Contacts of the helix formed by residues 260 - 274 (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 GLY 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A GLU* 3.0 16.9 + - - -
259A LEU* 1.3 83.3 - - - +
261A LEU* 1.3 57.6 + - - -
262A VAL 3.4 0.5 + - - -
263A HIS 3.5 2.4 + - - -
264A GLY 3.1 19.9 + - - -
362A CYS* 3.5 22.3 + - - +
363A THR* 4.2 2.5 - - - -
366A ASN* 3.8 14.8 - - - -
367A PRO* 5.5 0.9 - - - -
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Residues in contact with LEU 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A GLU* 3.2 0.6 + - - -
260A GLY* 1.3 69.8 - - - -
262A VAL* 1.3 65.3 + - - +
263A HIS 3.3 0.2 - - - -
264A GLY* 3.6 1.8 - - - +
265A MSE 2.9 49.4 + - + +
288A VAL* 3.9 7.9 - - + -
291A TYR* 3.8 21.5 - - + -
357A ALA 5.0 0.4 - - - +
363A THR* 3.9 28.0 - - + +
366A ASN* 3.0 24.2 + - - +
370A ALA* 4.0 12.6 - - + -
375A ILE* 3.9 18.8 - - + -
378A LEU* 3.4 31.0 - - + -
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Residues in contact with VAL 262 (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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199A THR* 3.5 14.8 - - + -
203A GLU* 2.9 27.6 + - + +
261A LEU* 1.3 77.2 - - - +
263A HIS* 1.3 58.7 + - - +
265A MSE 3.7 0.7 - - - -
266A ALA* 2.9 27.7 + - - +
281A ASN* 3.5 36.8 - - - +
284A LEU* 3.7 7.6 - - + +
285A LEU* 3.9 22.2 - - + +
288A VAL* 3.5 33.6 - - + +
289A MSE 5.8 0.7 - - + -
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Residues in contact with HIS 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ASP* 3.8 0.4 - - - -
199A THR* 3.4 22.3 - - + +
200A HIS* 3.0 23.9 + + - -
203A GLU* 2.8 23.4 + - - +
259A LEU* 3.6 15.1 - - + +
260A GLY 3.5 4.2 + - - +
262A VAL* 1.3 77.6 - - - +
264A GLY* 1.3 66.1 - - - +
266A ALA* 4.1 0.9 - - - -
267A HIS* 3.0 37.0 + + + -
277A HIS* 3.1 13.6 + + - -
281A ASN* 3.4 13.4 + - - -
360A ASP* 4.5 0.7 - - - -
362A CYS* 4.1 16.2 - - + -
387A ZN 2.2 34.4 - - - -
390A PGO 3.1 11.2 - - - -
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Residues in contact with GLY 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A GLY 3.1 12.9 + - - -
261A LEU 3.3 3.6 + - - -
262A VAL 3.2 0.4 - - - -
263A HIS* 1.3 77.2 - - - +
265A MSE 1.3 56.4 + - - +
268A PRO* 3.0 19.9 - - - +
357A ALA* 3.3 19.7 - - - -
360A ASP* 3.6 18.2 + - - +
362A CYS* 4.3 0.2 - - - +
363A THR* 3.3 22.7 - - - -
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Residues in contact with MSE 265 (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* 2.9 47.2 + - + +
264A GLY* 1.3 75.3 - - - +
266A ALA* 1.3 63.9 + - - +
267A HIS 3.4 0.2 - - - -
268A PRO* 3.3 4.1 - - - +
269A LEU* 3.5 11.8 - - - +
284A LEU* 3.7 20.4 - - + -
288A VAL* 4.1 11.9 - - - -
357A ALA* 3.9 11.2 - - + -
375A ILE* 3.6 7.6 - - + +
378A LEU* 3.5 37.2 - - + -
379A TYR* 2.6 66.3 + - + +
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Residues in contact with ALA 266 (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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162A LYS* 5.5 0.2 - - - -
262A VAL 2.9 10.4 + - - +
263A HIS* 3.2 5.1 + - - +
265A MSE 1.3 77.8 - - - +
267A HIS* 1.3 65.1 + - - +
269A LEU* 3.2 14.2 + - - +
270A GLY* 3.2 10.0 + - - -
277A HIS* 4.5 10.4 + - - +
280A ALA* 3.8 23.3 - - + +
281A ASN* 3.1 29.8 - - - +
284A LEU* 3.6 9.4 - - + +
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Residues in contact with HIS 267 (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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153A VAL* 4.7 3.3 - - + +
162A LYS* 3.2 43.5 + - + +
164A VAL* 3.4 27.2 - - + +
263A HIS* 3.0 20.3 + - + +
266A ALA* 1.3 76.6 - - - +
268A PRO* 1.3 68.6 - - + +
270A GLY 3.0 10.9 + - - -
271A ALA* 3.1 10.7 + - - +
277A HIS* 3.7 28.7 - + - -
360A ASP* 2.9 30.3 + - - +
362A CYS* 3.9 17.3 - - - -
389A APR 4.6 3.4 + - - -
390A PGO 4.2 10.5 + - - -
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Residues in contact with PRO 268 (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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161A ARG* 6.2 0.4 - - - -
162A LYS 5.8 0.4 - - - +
264A GLY 3.0 24.0 - - - +
265A MSE 3.3 9.0 - - - +
267A HIS* 1.3 93.4 - - + +
269A LEU* 1.3 56.0 + - - +
271A ALA* 3.3 6.5 + - + -
272A PHE* 2.8 38.1 + - + +
353A LEU* 3.8 19.1 - - + +
356A ALA* 3.6 21.1 - - + +
357A ALA* 3.6 21.5 - - - +
360A ASP* 5.4 1.1 - - + +
379A TYR* 3.9 6.7 - - - +
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Residues in contact with LEU 269 (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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265A MSE 3.5 17.5 - - - +
266A ALA 3.2 6.9 + - - +
267A HIS 3.1 0.6 - - - -
268A PRO* 1.3 75.7 - - - +
270A GLY* 1.3 59.8 + - - +
273A TYR* 2.9 49.8 + - + +
274A ASN 3.4 0.3 + - - -
275A THR* 3.3 26.4 + - + +
280A ALA* 4.0 18.2 - - + -
284A LEU* 4.1 9.9 - - + -
340A LEU* 3.9 26.2 - - + -
345A VAL* 3.8 14.1 - - + -
353A LEU* 3.8 18.4 - - + -
379A TYR* 4.1 11.2 - - + +
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Residues in contact with GLY 270 (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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71A ASN* 4.4 8.0 - - - +
155A THR* 5.4 1.0 + - - +
162A LYS* 3.8 15.7 - - - -
266A ALA 3.2 8.1 + - - -
267A HIS 3.0 7.7 + - - -
269A LEU* 1.3 80.6 - - - +
271A ALA* 1.3 56.3 + - - +
274A ASN* 2.9 27.9 + - - +
275A THR* 3.8 21.0 - - - -
277A HIS* 6.4 0.7 - - - -
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Residues in contact with ALA 271 (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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155A THR* 4.8 10.6 - - + +
160A ARG* 3.8 17.3 + - - +
161A ARG* 3.4 37.7 - - - +
162A LYS* 3.6 14.9 - - + +
267A HIS 3.1 7.5 + - - +
268A PRO* 3.7 9.6 - - + +
269A LEU 3.3 0.2 - - - -
270A GLY* 1.3 79.7 - - - +
272A PHE* 1.3 63.5 + - + +
274A ASN 4.6 0.7 + - - -
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Residues in contact with PHE 272 (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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160A ARG* 3.1 74.3 + - + +
268A PRO* 2.8 21.7 + - + +
271A ALA* 1.3 81.8 - - + +
273A TYR* 1.3 76.8 + - + +
274A ASN 3.8 0.2 - - - -
349A ASP* 4.1 24.0 - - + -
352A ALA* 3.9 33.9 - - + -
353A LEU* 3.5 22.9 - - + -
356A ALA* 5.1 9.2 - - + -
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Residues in contact with TYR 273 (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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160A ARG* 4.7 4.3 - - - -
269A LEU* 2.9 23.6 + - + -
272A PHE* 1.3 96.0 - - + +
274A ASN* 1.3 72.9 + - - +
275A THR* 3.0 17.2 + - - +
343A VAL 5.2 2.2 - - - +
344A GLY* 3.4 22.0 - - - +
345A VAL* 3.7 29.6 - - + +
346A ARG* 3.0 27.9 + - + -
349A ASP* 2.7 39.7 + - + +
353A LEU* 4.0 2.6 - - + +
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Residues in contact with ASN 274 (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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70A PRO* 3.7 15.9 + - - +
71A ASN* 2.9 32.2 + - - +
270A GLY 2.9 19.0 + - - +
271A ALA 4.5 0.8 + - - -
272A PHE 3.8 0.4 - - - -
273A TYR* 1.3 80.2 - - - +
275A THR* 1.3 65.2 + - - +
276A PRO* 3.5 6.4 - - - +
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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