - - - +
323B ILE 3.2 0.2 - - - -
324B ASP* 1.3 74.2 - - - +
326B ALA* 1.3 60.9 + - - +
328B ALA* 3.3 7.2 + - - +
329B ALA* 2.8 29.8 + - - +
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Residues in contact with ALA 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B LEU* 4.6 5.4 - - + +
307B TYR* 4.1 17.5 - - + -
308B ALA* 3.7 27.1 - - + -
312B TRP* 4.4 2.3 + - + -
314B ILE* 3.6 8.5 - - - +
322B ARG 3.0 16.5 + - - +
323B ILE* 3.2 6.7 + - - +
325B ALA* 1.3 75.1 - - - +
327B ILE* 1.3 59.8 + - + +
329B ALA* 3.4 4.5 + - - +
330B THR* 2.7 34.2 + - - -
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Residues in contact with ILE 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B PRO* 3.9 30.6 - - + +
293B TRP* 4.0 24.7 - - + +
294B ASN* 3.8 34.1 - - + +
297B ARG* 3.9 8.7 - - - +
304B LEU* 4.9 3.6 - - + -
323B ILE* 3.0 36.5 + - + +
324B ASP* 3.8 4.9 - - - +
326B ALA* 1.3 77.2 - - + +
328B ALA* 1.3 56.4 + - - +
330B THR* 3.3 6.6 + - - -
331B ARG* 3.0 33.6 + - - +
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Residues in contact with ALA 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B ASP 3.0 19.4 + - - +
325B ALA* 3.6 7.4 - - - +
327B ILE* 1.3 74.8 - - - +
329B ALA* 1.3 58.5 + - - +
331B ARG* 3.5 8.5 + - - +
332B ASN* 2.9 30.9 + - - +
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Residues in contact with ALA 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B TRP* 3.7 39.7 - - + -
314B ILE* 4.8 4.0 - - + -
325B ALA 2.8 17.6 + - - +
326B ALA* 3.8 4.3 - - - +
327B ILE 3.4 0.2 - - - -
328B ALA* 1.3 76.9 - - - +
330B THR* 1.3 56.6 + - - +
332B ASN* 3.5 8.9 + - - +
333B PHE* 2.9 29.6 + - - +
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Residues in contact with THR 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B PHE* 4.0 8.1 - - + -
289B LEU* 4.2 4.7 - - + -
290B PRO* 5.9 4.0 - - + -
293B TRP* 3.6 18.4 - - + -
307B TYR* 2.6 31.6 + - - +
312B TRP* 3.8 4.9 + - - -
326B ALA 2.7 21.9 + - - -
327B ILE* 3.5 5.4 - - - -
329B ALA* 1.3 74.1 - - - +
331B ARG* 1.3 63.6 - - - +
333B PHE* 3.2 8.1 + - - +
334B PHE* 3.1 49.7 + - + -
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Residues in contact with ARG 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ILE 5.2 0.6 + - - -
290B PRO* 3.3 38.1 - - + +
291B ALA* 4.3 5.9 - - - +
327B ILE* 3.0 21.4 + - - +
328B ALA* 3.7 8.4 - - - +
330B THR* 1.3 76.7 - - - +
332B ASN* 1.3 62.0 + - - +
334B PHE* 3.4 6.2 + - - +
335B GLU* 3.0 31.5 + - + +
341B THR* 3.0 58.6 + - + +
342B HIS* 3.3 29.8 + - - -
385B ALA 5.5 4.4 + - - -
386B ALA* 6.2 1.4 - - - +
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Residues in contact with ASN 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B ALA 2.9 19.4 + - - +
329B ALA* 3.6 8.5 + - - +
331B ARG* 1.3 77.0 - - - +
333B PHE* 1.3 60.2 + - - +
335B GLU* 3.3 6.4 + - - +
336B GLN* 2.9 54.8 + - - +
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Residues in contact with PHE 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B VAL* 3.9 9.2 - - + -
196B PHE* 3.7 34.1 - + + -
224B LEU 3.6 18.8 - - - -
225B ILE* 3.7 25.6 - - + -
229B PRO* 4.0 21.8 - - + -
312B TRP* 3.9 16.4 - + + -
329B ALA 2.9 17.7 + - - +
330B THR 3.2 5.3 + - - +
332B ASN* 1.3 80.5 - - - +
334B PHE* 1.3 79.2 + + - +
336B GLN* 3.8 5.1 - - + +
337B LEU* 3.1 50.5 + - + +
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Residues in contact with PHE 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B VAL* 3.8 23.3 - - + -
196B PHE* 3.9 30.1 - + + -
197B VAL* 4.0 12.3 - - + -
286B ALA* 3.7 39.3 - - + -
289B LEU* 4.0 22.7 - - + -
290B PRO* 5.0 2.2 - - + -
330B THR* 3.1 30.4 + - + -
331B ARG* 3.6 7.0 - - - +
333B PHE* 1.3 91.3 - + - +
335B GLU* 1.3 63.7 + - - +
337B LEU* 3.1 15.6 + - - +
338B GLY 3.3 0.3 + - - -
339B VAL* 3.0 31.5 + - - +
341B THR* 4.0 6.3 - - + -
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Residues in contact with GLU 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B ARG* 3.0 27.3 + - + +
332B ASN* 3.6 7.9 - - - +
334B PHE* 1.3 75.5 - - - +
336B GLN* 1.3 66.1 + - - +
338B GLY* 2.8 21.1 + - - -
339B VAL 3.6 4.9 + - - -
340B PRO* 3.6 18.8 - - - +
341B THR* 2.7 38.0 + - + +
342B HIS* 4.2 5.2 + - - -
345B ASP* 4.1 5.7 - - - +
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Residues in contact with GLN 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B LEU* 4.7 4.3 - - - +
332B ASN* 2.9 44.1 + - - +
333B PHE* 3.9 6.3 - - + +
335B GLU* 1.3 82.7 - - - +
337B LEU* 1.3 60.8 + - - +
338B GLY* 3.1 1.0 + - - -
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Residues in contact with LEU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B PRO 5.1 0.5 - - - +
186B ARG* 5.8 1.0 - - - +
189B ALA* 3.3 27.6 - - + +
192B VAL* 3.6 30.1 - - + -
193B VAL* 3.9 19.5 - - + -
228B GLY 4.1 5.6 - - - +
229B PRO* 3.9 32.5 - - + -
232B LEU* 3.6 29.6 - - + +
333B PHE* 3.1 35.6 + - + +
334B PHE* 3.1 8.9 + - - +
336B GLN* 1.3 77.5 - - + +
338B GLY* 1.3 56.5 + - - +
339B VAL* 4.6 2.5 - - + -
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Residues in contact with GLY 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ARG* 4.9 18.7 + - - +
189B ALA* 5.2 0.4 - - - -
283B GLN* 5.9 0.9 + - - -
335B GLU 2.8 13.2 + - - -
336B GLN 3.1 1.9 - - - -
337B LEU* 1.3 79.5 - - - +
339B VAL* 1.3 64.4 + - - +
340B PRO* 3.5 11.2 - - - +
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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