Contacts of the strand formed by residues 272 - 290 (chain B) in PDB entry 3RBH
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 LEU 272 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B HIS* 5.6 0.7 - - - -
270B MSE 3.6 15.4 - - - +
271B PRO* 1.3 82.5 - - + +
273B ASN* 1.3 78.9 + - - +
274B TYR* 4.7 11.1 - - + -
316B LEU* 4.6 22.0 - - + -
317B ARG 3.3 22.4 - - - +
318B TRP* 4.6 8.5 - - + +
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Residues in contact with ASN 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B GLY 3.1 15.0 + - - +
262B ASP 3.3 14.3 - - - +
263B ALA* 4.5 0.7 - - - +
268B SER* 3.1 27.4 + - - -
270B MSE 3.4 9.3 - - - +
272B LEU* 1.3 85.8 + - - +
274B TYR* 1.3 66.5 + - - +
275B TRP* 5.8 0.4 - - - -
316B LEU* 3.6 1.6 - - - -
317B ARG* 2.7 63.8 + - + +
319B ASN* 2.8 24.8 + - - +
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Residues in contact with TYR 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B TRP* 4.4 9.7 + - - -
219B HIS* 2.8 42.5 + + - +
220B ARG 5.2 0.5 + - - -
259B ALA* 4.3 12.1 - - + +
260B THR* 3.6 17.1 + - - -
261B GLY* 3.0 45.1 + - - -
263B ALA* 3.1 14.3 - - - +
272B LEU* 4.7 10.3 - - + -
273B ASN* 1.3 82.9 - - - +
275B TRP* 1.3 71.5 + - - +
276B ALA* 5.4 3.6 - - + -
315B GLY 3.2 13.9 - - - +
316B LEU* 4.0 13.2 - - + -
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Residues in contact with TRP 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ALA 3.4 6.3 - - - -
260B THR* 4.1 7.9 - - + -
263B ALA* 3.6 23.8 - - + -
264B TYR* 4.2 16.6 - + - +
274B TYR* 1.3 83.5 - - - +
276B ALA* 1.3 65.4 - - - +
277B SER* 5.5 1.3 - - - -
313B ASP* 2.9 41.7 + - - -
314B LEU* 3.3 9.2 - - - +
315B GLY* 2.9 59.3 + - - +
316B LEU 4.4 4.5 - - - -
317B ARG* 4.2 7.9 - - + -
328B VAL 4.4 2.7 - - - -
329B GLY* 4.7 1.1 - - - -
356B PHE* 3.8 46.0 - + + -
365B ARG* 4.0 21.3 - - - -
383B PHE* 4.3 15.0 - + - -
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Residues in contact with ALA 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B GLU* 3.3 1.7 - - - +
259B ALA* 2.7 48.1 + - + +
274B TYR* 5.4 3.6 - - + -
275B TRP* 1.3 78.1 - - - +
277B SER* 1.3 60.4 + - - +
313B ASP 3.3 7.2 - - - -
314B LEU* 3.8 15.5 - - + -
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Residues in contact with SER 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B GLN* 4.8 3.8 + - - -
160B TRP* 5.9 3.3 + - - -
257B ILE* 3.2 12.6 - - - -
258B GLU* 4.0 15.3 - - - -
275B TRP* 5.5 1.3 - - - -
276B ALA* 1.3 75.8 - - - +
278B ALA* 1.3 61.2 + - - +
279B THR* 5.0 5.8 + - - -
312B VAL* 3.2 10.4 - - - +
313B ASP* 2.9 50.0 + - - +
314B LEU* 4.4 0.4 - - - +
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Residues in contact with ALA 278 (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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256B GLY* 3.3 0.9 - - - -
257B ILE* 2.9 42.6 + - + +
277B SER* 1.3 73.9 - - - +
279B THR* 1.3 62.9 + - - +
280B TRP* 3.8 18.1 - - + -
310B PHE* 3.8 22.9 - - + -
311B GLY 3.5 5.6 - - - -
312B VAL* 4.4 3.6 - - + +
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Residues in contact with THR 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B TRP* 3.5 38.6 + - + -
254B TRP* 3.9 26.9 - - + -
255B LEU 3.4 9.2 - - - +
256B GLY* 4.0 0.9 - - - -
257B ILE 5.1 0.2 + - - -
277B SER* 5.0 6.2 + - - -
278B ALA* 1.3 81.2 + - - +
280B TRP* 1.3 62.7 + - - +
310B PHE* 3.2 10.1 - - - -
311B GLY 2.8 40.6 + - - -
344B PHE* 3.6 13.1 - - + -
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Residues in contact with TRP 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B THR 3.5 1.4 - - - +
254B TRP* 3.3 3.6 - - - -
255B LEU* 2.8 61.6 + - + +
256B GLY* 5.3 0.4 - - - -
257B ILE* 4.2 14.4 - - + -
278B ALA* 3.8 29.8 - - + -
279B THR* 1.3 76.9 - - - +
281B LEU* 1.3 61.9 + - - +
282B THR* 6.2 1.6 - - + -
309B ALA 3.7 7.9 - - - +
310B PHE* 3.6 29.9 - + + -
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B LEU* 3.9 17.5 - - + -
253B THR 3.3 16.6 - - - +
254B TRP* 3.4 29.6 - - + +
279B THR 4.0 0.4 + - - -
280B TRP* 1.3 73.7 - - - +
282B THR* 1.3 66.2 + - - +
307B VAL* 4.1 22.2 - - + -
308B ASN* 3.4 4.5 - - - +
309B ALA* 2.9 34.5 + - + +
343B GLN 4.4 0.2 - - - +
344B PHE* 3.9 22.7 - - + -
345B GLN* 3.8 44.4 - - + +
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Residues in contact with THR 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B LEU* 3.7 5.1 - - - -
253B THR* 2.8 40.7 + - - +
255B LEU* 4.2 7.9 - - + -
280B TRP* 5.7 1.8 - - + -
281B LEU* 1.3 76.7 - - - +
283B GLY* 1.3 60.1 + - - +
307B VAL 3.1 6.8 + - - -
308B ASN* 3.0 22.3 + - - -
176C LEU* 3.7 38.5 - - + +
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Residues in contact with GLY 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B GLN* 3.3 25.1 - - - -
252B LEU* 4.3 1.3 - - - -
282B THR* 1.3 81.6 + - - +
284B ASP* 1.3 65.4 + - - +
306B ASP* 3.6 8.3 - - - +
307B VAL* 2.9 25.9 + - - +
308B ASN* 5.2 0.2 + - - -
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Residues in contact with ASP 284 (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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250B GLY* 4.1 5.2 - - - -
251B GLN* 2.9 59.7 + - - +
252B LEU* 4.2 2.4 - - - +
283B GLY* 1.3 73.9 - - - +
285B ARG* 1.3 73.4 + - - +
305B GLY 3.3 14.1 - - - +
306B ASP* 3.8 13.7 - - - +
307B VAL* 4.1 3.8 - - - +
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Residues in contact with ARG 285 (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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247B THR* 5.3 4.9 - - - +
248B TYR* 3.5 52.2 - - + +
249B THR 3.3 5.4 - - - +
250B GLY* 4.3 1.3 - - - -
252B LEU* 4.9 8.5 - - + -
284B ASP* 1.3 84.1 - - - +
286B ASP* 1.3 58.8 + - - +
287B ASN* 2.9 34.9 + - - +
303B GLN 3.9 1.0 - - - +
304B SER* 3.2 3.2 - - - -
305B GLY 2.8 34.3 + - - +
307B VAL* 4.1 19.3 - - + -
345B GLN* 3.1 26.9 + - - +
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Residues in contact with ASP 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LEU* 3.2 17.4 - - + +
248B TYR* 3.4 0.4 - - - -
249B THR* 2.7 42.3 + - - +
250B GLY* 4.7 0.2 - - - -
284B ASP* 5.2 0.2 + - - -
285B ARG* 1.3 73.0 - - - +
287B ASN* 1.3 60.7 + - - +
302B LYS* 4.9 9.0 - - + -
303B GLN 3.8 4.5 - - - -
304B SER* 3.9 14.6 - - - +
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Residues in contact with ASN 287 (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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234B LEU* 4.5 0.2 - - - -
247B THR* 3.9 7.7 - - + +
248B TYR* 3.5 5.7 - - - +
285B ARG* 2.9 49.5 + - - +
286B ASP* 1.3 71.4 - - - +
288B LEU* 1.3 69.4 + - - +
289B THR* 3.4 3.3 + - + +
302B LYS* 4.3 1.6 - - - -
303B GLN* 2.8 54.4 + - + +
304B SER 5.5 0.2 - - - -
305B GLY* 5.4 2.4 - - - +
339B ASP* 4.4 17.4 + - - +
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Residues in contact with LEU 288 (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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234B LEU* 3.9 17.5 - - + +
235B ARG* 3.6 35.9 - - + +
241B VAL* 4.2 17.3 - - + -
245B ASP* 5.9 1.3 - - + -
246B LYS 4.0 16.2 - - - +
247B THR* 3.2 26.5 + - - +
286B ASP 3.7 3.6 + - - -
287B ASN* 1.3 76.5 - - - +
289B THR* 1.3 64.9 + - - +
290B THR* 3.9 19.4 - - + +
299B ALA* 3.7 13.7 - - + -
301B GLY 3.4 19.1 - - - +
302B LYS* 4.5 0.4 - - + +
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Residues in contact with THR 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ASN* 3.7 10.5 - - + +
288B LEU* 1.3 79.3 - - - +
290B THR* 1.3 59.6 + - - +
299B ALA* 3.5 2.3 - - - -
300B THR* 2.6 37.2 + - - -
301B GLY* 3.0 28.9 + - - +
302B LYS 3.7 1.0 + - - -
303B GLN* 4.0 20.6 - - + +
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Residues in contact with THR 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B VAL* 4.3 11.7 - - + -
288B LEU* 3.9 25.1 - - + +
289B THR* 1.3 81.3 - - - +
291B THR* 1.3 61.8 + - - +
297B ARG* 4.6 12.4 - - + +
298B ILE 3.3 17.5 - - - +
299B ALA* 4.2 4.5 - - - -
300B THR* 3.9 6.0 - - - +
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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