Contacts of the helix formed by residues 300 - 313 (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 LYS 300 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204D VAL* 2.8 26.2 + - + +
205D THR 3.7 10.8 - - - +
263D ASP* 2.8 29.7 + - - -
292D LEU* 3.8 18.6 - - - -
293D TRP* 3.7 22.4 - - + +
296D LYS* 2.9 31.7 + - + +
297D ARG 3.9 1.3 - - - -
299D THR* 1.3 79.8 - - - +
301D ARG* 1.3 64.6 + - - +
302D ALA 3.2 3.0 + - - -
303D LYS* 3.3 3.8 + - - +
304D LEU* 2.9 34.8 + - + +
370D GLU* 2.8 36.4 + - - +
374D ILE* 6.2 0.7 - - - -
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Residues in contact with ARG 301 (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 3.2 12.5 + - - +
298D ASP* 3.4 16.8 - - - +
299D THR 3.4 3.0 - - - -
300D LYS* 1.3 76.4 - - - +
302D ALA* 1.3 85.4 + - - +
304D LEU* 3.3 2.0 + - - +
305D LEU* 3.0 49.8 + - + +
319D ASP* 2.9 28.9 + - + +
323D ILE* 4.1 16.3 - - + +
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Residues in contact with ALA 302 (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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207D PRO* 3.7 33.2 - - + +
299D THR 5.3 0.4 + - - -
300D LYS 3.4 0.6 - - - -
301D ARG* 1.3 100.9 - - - +
303D LYS* 1.3 60.0 + - + +
305D LEU* 3.3 4.9 + - - +
306D GLN* 3.1 25.8 + - - +
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Residues in contact with LYS 303 (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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-2D LYS* 5.1 2.2 - - - +
203D TYR* 2.8 54.7 + - + +
204D VAL* 3.9 8.0 - - - +
205D THR* 3.8 24.5 + - - +
206D LYS 3.9 20.7 + - - -
207D PRO* 3.9 19.7 - - + +
208D VAL 5.1 4.8 + - - +
214D ASP* 3.0 27.1 + - - +
300D LYS 3.3 2.8 + - - +
302D ALA* 1.3 75.0 - - - +
304D LEU* 1.3 60.9 + - - +
306D GLN* 3.8 22.5 - - - +
307D TYR* 2.8 30.7 + - - +
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Residues in contact with LEU 304 (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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204D VAL* 3.7 20.8 - - + +
293D TRP* 3.8 40.6 - - + +
297D ARG* 4.0 22.7 - - - +
300D LYS* 2.9 34.3 + - + +
301D ARG 3.7 3.8 - - - +
303D LYS* 1.3 78.3 - - - +
305D LEU* 1.3 57.9 + - - +
307D TYR* 3.4 11.9 - - + +
308D ALA* 2.8 29.1 + - - +
323D ILE* 4.0 26.9 - - + +
326D ALA* 4.5 4.9 - - + +
327D ILE* 4.9 6.1 - - + -
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Residues in contact with LEU 305 (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* 3.0 56.7 + - + +
302D ALA 3.7 4.7 - - - +
304D LEU* 1.3 75.6 - - - +
306D GLN* 1.3 63.7 + - - +
308D ALA* 3.4 4.3 + - - +
309D GLU* 3.1 23.8 + - - +
319D ASP* 3.7 44.9 - - - +
322D ARG* 3.8 42.5 + - + +
323D ILE* 3.9 9.4 - - + -
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Residues in contact with GLN 306 (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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-2D LYS* 3.6 21.9 + - - +
203D TYR* 3.7 8.2 + - - +
214D ASP* 3.1 26.7 + - - +
218D GLU* 2.7 23.2 + - - +
302D ALA 3.1 17.2 + - - +
303D LYS* 3.8 16.5 - - - +
305D LEU* 1.3 72.8 - - - +
307D TYR* 1.3 57.5 + - - +
309D GLU* 3.3 6.0 + - - -
310D ARG* 2.8 65.3 + - + +
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Residues in contact with TYR 307 (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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196D PHE* 3.3 20.9 - + - -
200D VAL* 4.3 2.0 - - + -
203D TYR* 3.6 25.2 + + + -
204D VAL* 4.1 9.9 - - + -
221D LEU* 4.0 17.0 - - + -
293D TRP* 3.6 25.4 - + - -
303D LYS 2.8 20.1 + - - +
304D LEU* 3.4 10.8 - - + +
306D GLN* 1.3 75.4 - - - +
308D ALA* 1.3 64.3 + - - +
311D VAL* 2.9 46.2 + - + +
312D TRP* 3.1 27.2 + + - -
326D ALA* 4.0 16.6 - - + -
330D THR* 2.6 30.3 + - - +
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Residues in contact with ALA 308 (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 2.8 18.1 + - - +
305D LEU* 3.5 10.1 - - - +
306D GLN 3.2 0.2 - - - -
307D TYR* 1.3 75.9 - - - +
309D GLU* 1.3 57.6 + - - +
312D TRP* 3.1 19.8 + - - +
314D ILE* 2.9 39.0 + - + +
322D ARG* 4.0 12.3 - - + +
326D ALA* 3.7 24.9 - - + -
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Residues in contact with GLU 309 (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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305D LEU 3.1 17.0 + - - +
306D GLN* 3.9 5.3 - - - +
308D ALA* 1.3 76.1 - - - +
310D ARG* 1.3 72.7 + - + +
313D ASN* 3.0 27.1 + - - +
314D ILE 3.4 15.8 + - - +
315D THR* 3.8 21.7 - - + +
322D ARG* 4.3 12.6 + - - +
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Residues in contact with ARG 310 (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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226A GLU* 5.2 4.4 + - - -
203D TYR* 4.5 0.7 - - - +
214D ASP* 4.7 3.6 - - - +
215D ARG* 3.4 45.7 - - - +
218D GLU* 2.9 52.1 + - + +
222D LEU* 3.8 20.3 - - - +
306D GLN* 2.8 45.0 + - + +
309D GLU* 1.3 85.9 + - + +
311D VAL* 1.3 59.2 + - - +
313D ASN 4.7 0.4 + - - -
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Residues in contact with VAL 311 (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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196D PHE* 5.1 0.4 - - + -
203D TYR* 4.7 0.2 - - - +
218D GLU* 4.2 24.0 - - + +
221D LEU* 4.0 27.6 - - + -
222D LEU* 3.5 19.7 - - + +
225D ILE* 3.4 31.4 - - + +
307D TYR* 2.9 38.5 + - + +
310D ARG* 1.3 82.1 - - - +
312D TRP* 1.3 73.2 + - + +
313D ASN 3.7 0.4 - - - -
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Residues in contact with TRP 312 (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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196D PHE* 4.6 3.1 - + - -
225D ILE* 3.5 41.7 - - + +
307D TYR* 3.1 45.9 + + - -
308D ALA* 3.1 13.5 + - - +
311D VAL* 1.3 88.4 - - + +
313D ASN* 1.3 72.0 + - - +
314D ILE* 3.1 21.5 + - + +
326D ALA* 4.5 2.9 - - - -
329D ALA* 3.6 44.2 - - + +
330D THR* 3.9 5.3 + - - -
333D PHE* 3.9 20.4 - + + -
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Residues in contact with ASN 313 (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 GLU* 3.0 20.4 + - - +
310D ARG 4.7 0.4 - - - -
311D VAL 3.7 1.6 - - - -
312D TRP* 1.3 79.9 - - - +
314D ILE* 1.3 60.9 + - - +
315D THR* 3.6 15.8 + - - +
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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