Contacts of the helix formed by residues 260 - 274 (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 GLY 260 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B GLU* 3.0 16.1 + - - -
259B LEU* 1.3 85.2 - - - +
261B LEU* 1.3 59.0 + - - -
262B VAL 3.3 0.7 + - - -
263B HIS 3.4 2.3 + - - -
264B GLY 3.1 20.3 + - - -
362B CYS* 3.5 24.4 + - - +
363B THR* 4.2 1.1 - - - -
366B ASN* 3.9 13.9 - - - -
367B PRO* 5.6 0.4 - - - -
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Residues in contact with LEU 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B GLU* 3.2 0.4 + - - -
260B GLY* 1.3 68.5 - - - -
262B VAL* 1.3 65.9 + - - +
264B GLY* 3.6 2.5 - - - +
265B MSE 2.9 43.4 + - + +
288B VAL* 3.9 8.1 - - + -
291B TYR* 3.8 23.3 - - + -
357B ALA* 5.0 0.4 - - + -
363B THR* 3.9 27.8 - - + +
366B ASN* 3.0 28.7 - - + +
370B ALA* 4.1 11.2 - - + -
375B ILE* 3.9 17.3 - - + -
378B LEU* 3.5 30.3 - - + -
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Residues in contact with VAL 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B THR* 3.6 13.7 - - + -
203B GLU* 2.9 29.9 + - + +
261B LEU* 1.3 74.3 - - - +
263B HIS* 1.3 59.2 + - - +
265B MSE 3.2 3.7 + - - +
266B ALA* 2.9 26.3 + - - +
281B ASN* 3.5 37.5 - - - +
284B LEU* 3.8 4.9 - - + +
285B LEU* 3.9 25.4 - - + +
288B VAL* 3.5 32.5 - - + +
289B MSE 5.9 0.2 - - + -
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Residues in contact with HIS 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B THR* 3.4 23.3 - - + +
200B HIS* 3.0 22.6 + + - -
203B GLU* 2.8 24.6 + - - +
259B LEU* 3.6 13.8 - - + +
260B GLY 3.4 4.0 + - - +
261B LEU 3.4 0.2 - - - -
262B VAL* 1.3 78.8 - - - +
264B GLY* 1.3 63.4 + - - +
266B ALA* 4.2 0.9 - - - -
267B HIS* 3.1 36.4 + + + -
277B HIS* 3.1 14.0 + + - -
281B ASN* 3.5 13.2 + - - -
362B CYS* 4.0 17.0 - - + -
387B ZN 2.1 34.4 - - - -
390B PGO 3.0 11.9 - - - -
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Residues in contact with GLY 264 (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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260B GLY 3.1 13.4 + - - -
261B LEU 3.3 3.1 + - - -
262B VAL 3.2 0.6 - - - -
263B HIS* 1.3 77.2 - - - +
265B MSE 1.3 55.6 + - - +
268B PRO* 3.0 20.4 - - - +
357B ALA* 3.3 18.6 - - - -
360B ASP* 3.6 18.1 - - - +
362B CYS* 4.1 0.8 - - - +
363B THR* 3.4 22.2 - - - -
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Residues in contact with MSE 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B LEU* 2.9 46.9 + - + +
264B GLY* 1.3 75.0 - - - +
266B ALA* 1.3 64.2 + - - +
267B HIS 3.4 0.4 - - - -
268B PRO* 3.4 3.7 - - - +
269B LEU* 3.5 12.0 - - - +
284B LEU* 3.7 22.4 - - + -
288B VAL* 4.1 10.1 - - - -
357B ALA* 3.9 12.3 - - + -
375B ILE* 3.6 7.0 - - + +
378B LEU* 3.5 37.2 - - + -
379B TYR* 2.6 65.2 + - + +
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Residues in contact with ALA 266 (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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262B VAL 2.9 10.8 + - - +
263B HIS* 3.8 4.3 - - - +
265B MSE 1.3 78.1 - - - +
267B HIS* 1.3 67.2 + - - +
269B LEU* 3.1 13.8 + - - +
270B GLY* 3.1 10.4 + - - -
277B HIS* 4.5 10.6 + - - +
280B ALA* 3.8 24.1 - - + +
281B ASN* 3.1 28.9 - - - +
284B LEU* 3.8 10.1 - - + -
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Residues in contact with HIS 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B VAL* 4.7 7.1 - - + +
162B LYS* 3.5 29.8 - - + +
164B VAL* 3.4 27.5 - - + +
263B HIS* 3.1 21.0 + + + +
266B ALA* 1.3 77.3 - - - +
268B PRO* 1.3 69.3 - - + +
270B GLY 3.0 2.5 + - - +
271B ALA* 3.0 17.0 + - - +
277B HIS* 3.7 31.3 - + - -
360B ASP* 2.9 27.7 + - - +
362B CYS* 3.8 16.8 - - - -
389B APR 4.5 8.8 + - - -
390B PGO 4.3 10.6 + - - -
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Residues in contact with PRO 268 (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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161B ARG* 6.1 0.4 - - - -
162B LYS 5.7 0.9 - - - +
264B GLY 3.0 28.5 - - - +
265B MSE 3.4 8.5 - - - +
267B HIS* 1.3 88.9 - - + +
269B LEU* 1.3 54.8 + - - +
271B ALA* 3.3 6.4 + - + +
272B PHE* 2.9 37.5 + - + +
353B LEU* 3.8 23.8 - - + +
356B ALA* 3.7 20.6 - - + +
357B ALA* 3.7 21.3 - - - +
360B ASP* 5.4 0.9 - - + +
379B TYR* 3.9 4.9 - - - +
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Residues in contact with LEU 269 (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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265B MSE 3.5 18.8 - - - +
266B ALA 3.1 6.4 + - - +
268B PRO* 1.3 73.9 - - - +
270B GLY* 1.3 61.8 + - - +
273B TYR* 2.9 40.2 + - + +
274B ASN 3.5 3.1 + - - -
275B THR* 3.5 22.2 + - + +
280B ALA* 4.0 20.0 - - + -
284B LEU* 4.0 9.6 - - + -
340B LEU* 4.0 24.5 - - + -
345B VAL* 3.9 24.7 - - + -
353B LEU* 4.0 17.9 - - + -
379B TYR* 4.0 11.7 - - + -
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Residues in contact with GLY 270 (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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71B ASN* 4.2 8.2 - - - +
155B THR* 5.2 1.2 + - - +
162B LYS* 4.0 13.9 - - - -
266B ALA 3.1 8.9 + - - -
267B HIS 3.0 8.2 + - - -
269B LEU* 1.3 77.5 - - - +
271B ALA* 1.3 57.2 + - - +
274B ASN* 2.8 29.0 + - - +
275B THR* 3.9 20.3 - - - -
277B HIS* 6.4 0.4 - - - -
280B ALA* 5.7 0.4 - - - +
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Residues in contact with ALA 271 (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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155B THR* 4.5 11.6 - - + +
160B ARG* 3.8 15.9 + - - +
161B ARG* 3.5 36.8 - - - +
162B LYS* 3.5 17.8 - - + +
267B HIS 3.0 7.4 + - - +
268B PRO* 3.6 9.6 - - + +
269B LEU 3.2 0.2 - - - -
270B GLY* 1.3 79.1 - - - +
272B PHE* 1.3 62.0 + - + +
274B ASN 4.6 0.3 + - - -
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Residues in contact with PHE 272 (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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160B ARG* 3.2 77.6 + - + +
268B PRO* 2.9 24.0 + - + +
271B ALA* 1.3 82.1 - - + +
273B TYR* 1.3 77.6 + - + +
349B ASP* 4.1 27.1 - - + -
352B ALA* 3.9 30.5 - - + -
353B LEU* 3.6 20.2 - - + -
356B ALA* 5.3 5.6 - - + -
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Residues in contact with TYR 273 (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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160B ARG* 4.8 3.8 - - - -
269B LEU* 2.9 30.6 + - + -
272B PHE* 1.3 94.6 - - + +
274B ASN* 1.3 73.7 + - - +
275B THR* 3.2 18.1 + - - +
343B VAL 5.1 2.0 - - - +
344B GLY* 3.4 22.0 - - - +
345B VAL* 3.7 24.9 - - + +
346B ARG* 3.1 27.8 + - + -
349B ASP* 2.6 39.8 + - - +
353B LEU* 3.9 2.9 - - + +
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Residues in contact with ASN 274 (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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70B PRO* 3.6 17.0 + - - +
71B ASN* 2.9 31.6 - - - +
270B GLY 2.8 18.8 + - - +
271B ALA 4.5 0.8 + - - -
272B PHE 3.8 0.6 - - - -
273B TYR* 1.3 80.8 - - - +
275B THR* 1.3 67.0 + - - +
276B PRO* 3.6 4.7 - - - +
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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