Contacts of the strand formed by residues 272 - 287 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219C HIS* 5.5 0.5 - - - -
270C MSE 3.6 16.0 - - - +
271C PRO* 1.3 85.1 - - + +
273C ASN* 1.3 78.7 + - - +
274C TYR* 4.8 9.7 - - + -
316C LEU* 4.6 22.9 - - + -
317C ARG 3.4 21.5 - - - +
318C TRP* 4.7 7.0 - - + -
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Residues in contact with ASN 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C GLY 3.1 20.0 + - - +
262C ASP* 3.3 12.9 - - - +
263C ALA* 4.5 0.9 - - - +
268C SER* 3.1 25.9 + - - -
270C MSE 3.4 11.5 + - - +
272C LEU* 1.3 88.0 + - - +
274C TYR* 1.3 65.6 + - - +
275C TRP* 5.8 0.4 - - - -
316C LEU* 3.6 1.9 - - - -
317C ARG* 2.8 64.0 + - + +
319C ASN* 2.9 22.9 + - - -
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Residues in contact with TYR 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C TRP* 4.3 9.9 + - - -
219C HIS* 2.7 44.3 + + - +
220C ARG 5.2 0.2 + - - -
259C ALA* 4.2 12.1 - - + +
260C THR* 3.5 16.6 + - - -
261C GLY* 3.0 42.8 + - - -
263C ALA* 3.1 13.8 - - - +
272C LEU* 4.8 9.9 - - + -
273C ASN* 1.3 82.3 - - - +
275C TRP* 1.3 73.0 + - - +
276C ALA* 4.8 2.9 - - + -
315C GLY 3.2 13.9 - - - +
316C LEU* 3.9 13.5 - - + -
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Residues in contact with TRP 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C ALA 3.5 6.5 - - - -
260C THR* 4.1 8.3 - - + -
263C ALA* 3.6 24.5 - - + -
264C TYR* 4.1 16.1 + + - +
273C ASN 5.8 0.2 - - - -
274C TYR* 1.3 83.3 - - - +
276C ALA* 1.3 64.9 + - - +
277C SER* 5.6 1.1 - - - -
313C ASP* 2.9 43.4 + - - -
314C LEU* 3.4 8.5 - - - +
315C GLY* 2.9 58.7 + - - +
316C LEU 4.3 4.5 - - - -
317C ARG* 4.3 7.2 - - + -
328C VAL 4.4 2.2 - - - -
329C GLY* 4.7 0.9 - - - -
356C PHE* 3.9 43.1 - + + -
365C ARG* 4.0 21.1 - - - -
383C PHE* 4.3 14.6 - + - -
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Residues in contact with ALA 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C GLU* 3.4 2.1 - - - +
259C ALA* 2.7 47.9 + - + +
260C THR* 6.1 0.2 - - - -
274C TYR* 5.4 3.6 - - + -
275C TRP* 1.3 77.5 - - - +
277C SER* 1.3 60.0 + - - +
313C ASP 3.3 7.0 - - - -
314C LEU* 3.8 15.3 - - + -
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Residues in contact with SER 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C GLN* 4.8 4.3 + - - -
160C TRP* 5.8 3.1 + - - -
257C ILE 3.2 13.5 - - - -
258C GLU* 4.0 15.9 - - - -
275C TRP* 5.6 1.2 - - - -
276C ALA* 1.3 75.2 - - - +
278C ALA* 1.3 61.2 + - - +
279C THR* 5.1 6.0 + - - -
312C VAL* 3.3 10.0 - - - +
313C ASP* 2.9 48.6 + - - +
314C LEU* 4.4 0.6 - - - +
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Residues in contact with ALA 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C GLY* 3.3 0.7 - - - -
257C ILE* 2.8 48.4 + - + +
277C SER* 1.3 74.6 - - - +
279C THR* 1.3 64.2 + - - +
280C TRP* 3.9 11.9 - - + -
310C PHE* 3.8 23.1 - - + -
311C GLY 3.4 5.2 - - - -
312C VAL* 4.8 3.4 - - + -
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Residues in contact with THR 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C TRP* 3.5 39.0 + - + -
254C TRP* 3.9 26.7 - - + -
255C LEU 3.4 9.4 - - - +
256C GLY* 3.9 0.7 - - - -
257C ILE 5.0 0.9 + - - -
277C SER* 5.1 5.4 + - - -
278C ALA* 1.3 80.8 + - - +
280C TRP* 1.3 64.9 + - - +
310C PHE* 3.2 7.7 - - - -
311C GLY 2.7 39.0 + - - -
344C PHE* 3.6 14.1 - - + -
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Residues in contact with TRP 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C THR 3.5 1.6 - - - +
254C TRP* 3.3 3.6 - - - -
255C LEU* 2.8 62.2 + - + +
256C GLY 5.3 0.4 - - - -
257C ILE* 4.1 15.0 - - + -
278C ALA* 3.9 30.1 - - + -
279C THR* 1.3 76.6 - - - +
281C LEU* 1.3 61.3 + - - +
282C THR* 4.2 1.3 - - - -
309C ALA 3.6 7.6 - - - +
310C PHE* 3.6 29.3 - + + +
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Residues in contact with LEU 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C LEU* 3.9 19.5 - - + -
253C THR 3.3 17.3 - - - +
254C TRP* 3.4 26.9 - - + -
279C THR 4.0 0.2 + - - -
280C TRP* 1.3 74.7 - - - +
282C THR* 1.3 66.1 + - - +
307C VAL* 4.0 22.0 - - + -
308C ASN* 3.3 4.9 - - - -
309C ALA* 2.9 34.0 + - + +
343C GLN 4.3 4.3 - - - +
344C PHE* 3.9 19.7 - - + -
345C GLN* 3.8 43.7 - - + +
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Residues in contact with THR 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B LEU* 3.7 38.3 - - + +
251C GLN* 4.8 0.3 - - - +
252C LEU* 3.6 5.5 - - - -
253C THR* 2.8 39.2 + - - +
255C LEU* 4.2 7.9 - - + -
280C TRP* 5.7 1.6 - - + -
281C LEU* 1.3 77.7 - - - +
283C GLY* 1.3 61.5 + - - +
307C VAL 3.1 7.1 + - - -
308C ASN* 3.0 21.7 + - - -
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Residues in contact with GLY 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C GLN* 3.2 24.9 - - - -
252C LEU* 4.2 1.1 - - - -
282C THR* 1.3 82.2 + - - +
284C ASP* 1.3 66.3 + - - +
306C ASP* 3.5 5.7 - - - +
307C VAL* 2.9 26.3 + - - +
308C ASN* 5.3 0.3 + - - -
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Residues in contact with ASP 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C GLY* 4.1 5.4 - - - -
251C GLN* 2.9 59.3 + - - +
252C LEU* 4.2 2.9 - - - +
283C GLY* 1.3 74.8 - - - +
285C ARG* 1.3 73.4 + - - +
305C GLY 3.3 16.8 - - - +
306C ASP* 4.2 3.1 - - + +
307C VAL* 4.2 4.7 - - - +
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Residues in contact with ARG 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C TYR* 3.5 54.0 + - + +
249C THR 3.3 4.9 - - - +
250C GLY* 4.3 1.3 - - - -
252C LEU* 4.9 8.1 - - + -
284C ASP* 1.3 84.1 - - - +
286C ASP* 1.3 61.1 + - - +
287C ASN* 3.0 33.8 + - - +
303C GLN 3.9 1.4 - - - +
304C SER* 3.1 4.4 - - - -
305C GLY 2.8 34.7 + - - +
307C VAL* 4.2 18.4 - - + -
345C GLN* 3.2 27.6 + - - +
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Residues in contact with ASP 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C TYR* 3.1 5.2 - - - -
249C THR* 2.7 46.3 + - - +
250C GLY* 4.7 0.4 - - - -
285C ARG* 1.3 72.9 - - - +
287C ASN* 1.3 64.4 + - - +
303C GLN 5.9 0.2 - - - +
304C SER* 4.1 15.3 - - - +
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Residues in contact with ASN 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C THR 4.8 0.9 - - - +
248C TYR* 3.6 9.5 - - + +
285C ARG* 3.0 44.4 + - - +
286C ASP* 1.3 77.1 - - - +
288C LEU* 1.3 67.4 + - - +
303C GLN* 3.0 54.8 + - + +
305C GLY* 5.4 0.8 - - - +
339C ASP* 4.9 13.3 + - - +
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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