Contacts of the helix formed by residues 276 - 293 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ASN* 5.1 3.1 - - - +
192A ALA* 5.5 3.4 - - + -
274A ASN 3.8 6.1 - - - +
275A THR* 1.3 92.2 - - + +
277A HIS* 1.3 66.7 + - - +
278A GLY 4.7 1.1 - - - +
279A VAL* 3.1 26.7 + - + +
280A ALA* 3.1 18.4 + - - +
343A VAL* 6.2 0.7 - - + -
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Residues in contact with HIS 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ASN* 4.9 6.0 - - - +
162A LYS* 5.1 2.0 - - - -
196A ASP* 3.1 20.9 - - - -
263A HIS* 3.4 15.3 - + - -
266A ALA* 4.5 8.0 + - + +
267A HIS* 3.7 25.3 - + - -
270A GLY* 6.4 0.2 - - - -
275A THR 3.2 5.6 + - - -
276A PRO* 1.3 70.4 - - - +
278A GLY* 1.3 61.7 + - - +
280A ALA* 3.3 7.5 + - - +
281A ASN* 3.0 42.9 + - - -
387A ZN 2.2 36.5 - - - -
389A APR 3.6 46.8 + - - +
390A PGO 3.1 2.7 + - - -
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Residues in contact with GLY 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ALA* 3.3 33.3 - - - +
193A THR* 5.1 0.9 - - - -
195A VAL* 4.6 1.9 - - - +
196A ASP* 3.9 15.0 - - - +
276A PRO* 3.3 1.8 - - - +
277A HIS* 1.3 80.9 - - - +
279A VAL* 1.3 57.0 + - - +
281A ASN* 3.5 2.3 + - - +
282A ALA* 2.9 30.0 + - - +
389A APR 5.4 3.8 + - - -
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Residues in contact with VAL 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ALA* 3.9 17.7 - - + +
275A THR* 4.6 4.0 - - + -
276A PRO* 3.1 31.5 + - + +
278A GLY* 1.3 72.4 - - - +
280A ALA* 1.3 67.0 + - - +
282A ALA* 3.3 5.9 + - - +
283A ILE* 3.1 31.4 + - + +
336A ILE* 4.3 15.7 - - + -
337A PRO* 4.6 5.2 - - + -
343A VAL* 3.8 30.5 - - + -
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Residues in contact with ALA 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A ALA* 3.8 22.7 - - + +
269A LEU* 4.0 21.8 - - + -
275A THR* 4.2 13.9 - - + +
276A PRO 3.1 11.7 + - - +
277A HIS* 3.5 10.1 - - - +
279A VAL* 1.3 79.3 - - - +
281A ASN* 1.3 61.6 + - - +
283A ILE* 3.3 6.4 + - - +
284A LEU* 3.1 29.3 + - - +
340A LEU* 5.0 1.3 - - - +
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Residues in contact with ASN 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ASP* 3.0 30.4 + - - +
199A THR* 3.6 16.4 - - - +
262A VAL* 3.5 17.5 - - + +
263A HIS* 3.4 19.7 + - - -
266A ALA* 3.1 21.2 - - - +
277A HIS* 3.0 36.3 + - - +
278A GLY* 3.8 4.5 - - - +
280A ALA* 1.3 76.2 - - - +
282A ALA* 1.3 57.2 + - - +
284A LEU 3.2 0.2 + - - -
285A LEU* 2.7 37.1 + - - +
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Residues in contact with ALA 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A VAL* 3.5 26.9 - - + +
278A GLY 2.9 19.2 + - - +
279A VAL 3.5 5.4 - - - +
280A ALA 3.3 0.2 - - - -
281A ASN* 1.3 76.7 - - - +
283A ILE* 1.3 62.0 + - - +
285A LEU* 4.0 1.0 - - - +
286A PRO* 3.2 10.7 - - - +
331A ASN* 2.8 26.3 + - - +
336A ILE* 3.7 30.5 - - + -
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Residues in contact with ILE 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A VAL* 3.1 21.3 + - + +
280A ALA* 3.9 3.8 - - - +
282A ALA* 1.3 76.3 - - - +
284A LEU* 1.3 59.3 + - - +
286A PRO* 3.7 5.2 - - - +
287A HIS* 3.2 21.5 + - - -
331A ASN* 5.0 0.7 - - - +
336A ILE* 4.7 2.2 - - + -
337A PRO 3.1 26.9 - - - +
338A PRO* 3.5 20.0 - - - +
339A HIS 3.8 17.3 - - - +
340A LEU* 3.5 33.0 - - + +
343A VAL* 3.9 29.8 - - + -
382A ALA* 4.1 7.6 - - + +
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Residues in contact with LEU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A VAL* 3.7 12.1 - - + +
265A MSE 3.7 41.1 - - + +
266A ALA* 3.6 33.9 - - + +
269A LEU* 4.1 10.3 - - + -
280A ALA 3.1 21.2 + - - +
281A ASN 3.8 1.6 - - - +
283A ILE* 1.3 78.1 - - - +
285A LEU* 1.3 66.2 + - - +
287A HIS* 3.0 11.0 + - + +
288A VAL* 3.0 28.4 + - + +
340A LEU* 4.4 12.6 - - + -
378A LEU* 5.1 0.7 - - + +
379A TYR* 4.6 1.6 - - + -
382A ALA* 4.1 19.5 - - + -
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A VAL* 4.4 8.1 - - + -
198A LEU* 4.4 10.8 - - + -
199A THR* 3.6 30.1 - - + +
202A ILE* 4.3 26.9 - - + -
203A GLU* 5.1 1.3 - - + -
262A VAL* 3.9 21.7 - - + +
281A ASN 2.7 21.2 + - - +
282A ALA 4.0 2.0 - - - +
284A LEU* 1.3 71.1 - - - +
286A PRO* 1.3 65.6 - - + +
288A VAL* 3.3 1.2 + - - +
289A MSE 2.9 51.8 + - + +
327A VAL* 3.6 22.9 - - + -
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Residues in contact with PRO 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ALA 3.2 17.9 - - - +
283A ILE* 3.8 9.2 - - - +
284A LEU 3.6 1.8 - - - -
285A LEU* 1.3 92.7 - - + +
287A HIS* 1.3 62.2 + - + +
289A MSE 3.5 9.6 + - + +
290A ARG* 3.1 19.6 + - - +
324A VAL* 3.7 16.0 - - + +
327A VAL* 3.9 19.1 - - + -
328A PHE* 3.5 49.4 - - + -
331A ASN* 4.1 3.6 - - - +
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Residues in contact with HIS 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ILE 3.2 25.7 + - - -
284A LEU* 3.0 7.7 + - + +
286A PRO* 1.3 75.7 - - + +
288A VAL* 1.3 67.7 + - + +
290A ARG* 3.3 16.9 + - - +
291A TYR* 3.1 20.3 + - - +
328A PHE* 3.7 27.6 - + - -
338A PRO 4.8 7.9 + - - -
339A HIS* 5.8 0.8 - - - -
378A LEU* 3.8 19.1 - - + +
381A THR* 3.5 34.1 + - + +
382A ALA* 4.0 25.1 - - + -
385A GLY* 4.3 13.8 - - - -
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Residues in contact with VAL 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A GLU* 4.9 0.4 - - - +
261A LEU* 3.9 20.2 - - + +
262A VAL* 3.5 42.2 - - + +
265A MSE 4.1 23.3 - - - -
284A LEU* 3.0 23.2 + - + +
287A HIS* 1.3 73.5 - - + +
289A MSE 1.3 60.5 + - - +
291A TYR* 3.1 7.9 + - + +
292A ASN* 2.9 46.1 + - - +
366A ASN* 4.2 0.2 - - - +
378A LEU* 4.6 7.9 - - + -
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Residues in contact with MSE 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ILE* 4.1 23.8 - - + -
206A ILE* 5.7 2.2 - - + -
285A LEU* 2.9 44.0 + - + +
286A PRO* 3.6 8.1 - - - +
288A VAL* 1.3 79.1 - - + +
290A ARG* 1.3 57.1 + - - +
292A ASN* 3.1 2.3 + - - +
293A ALA 2.8 18.5 + - - -
300A TYR* 2.6 43.7 + - + +
303A ILE* 4.7 5.2 - - + -
323A ALA* 3.9 38.8 - - + +
324A VAL* 4.1 6.5 - - + +
327A VAL* 3.6 28.3 - - + -
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Residues in contact with ARG 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A PRO 3.1 10.0 + - - +
287A HIS* 3.6 19.9 + - - +
288A VAL 3.3 0.2 - - - -
289A MSE 1.3 78.5 - - - +
291A TYR* 1.3 62.7 + - - +
293A ALA* 3.3 21.9 - - + +
321A ASN* 5.8 2.0 + - - -
324A VAL* 3.7 25.9 - - + +
325A GLU* 5.8 0.6 + - - -
328A PHE* 3.7 31.2 - - - -
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Residues in contact with TYR 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A LEU* 3.8 19.1 - - + -
287A HIS 3.1 13.5 + - - +
288A VAL* 3.2 9.0 - - + +
290A ARG* 1.3 80.0 - - - +
292A ASN* 1.3 81.5 + - - +
293A ALA 3.7 0.2 + - - -
294A ASP* 4.9 1.7 + - - +
295A PHE* 4.9 0.9 - - - -
366A ASN* 3.8 6.7 - - - -
368A ARG* 2.9 73.7 + - + +
369A GLU 3.6 2.3 + - - -
370A ALA* 3.3 18.6 - - + -
374A ASP* 3.0 39.5 + - + -
378A LEU* 3.9 29.4 - - + -
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Residues in contact with ASN 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A GLU* 5.5 1.2 + - - -
206A ILE* 4.1 10.2 - - + +
288A VAL* 2.9 30.5 + - - +
289A MSE 4.9 0.6 - - - +
291A TYR* 1.3 85.9 - - - +
293A ALA* 1.3 65.6 + - - +
294A ASP 3.3 1.8 - - - -
295A PHE* 2.8 19.8 + - - +
296A THR* 3.4 10.2 - - + +
300A TYR* 3.8 10.5 - - - +
366A ASN* 2.7 43.9 + - - -
367A PRO* 3.8 21.9 - - + +
368A ARG* 3.5 9.5 - - - +
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Residues in contact with ALA 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A MSE 2.8 12.5 + - - +
290A ARG* 3.3 19.4 + - + +
291A TYR 3.4 0.2 - - - -
292A ASN* 1.3 74.2 - - - +
294A ASP* 1.3 62.6 + - - +
295A PHE 3.0 3.3 + - - -
296A THR* 2.7 21.3 + - - -
300A TYR* 4.0 17.5 - - + -
320A ARG* 3.2 30.2 + - + -
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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