Contacts of the helix formed by residues 276 - 293 (chain B) in PDB entry 1RRM
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 PRO 276 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ASN* 5.0 2.0 - - - +
189B LEU* 6.5 1.3 - - + -
192B ALA* 5.4 3.8 - - + -
274B ASN 4.0 4.9 - - - +
275B THR* 1.3 94.5 - - + +
277B HIS* 1.3 66.5 + - - +
278B GLY 3.3 1.3 - - - +
279B VAL* 3.1 27.5 + - + +
280B ALA* 3.0 19.1 + - - +
343B VAL* 6.0 1.1 - - + -
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Residues in contact with HIS 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ASN* 4.8 5.5 - - - +
162B LYS* 5.4 0.8 + - - +
196B ASP* 3.1 22.2 - - - -
263B HIS* 3.4 14.4 - + - -
266B ALA* 4.5 7.2 - - + +
267B HIS* 3.7 23.2 - + - -
270B GLY* 6.4 0.7 - - - -
275B THR 3.1 5.6 + - - -
276B PRO* 1.3 70.0 - - - +
278B GLY* 1.3 57.5 + - - +
280B ALA* 3.3 8.0 + - - +
281B ASN* 2.9 47.7 + - - -
387B ZN 2.2 36.6 - - - -
389B APR 3.6 48.0 + - - +
390B PGO 3.1 4.9 + - - -
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Residues in contact with GLY 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ALA* 3.3 32.6 - - - +
193B THR* 5.1 1.1 - - - +
195B VAL* 4.6 1.2 - - - +
196B ASP* 3.8 15.9 - - - +
276B PRO* 3.3 2.2 - - - +
277B HIS* 1.3 77.4 - - - +
279B VAL* 1.3 60.3 + - - +
281B ASN* 3.8 2.3 - - - +
282B ALA* 2.9 30.1 + - - +
389B APR 5.4 3.6 + - - -
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Residues in contact with VAL 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ALA* 3.9 16.6 - - + -
275B THR* 4.6 2.9 - - + -
276B PRO* 3.1 33.2 + - + +
278B GLY* 1.3 73.0 - - - +
280B ALA* 1.3 67.8 + - - +
282B ALA* 3.3 6.4 + - - +
283B ILE* 3.0 32.8 + - + +
336B ILE* 4.1 16.6 - - + -
337B PRO* 4.5 5.6 - - + -
343B VAL* 3.9 29.8 - - + -
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Residues in contact with ALA 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ALA* 3.8 22.4 - - + +
269B LEU* 4.0 23.1 - - + +
270B GLY* 6.4 0.2 - - - -
275B THR* 4.2 12.7 - - + +
276B PRO 3.0 11.3 + - - +
277B HIS* 3.4 11.2 - - - +
279B VAL* 1.3 78.4 - - - +
281B ASN* 1.3 61.6 + - - +
283B ILE* 3.5 5.8 + - - +
284B LEU* 3.1 30.8 + - - +
340B LEU* 5.4 0.7 - - - -
343B VAL* 6.2 0.2 - - - -
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Residues in contact with ASN 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B ASP* 2.9 31.2 + - - +
199B THR* 3.6 16.8 - - - +
262B VAL* 3.5 18.1 - - + +
263B HIS* 3.4 18.5 + - - -
266B ALA* 3.1 20.6 - - - +
277B HIS* 2.9 37.5 + - - +
278B GLY* 3.8 4.5 - - - +
280B ALA* 1.3 75.7 - - - +
282B ALA* 1.3 56.6 - - - +
284B LEU 3.3 0.3 + - - -
285B LEU* 2.7 37.8 + - - +
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Residues in contact with ALA 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B VAL* 3.5 27.3 - - + +
278B GLY 2.9 19.8 + - - +
279B VAL 3.6 4.7 - - - +
281B ASN* 1.3 76.2 - - - +
283B ILE* 1.3 62.7 + - - +
285B LEU* 3.9 0.8 - - - +
286B PRO* 3.2 12.8 - - - +
331B ASN* 3.0 24.8 + - - +
336B ILE* 3.6 29.4 - - + -
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Residues in contact with ILE 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B VAL* 3.0 27.7 + - + +
280B ALA 3.9 3.1 - - - +
282B ALA* 1.3 77.3 - - - +
284B LEU* 1.3 61.4 + - - +
286B PRO* 3.7 4.7 - - - +
287B HIS* 3.3 18.9 + - - -
331B ASN* 5.1 0.9 - - - +
336B ILE* 4.6 1.1 - - + -
337B PRO 3.2 28.0 - - - +
338B PRO* 3.6 19.2 - - - +
339B HIS 3.8 16.4 - - - +
340B LEU* 3.5 34.3 - - + +
343B VAL* 3.8 25.8 - - + -
382B ALA* 4.1 7.0 - - + +
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Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B VAL* 3.8 11.4 - - + +
265B MSE 3.7 42.0 - - + +
266B ALA* 3.6 34.8 - - + +
269B LEU* 4.0 9.9 - - + -
280B ALA 3.1 21.8 + - - +
281B ASN* 3.9 1.8 - - - +
283B ILE* 1.3 77.5 - - - +
285B LEU* 1.3 65.2 + - - +
287B HIS* 3.0 11.5 + - + +
288B VAL* 3.0 29.0 + - + +
340B LEU* 4.4 5.6 - - + -
378B LEU* 5.1 1.3 - - + +
379B TYR* 4.3 8.7 - - + -
382B ALA* 4.3 17.5 - - + -
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B VAL* 4.4 11.9 - - + -
198B LEU* 4.5 5.4 - - + -
199B THR* 3.6 29.6 - - + +
202B ILE* 4.3 27.6 - - + -
203B GLU* 5.1 1.6 - - + -
262B VAL* 3.9 23.1 - - + +
281B ASN 2.7 21.7 + - - +
282B ALA 3.9 2.5 - - - +
284B LEU* 1.3 71.8 - - - +
286B PRO* 1.3 64.4 - - + +
288B VAL* 3.2 1.2 + - - +
289B MSE 2.9 53.9 + - + +
327B VAL* 3.6 20.0 - - + -
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Residues in contact with PRO 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ALA 3.2 20.9 - - - +
283B ILE 3.7 8.3 - - - +
284B LEU 3.6 1.1 - - - -
285B LEU* 1.3 89.3 - - + +
287B HIS* 1.3 59.2 + - + +
289B MSE 3.4 13.5 + - + +
290B ARG* 3.1 23.0 + - - +
324B VAL* 3.6 16.0 - - + +
327B VAL* 3.9 15.5 - - + -
328B PHE* 3.4 50.2 - - + -
331B ASN* 4.4 4.5 - - - +
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Residues in contact with HIS 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ILE 3.3 25.2 + - - -
284B LEU* 3.0 6.6 + - + +
286B PRO* 1.3 76.2 - - + +
288B VAL* 1.3 66.1 + - + +
290B ARG* 3.3 17.6 + - - +
291B TYR* 3.1 16.8 + - - +
328B PHE* 3.7 28.3 - + - -
338B PRO 4.8 7.9 + - - -
339B HIS* 5.9 0.2 + - - -
378B LEU* 3.5 23.3 - - + +
381B THR* 3.6 33.2 + - + +
382B ALA* 3.7 27.1 - - + -
385B GLY* 4.4 14.0 - - - -
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Residues in contact with VAL 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B GLU* 4.9 0.2 - - - +
261B LEU* 3.9 20.9 - - + -
262B VAL* 3.5 38.8 - - + +
265B MSE 4.1 25.1 - - - -
284B LEU* 3.0 23.3 + - + +
287B HIS* 1.3 73.6 - - + +
289B MSE 1.3 60.2 + - + +
291B TYR* 3.2 8.3 + - + +
292B ASN* 2.9 46.3 + - - +
366B ASN* 4.3 0.7 - - - +
378B LEU* 4.2 8.1 - - + -
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Residues in contact with MSE 289 (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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202B ILE* 4.2 24.2 - - + -
206B ILE* 5.7 2.0 - - + -
262B VAL* 5.9 0.2 - - + -
285B LEU* 2.9 41.0 + - + +
286B PRO* 3.5 7.4 - - - +
288B VAL* 1.3 78.1 - - + +
290B ARG* 1.3 57.5 + - - +
292B ASN* 3.2 2.1 + - - +
293B ALA 2.8 18.0 + - - -
300B TYR* 2.7 45.7 + - + +
303B ILE* 4.6 5.4 - - + -
323B ALA* 3.9 39.3 - - + +
324B VAL* 4.0 7.9 - - + +
327B VAL* 3.6 26.7 - - + -
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Residues in contact with ARG 290 (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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286B PRO 3.1 14.0 + - - +
287B HIS* 3.6 19.6 + - - +
288B VAL 3.3 0.2 - - - -
289B MSE 1.3 78.1 - - - +
291B TYR* 1.3 64.6 + - - +
293B ALA* 3.4 18.1 - - + +
321B ASN* 5.5 7.0 + - - +
324B VAL* 3.6 36.0 - - + +
325B GLU* 5.6 1.0 + - - +
328B PHE* 3.6 23.3 - - - -
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Residues in contact with TYR 291 (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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261B LEU* 3.8 25.6 - - + -
287B HIS 3.1 13.7 + - - +
288B VAL 3.3 8.5 - - - +
289B MSE 3.2 0.2 - - - -
290B ARG* 1.3 78.0 - - - +
292B ASN* 1.3 82.7 + - - +
293B ALA 3.7 0.2 + - - -
294B ASP* 4.9 1.9 + - - +
295B PHE* 4.9 1.2 - - - -
366B ASN* 3.9 4.5 - - - -
368B ARG* 2.9 80.8 + - + +
369B GLU 3.8 0.2 + - - -
370B ALA* 3.1 20.9 + - + -
374B ASP* 2.7 39.4 + - + -
378B LEU* 4.0 21.1 - - + -
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Residues in contact with ASN 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B GLU* 5.5 0.8 + - - -
206B ILE* 4.1 10.3 - - + +
288B VAL* 2.9 29.1 + - - +
289B MSE 4.9 0.6 - - - +
291B TYR* 1.3 87.9 - - - +
293B ALA* 1.3 65.1 + - - +
294B ASP 3.3 1.8 - - - -
295B PHE* 2.8 20.3 + - - +
296B THR* 3.4 7.7 - - + +
300B TYR* 3.7 12.5 + - - +
366B ASN* 2.7 43.4 - - - +
367B PRO* 3.8 20.7 - - + +
368B ARG* 3.5 10.4 - - - +
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B MSE 2.8 12.7 + - - +
290B ARG* 3.4 18.6 - - + +
291B TYR 3.4 1.4 - - - -
292B ASN* 1.3 73.5 - - - +
294B ASP* 1.3 65.8 + - - +
296B THR* 2.7 21.6 + - - -
300B TYR* 3.6 18.6 + - + -
320B ARG* 3.2 27.5 + - + -
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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