Contacts of the helix formed by residues 288 - 306 (chain B) in PDB entry 4OL0
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 ASP 288 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B SER* 4.7 6.6 + - - -
283B ALA* 2.9 15.1 + - - +
286B ARG* 3.2 24.8 + - + +
287B GLU* 1.3 73.4 - - - +
289B LEU* 1.3 63.1 + - - +
290B ASP* 3.5 18.0 + - - +
291B LYS* 3.4 39.7 + - + +
292B VAL* 3.3 23.6 + - - +
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Residues in contact with LEU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LYS* 4.8 11.2 - - - +
287B GLU 3.4 8.8 + - - +
288B ASP* 1.3 71.2 + - - +
290B ASP* 1.3 72.1 + - - +
292B VAL* 3.1 6.6 + - + +
293B LEU* 2.8 42.9 + - + +
333B HIS* 4.0 21.3 - - + +
335B GLN* 3.9 31.2 - - + +
337B GLU* 3.8 20.6 - - - +
338B VAL* 4.6 5.6 - - + -
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Residues in contact with ASP 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LYS* 2.5 38.9 + - - +
239B SER* 3.6 28.6 + - - +
243B GLU* 6.2 1.6 - - + -
288B ASP* 3.4 10.2 - - - +
289B LEU* 1.3 77.5 + - - +
291B LYS* 1.3 59.5 + - + +
293B LEU* 3.3 10.6 + - - +
294B ASN* 2.9 39.8 + - - +
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Residues in contact with LYS 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B GLN 4.2 3.6 + - - -
235B ASP* 2.9 29.1 + - - +
237B THR* 2.6 34.8 + - - +
238B SER 4.7 5.6 - - - -
239B SER* 5.0 3.8 - - - +
242B HIS* 3.7 42.1 - - + +
283B ALA* 3.8 22.4 - - + -
288B ASP* 3.4 30.6 + - + +
289B LEU 3.3 0.6 - - - -
290B ASP* 1.3 75.0 - - + +
292B VAL* 1.3 60.1 + - - +
294B ASN* 3.4 1.2 + - - +
295B TYR* 2.8 40.6 + - + +
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Residues in contact with VAL 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B TYR* 3.8 18.4 - - + -
283B ALA* 4.0 4.3 - - + +
284B VAL* 3.7 35.9 - - + +
287B GLU 5.8 0.2 - - - -
288B ASP 3.3 16.2 - - - +
289B LEU* 3.1 10.3 + - + +
291B LYS* 1.3 77.6 - - - +
293B LEU* 1.3 57.4 + - - +
295B TYR* 3.3 8.8 + - - +
296B CYS* 2.8 28.6 + - - +
333B HIS* 4.0 19.1 - - + +
338B VAL* 3.9 27.4 - - + -
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Residues in contact with LEU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG 5.8 3.6 - - - +
142A LYS* 4.1 35.9 - - + -
289B LEU* 2.8 32.5 + - + +
290B ASP* 3.5 8.1 - - - +
292B VAL* 1.3 75.6 - - - +
294B ASN* 1.3 59.2 + - - +
296B CYS* 3.0 7.1 + - - +
297B ARG* 2.8 36.9 + - + +
337B GLU* 4.2 14.1 - - + +
338B VAL* 3.7 40.6 - - + +
341B ILE* 4.2 10.6 - - + +
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Residues in contact with ASN 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B SER 4.5 1.0 + - - -
242B HIS* 3.2 27.9 + - - +
243B GLU* 3.6 33.5 - - - +
246B SER* 3.4 17.8 - - - +
290B ASP* 2.9 26.1 + - - +
291B LYS* 3.6 0.9 - - - +
293B LEU* 1.3 76.9 - - - +
295B TYR* 1.3 58.2 + - - +
297B ARG* 2.8 36.7 + - - +
298B ILE* 2.9 34.3 + - - +
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Residues in contact with TYR 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B LEU* 2.4 34.0 + - + -
234B GLN 5.0 2.1 + - - -
242B HIS* 3.1 28.6 + + - -
276B LEU* 4.4 26.5 - - + -
279B ALA* 3.2 31.6 + - + +
280B TYR* 3.5 33.0 - + + -
283B ALA* 3.8 11.9 - - + -
291B LYS* 2.8 30.3 + - + +
292B VAL 3.6 4.0 - - - +
294B ASN* 1.3 72.5 - - - +
296B CYS* 1.3 58.5 + - - +
298B ILE* 3.1 16.0 + - + +
299B PHE* 2.8 41.1 + + + -
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Residues in contact with CYS 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B VAL 2.8 18.0 + - - +
293B LEU* 3.4 5.6 - - - +
295B TYR* 1.3 76.7 - - - +
297B ARG* 1.3 53.6 + - - +
299B PHE* 3.8 1.0 - - - +
300B THR* 2.4 48.8 + - - -
327B LEU* 5.0 1.3 - - - -
330B CYS* 3.8 36.1 - - - -
338B VAL* 3.5 34.1 - - + -
339B VAL* 5.3 0.7 - - - -
341B ILE* 4.2 12.1 - - + -
342B SER* 5.0 3.8 - - - -
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Residues in contact with ARG 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 3.8 42.9 + - + +
141A LYS* 3.3 33.0 - - - +
243B GLU* 4.5 1.2 + - - +
246B SER* 3.9 12.0 - - - -
247B ASP* 3.2 21.6 + - - -
250B CYS* 4.1 18.2 - - - +
293B LEU* 2.8 16.4 + - - +
294B ASN* 2.8 40.7 + - - +
296B CYS* 1.3 76.8 - - - +
298B ILE* 1.3 56.4 + - - +
300B THR* 3.4 5.4 + - - -
301B GLU* 2.9 34.7 + - + +
341B ILE* 3.9 19.5 - - + -
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Residues in contact with ILE 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B LEU* 3.8 29.4 - - + -
246B SER* 3.8 22.7 - - - +
249B VAL* 3.9 13.2 - - + -
250B CYS* 3.9 18.8 - - - -
253B LEU* 3.8 1.5 - - + +
273B VAL* 3.7 33.0 - - + -
276B LEU* 4.2 12.8 - - + -
294B ASN 2.9 18.9 + - - +
295B TYR* 3.4 17.0 - - + +
297B ARG* 1.3 76.6 - - - +
299B PHE* 1.3 58.3 + - + +
301B GLU* 3.3 3.3 + - - +
302B LEU* 2.9 27.4 + - - +
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Residues in contact with PHE 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B VAL* 3.4 37.5 - - + -
276B LEU* 4.3 18.4 - - + -
277B GLU 4.7 0.2 - - - -
280B TYR* 4.1 26.5 - + + -
295B TYR* 2.8 43.4 + - + +
296B CYS* 3.8 3.8 - - - +
298B ILE* 1.3 72.1 - - + +
300B THR* 1.3 57.9 + - - +
302B LEU* 3.2 8.2 + - - +
303B CYS* 2.9 32.9 + - - -
326B LEU* 3.8 42.0 - - + -
327B LEU* 4.3 11.7 - - + -
329B ILE* 6.5 0.4 - - + -
330B CYS* 3.5 22.0 - - - -
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Residues in contact with THR 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 3.4 25.8 - - - +
296B CYS* 2.4 35.2 + - - -
297B ARG 3.7 3.6 - - - -
299B PHE* 1.3 72.5 - - - +
301B GLU* 1.3 61.3 + - - +
303B CYS* 3.3 2.3 + - - +
304B GLU* 2.8 33.8 + - - +
327B LEU* 3.7 16.3 - - + +
341B ILE* 3.8 4.7 - - - +
342B SER* 3.3 35.3 - - - +
345B PHE* 4.5 8.7 - - + -
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Residues in contact with GLU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 3.5 19.7 + - - +
250B CYS* 3.4 40.9 - - + +
253B LEU* 3.8 12.6 - - + -
254B TYR* 3.7 28.2 + - - +
297B ARG* 2.9 20.7 + - + +
298B ILE 3.5 4.0 - - - +
300B THR* 1.3 77.3 - - - +
302B LEU* 1.3 51.4 + - - +
304B GLU* 4.0 6.9 - - - +
305B THR* 2.6 47.8 + - - -
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Residues in contact with LEU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B LEU* 3.6 13.8 - - + +
270B PHE* 3.8 24.2 - - + +
273B VAL* 3.7 33.4 - - + -
274B LEU* 4.9 3.1 - - + -
298B ILE 2.9 14.9 + - - +
299B PHE* 3.2 9.8 + - - +
301B GLU* 1.3 77.5 - - - +
303B CYS* 1.3 62.8 + - - +
305B THR* 3.3 3.2 + - - -
306B PHE* 3.1 58.8 + - + +
323B THR* 3.7 28.5 - - + -
326B LEU* 4.7 11.2 - - + -
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Residues in contact with CYS 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B PHE* 2.9 19.4 + - - +
300B THR 3.8 2.7 - - - +
301B GLU 3.3 0.2 - - - -
302B LEU* 1.3 73.1 - - - +
304B GLU* 1.3 63.7 + - - +
306B PHE 3.3 3.1 + - - -
307B LEU* 3.1 19.6 + - - -
310B ILE* 3.9 8.2 - - + +
323B THR* 3.4 41.5 - - - -
324B LEU* 4.1 1.1 - - - -
327B LEU* 3.3 39.5 - - + -
345B PHE* 3.4 22.9 - - + -
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Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 5.0 3.0 - - - +
140A ARG* 3.0 30.3 + - - -
257B GLU* 5.5 1.2 - - - +
300B THR* 2.8 20.2 + - - +
301B GLU* 4.0 7.1 - - - +
303B CYS* 1.3 72.7 - - - +
305B THR* 1.3 61.8 + - - +
307B LEU* 3.8 6.8 + - - +
344B ASN* 2.8 25.2 - - - +
345B PHE* 3.7 18.6 + - + -
348B ARG* 3.4 43.2 + - - +
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Residues in contact with THR 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B LEU* 3.2 39.7 + - - +
254B TYR* 4.7 0.7 - - - -
256B ILE* 4.3 3.8 - - + -
257B GLU* 3.9 29.7 - - + +
301B GLU* 2.6 31.0 + - - -
302B LEU* 3.6 6.3 - - - -
304B GLU* 1.3 80.9 - - - +
306B PHE* 1.3 81.2 + - + +
307B LEU 3.4 2.3 + - - -
308B GLU* 5.2 8.3 - - - +
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Residues in contact with PHE 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B LEU* 4.5 11.2 - - + -
256B ILE* 4.6 9.6 - - + -
266B ALA* 3.8 29.8 - - + -
270B PHE* 3.5 26.2 - + - -
302B LEU* 3.1 44.1 + - + +
303B CYS 3.5 3.8 - - - +
305B THR* 1.3 96.4 - - + +
307B LEU* 1.3 58.0 + - - +
308B GLU* 3.5 2.2 - - - -
309B LYS* 3.4 9.7 + - + -
310B ILE* 2.9 33.3 + - + +
318B LEU* 3.7 44.2 - - + +
323B THR* 5.6 0.7 - - + -
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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