Contacts of the helix formed by residues 249 - 266 (chain B) in PDB entry 2M6I
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 ALA 249 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244B ILE* 6.1 0.7 - - + -
245B ASN* 3.0 27.9 - - - +
248B ALA* 1.3 84.1 - - + +
250B PRO* 1.3 60.7 - - - +
251B ALA 3.0 10.4 + - - +
252B ARG 3.5 5.5 + - - -
246C LEU 4.0 9.9 - - - +
247C ASP* 4.7 1.3 - - - +
250C PRO* 3.9 15.0 - - + -
301C TYR* 2.9 32.6 - - + +
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Residues in contact with PRO 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ALA 5.2 0.4 - - - +
249A ALA* 4.0 16.4 - - + -
251A ALA* 4.4 18.3 - - + +
245B ASN* 2.8 21.5 - - + +
247B ASP 3.3 15.3 - - - +
248B ALA 4.3 0.2 - - - +
249B ALA* 1.3 87.1 - - - +
251B ALA* 1.3 64.0 + - + +
252B ARG 3.2 0.9 - - - -
253B VAL* 3.1 7.0 + - + +
254B GLY* 3.1 19.6 + - - -
301B TYR* 2.9 31.4 - - + +
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Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ALA* 5.0 8.0 - - + +
249B ALA* 3.0 1.2 - - - +
250B PRO* 1.3 82.7 - - + +
252B ARG* 1.3 60.9 + - - +
254B GLY* 3.5 2.1 + - - -
255B LEU* 3.3 29.1 + - + +
250C PRO* 4.4 34.5 - - + +
251C ALA* 4.9 5.6 - - + +
254C GLY* 6.4 0.4 - - - -
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Residues in contact with ARG 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B ILE* 4.7 10.9 + - - +
238B SER* 3.6 24.4 + - - +
241B SER* 3.2 24.7 + - - -
245B ASN* 3.3 7.6 - - - +
249B ALA 3.5 1.6 + - - -
250B PRO 3.2 0.6 - - - -
251B ALA* 1.3 77.5 - - - +
253B VAL* 1.3 63.3 + - - +
255B LEU* 3.1 11.1 + - + +
256B GLY* 2.9 50.4 + - - -
294C VAL* 4.2 11.3 - - - +
298C LEU* 3.1 34.7 - - + +
301C TYR* 3.2 36.0 + - + +
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Residues in contact with VAL 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B SER* 5.0 4.9 - - - +
242B PHE* 3.5 44.6 - - + +
245B ASN* 3.2 33.8 - - + +
250B PRO* 3.1 12.0 + - + +
252B ARG* 1.3 81.8 - - - +
254B GLY* 1.3 60.7 + - - +
256B GLY* 4.1 0.4 - - - -
257B ILE* 3.1 44.9 + - + +
301B TYR* 4.9 12.3 - - + -
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Residues in contact with GLY 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ALA* 6.4 0.9 - - - -
255A LEU* 3.3 30.5 - - - +
250B PRO 3.1 12.3 + - - -
251B ALA* 3.5 4.0 + - - -
252B ARG 3.2 0.4 - - - -
253B VAL* 1.3 79.5 - - - +
255B LEU* 1.3 59.3 + - - +
257B ILE* 4.1 3.4 - - - +
258B THR* 2.6 31.0 + - - -
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Residues in contact with LEU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ALA* 3.3 17.9 + - + +
252B ARG* 3.1 12.2 + - + +
254B GLY* 1.3 80.0 - - - +
256B GLY* 1.3 55.5 + - - +
258B THR* 3.8 3.5 - - - +
259B THR* 2.6 39.5 + - - +
254C GLY* 3.3 40.8 - - - +
257C ILE* 6.1 2.5 - - + -
258C THR* 4.4 10.5 - - + +
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Residues in contact with GLY 256 (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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238B SER* 5.2 7.5 - - - -
252B ARG* 2.9 37.0 + - - +
253B VAL 4.2 0.9 - - - -
255B LEU* 1.3 78.6 - - - +
257B ILE* 1.3 60.1 + - - +
259B THR* 3.4 7.1 + - - -
260B VAL* 3.3 29.3 + - - +
293B PHE* 5.9 0.2 - - - -
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Residues in contact with ILE 257 (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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255A LEU* 6.0 2.0 - - + -
238B SER* 5.5 4.7 - - - +
242B PHE* 6.1 0.2 - - + -
253B VAL* 3.1 37.0 + - + +
254B GLY* 4.4 5.2 - - - +
256B GLY* 1.3 77.4 - - - +
258B THR* 1.3 62.8 + - - +
259B THR 3.7 0.2 + - - -
260B VAL* 3.8 8.5 + - - +
261B LEU* 3.9 23.1 + - + +
293B PHE* 3.8 37.3 - - + -
294B VAL* 5.1 14.4 - - + -
297B ALA* 5.0 15.7 - - + -
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Residues in contact with THR 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A LEU* 4.4 13.5 - - + +
254B GLY 2.6 24.3 + - - -
255B LEU* 3.5 7.2 + - - -
256B GLY 3.3 0.2 - - - -
257B ILE* 1.3 77.1 - - - +
259B THR* 1.3 58.6 + - - +
260B VAL 3.3 0.7 - - - -
261B LEU* 3.8 6.3 + - + +
262B THR* 2.6 46.1 + - - +
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Residues in contact with THR 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B ILE* 5.8 8.3 - - + -
255B LEU* 2.6 25.0 + - - +
256B GLY* 3.7 9.3 - - - +
257B ILE 3.3 0.4 - - - -
258B THR* 1.3 77.5 - - - +
260B VAL* 1.3 62.1 - - + +
262B THR* 3.8 5.2 - - - -
263B LEU* 2.8 61.3 + - + +
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Residues in contact with VAL 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B SER* 4.9 6.3 - - - +
234B ILE* 6.5 0.9 - - + -
235B VAL* 3.2 37.2 - - + -
238B SER* 6.5 0.4 - - - -
256B GLY 3.3 17.0 + - - +
257B ILE* 4.1 7.2 - - - +
258B THR 3.3 0.2 - - - -
259B THR* 1.3 81.0 - - + +
261B LEU* 1.3 67.1 + - + +
263B LEU* 3.6 6.4 + - + +
264B THR* 2.6 35.8 + - - +
293B PHE* 5.3 12.1 - - + -
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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
----------------------------------------------------------
263A LEU* 6.5 1.1 - - + -
257B ILE* 3.9 20.5 + - + +
258B THR* 3.8 7.3 + - + +
259B THR 3.4 0.2 - - - -
260B VAL* 1.3 92.5 - - + +
262B THR* 1.3 57.4 + - - +
264B THR* 4.1 4.0 - - - +
265B THR* 2.6 33.6 + - - -
290B CYS* 5.5 15.3 - - + -
293B PHE* 5.3 11.7 - - + -
294B VAL* 6.0 4.9 - - + -
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Residues in contact with THR 262 (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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258B THR* 2.6 34.8 + - - +
259B THR* 4.1 4.3 - - - -
261B LEU* 1.3 79.3 - - - +
263B LEU* 1.3 59.3 - - + +
264B THR 3.3 0.7 - - - -
265B THR* 4.1 4.2 - - - -
266B GLN* 3.2 30.4 + - + +
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Residues in contact with LEU 263 (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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227B LEU* 4.9 6.3 - - + +
231B SER* 5.5 15.0 - - - -
234B ILE* 5.2 14.6 - - + -
259B THR* 2.8 45.7 + - + +
260B VAL* 4.0 6.7 - - + +
261B LEU 3.4 0.2 - - - -
262B THR* 1.3 80.9 - - + +
264B THR* 1.3 59.1 + - - +
266B GLN* 4.2 11.8 + - - +
267B SER* 3.1 25.6 + - - -
261C LEU* 6.5 1.6 - - + -
286C TRP* 4.9 22.2 - - + -
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Residues in contact with THR 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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224B LEU* 4.9 7.6 - - + -
227B LEU* 5.7 3.4 - - + -
228B TYR* 4.3 23.1 - - + +
231B SER* 6.0 2.4 - - - -
260B VAL* 2.6 28.1 + - - +
261B LEU* 4.5 4.1 - - - +
263B LEU* 1.3 77.2 - - - +
265B THR* 1.3 65.6 + - - +
266B GLN 3.2 1.6 - - - -
267B SER* 3.1 19.2 + - - -
268B SER* 3.6 9.0 + - - -
286B TRP* 3.5 34.4 - - + +
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Residues in contact with THR 265 (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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266A GLN* 4.6 18.2 + - + +
261B LEU* 2.6 24.2 + - - +
262B THR* 4.0 4.2 + - - -
264B THR* 1.3 78.8 - - - +
266B GLN* 1.3 59.4 + - - +
268B SER* 3.8 15.0 + - - +
269B GLY* 4.2 2.6 + - - -
271B ARG* 5.2 1.7 + - - -
279B TYR* 5.6 5.6 - - - +
286B TRP* 5.5 9.3 - - - -
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Residues in contact with GLN 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 THR* 3.2 23.0 + - + +
263B LEU* 4.6 12.3 + - - +
264B THR 3.2 0.4 - - - -
265B THR* 1.3 75.8 - - - +
267B SER* 1.3 64.0 + - - +
268B SER 3.0 6.9 + - - -
269B GLY* 3.4 12.9 + - - +
265C THR* 4.6 19.1 + - + +
279C TYR* 5.1 7.9 + - - -
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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