Contacts of the helix formed by residues 300 - 313 (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 LYS 300 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204B VAL* 2.9 26.1 + - + +
205B THR 3.6 10.3 - - - +
263B ASP* 2.6 30.3 + - - -
292B LEU* 3.8 18.6 - - - -
293B TRP* 3.8 21.9 - - + +
296B LYS* 3.0 34.0 + - + +
297B ARG 3.9 1.3 - - - -
299B THR* 1.3 77.6 - - - +
301B ARG* 1.3 64.1 + - - +
302B ALA 3.3 2.9 + - - -
303B LYS* 3.3 4.0 + - - -
304B LEU* 2.9 35.3 + - + +
370B GLU* 2.8 35.2 + - - +
374B ILE* 6.1 0.4 - - - -
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Residues in contact with ARG 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ARG 3.1 17.9 + - - +
298B ASP* 3.4 13.4 + - - +
299B THR 3.4 3.0 + - - -
300B LYS* 1.3 78.0 - - - +
302B ALA* 1.3 71.8 + - - +
304B LEU* 3.3 1.7 + - - +
305B LEU* 2.9 54.4 + - + +
319B ASP* 3.1 28.9 + - + +
323B ILE* 4.0 20.2 - - + -
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Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B PRO* 3.9 32.8 - - + -
299B THR 5.3 0.2 + - - -
300B LYS 3.4 0.8 - - - -
301B ARG* 1.3 96.6 - - - +
303B LYS* 1.3 60.5 + - + +
305B LEU* 3.3 7.8 + - - +
306B GLN* 3.0 26.3 + - - +
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Residues in contact with LYS 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-2B LYS* 6.3 1.1 - - - +
203B TYR* 2.8 46.9 + - + +
204B VAL* 3.9 7.7 - - - +
205B THR* 3.7 29.2 + - - +
206B LYS 4.0 20.7 + - - +
207B PRO* 4.1 18.1 - - + +
208B VAL* 5.1 5.5 + - - +
214B ASP* 2.8 36.5 + - - -
300B LYS 3.3 3.2 + - - +
302B ALA* 1.3 75.3 - - + +
304B LEU* 1.3 62.1 + - - +
306B GLN* 3.8 16.8 - - - +
307B TYR* 2.9 30.1 + - - +
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B VAL* 3.7 21.5 - - + +
293B TRP* 3.8 39.5 - - + +
297B ARG* 3.8 24.2 - - - +
300B LYS* 2.9 34.9 + - + +
301B ARG 3.6 3.6 - - - +
303B LYS* 1.3 76.2 - - - +
305B LEU* 1.3 58.6 + - - +
307B TYR* 3.6 11.9 - - + +
308B ALA* 2.9 28.4 + - - +
323B ILE* 4.0 30.7 - - + -
326B ALA* 4.6 5.0 - - + +
327B ILE* 4.9 3.1 - - + -
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Residues in contact with LEU 305 (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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301B ARG* 2.9 53.6 + - + +
302B ALA* 3.6 6.5 - - - +
303B LYS 3.3 0.2 - - - -
304B LEU* 1.3 74.5 - - - +
306B GLN* 1.3 63.2 + - - +
308B ALA* 3.4 4.7 + - - +
309B GLU* 3.1 22.5 + - - +
319B ASP* 3.7 39.0 - - - +
322B ARG* 3.8 47.1 + - + +
323B ILE* 3.9 9.0 - - + -
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Residues in contact with GLN 306 (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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-2B LYS* 4.3 14.9 + - - -
203B TYR* 3.7 3.6 + - - +
214B ASP* 3.0 30.0 + - - +
218B GLU* 2.7 26.5 + - - +
302B ALA 3.0 15.8 + - - +
303B LYS* 3.8 19.1 - - - +
304B LEU 3.4 0.2 - - - -
305B LEU* 1.3 75.2 - - - +
307B TYR* 1.3 56.2 + - - +
309B GLU* 3.3 6.3 + - - +
310B ARG* 2.8 68.0 + - + +
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Residues in contact with TYR 307 (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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196B PHE* 3.2 22.0 - + - -
200B VAL* 4.3 2.2 - - + -
203B TYR* 3.5 27.6 + + + -
204B VAL* 4.2 8.7 - - + -
221B LEU* 3.9 16.8 - - + -
293B TRP* 3.6 24.0 - + - -
303B LYS 2.9 18.9 + - - +
304B LEU* 3.6 11.0 - - + +
306B GLN* 1.3 76.7 - - - +
308B ALA* 1.3 65.0 + - - +
311B VAL* 2.9 48.8 + - + +
312B TRP* 3.0 26.6 + + - -
326B ALA* 4.1 15.9 - - + -
330B THR* 2.6 29.4 + - - +
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Residues in contact with ALA 308 (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 2.9 19.6 + - - +
305B LEU* 3.5 9.4 - - - +
306B GLN 3.3 0.2 - - - -
307B TYR* 1.3 76.6 - - - +
309B GLU* 1.3 56.9 + - - +
312B TRP* 3.2 10.2 + - - +
313B ASN 3.1 10.4 + - - -
314B ILE* 2.9 35.0 + - + +
322B ARG* 4.0 16.2 - - + +
326B ALA* 3.7 24.7 - - + -
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Residues in contact with GLU 309 (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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305B LEU 3.1 16.1 + - - +
306B GLN* 3.9 5.7 - - - +
308B ALA* 1.3 77.1 - - - +
310B ARG* 1.3 67.3 + - + +
313B ASN* 3.1 26.7 + - - +
314B ILE 3.5 14.7 + - - +
315B THR* 3.5 26.0 - - + +
322B ARG* 4.6 12.8 + - - +
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Residues in contact with ARG 310 (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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203B TYR* 4.5 0.2 - - - +
211B LYS 5.6 0.2 + - - -
214B ASP* 4.6 3.4 - - - +
215B ARG* 3.3 47.2 - - - +
218B GLU* 3.0 49.5 + - + +
222B LEU* 3.7 21.4 - - - +
306B GLN* 2.8 45.6 + - + +
309B GLU* 1.3 82.2 + - + +
311B VAL* 1.3 59.8 + - - +
313B ASN 4.7 0.2 - - - -
226C GLU* 5.0 4.2 + - - -
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Residues in contact with VAL 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B TYR* 4.7 0.2 - - - +
218B GLU* 4.2 21.8 - - + +
221B LEU* 3.9 25.8 - - + -
222B LEU* 3.5 18.8 - - - +
225B ILE* 3.4 31.6 - - + +
307B TYR* 2.9 42.5 + - + +
310B ARG* 1.3 80.0 - - - +
312B TRP* 1.3 75.6 + - + +
313B ASN 3.7 0.7 - - - -
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Residues in contact with TRP 312 (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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196B PHE* 4.6 2.5 - + - -
225B ILE* 3.6 42.4 - - + -
307B TYR* 3.0 46.6 + + - -
308B ALA* 3.2 11.9 + - - +
311B VAL* 1.3 87.6 - - + +
313B ASN* 1.3 71.9 + - - +
314B ILE* 3.2 20.3 + - + +
326B ALA* 4.5 5.4 - - - -
329B ALA* 3.7 44.6 - - + -
330B THR* 3.8 6.1 + - - -
333B PHE* 3.9 19.7 - + + -
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Residues in contact with ASN 313 (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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308B ALA 3.1 2.6 + - - -
309B GLU* 3.1 18.8 + - - +
310B ARG 4.7 0.4 - - - -
311B VAL 3.7 1.0 - - - -
312B TRP* 1.3 79.1 - - - +
314B ILE* 1.3 59.5 + - - +
315B THR* 3.6 16.6 + - - +
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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