Contacts of the helix formed by residues 262 - 275 (chain B) in PDB entry 3MQT
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 THR 262 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B ARG* 3.4 12.6 - - - +
96B GLY* 2.9 34.0 + - - +
99B LEU* 3.9 14.8 - - - +
100B PHE* 4.0 17.3 - - + -
260B MET 4.2 6.1 - - - +
261B SER* 1.3 83.2 - - - +
263B THR* 1.3 78.4 + - - +
266B GLU* 3.2 18.4 + - - +
281B SER* 6.4 0.2 - - - -
285B ARG* 3.6 18.2 - - + +
286B CYS* 3.8 4.7 - - - +
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Residues in contact with THR 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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86B TYR* 4.4 5.8 - - + -
94B MET 3.2 27.1 - - - +
95B ARG* 3.5 15.1 + - - +
99B LEU* 3.9 19.7 - - + -
261B SER* 5.1 1.4 + - - -
262B THR* 1.3 86.8 + - - +
264B ARG* 1.3 63.8 + - - +
265B PHE* 3.3 27.4 + - + -
266B GLU 3.5 2.8 + - - -
267B ALA* 3.3 17.0 + - - +
281B SER* 5.1 0.7 + - - -
286B CYS* 3.1 19.6 + - - +
291B GLU* 3.4 11.4 - - - +
295B ILE* 4.1 7.6 - - - +
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Residues in contact with ARG 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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82B TYR* 4.6 9.7 - - - -
83B ASN* 5.2 5.5 + - - -
263B THR* 1.3 70.8 - - - +
265B PHE* 1.3 97.9 + - + +
266B GLU 3.3 0.2 - - - -
267B ALA* 3.6 1.2 - - - +
268B GLN* 2.8 33.4 + - - +
291B GLU* 2.8 42.9 + - - +
294B ARG* 3.4 50.2 - - + +
295B ILE* 3.6 26.5 - - + -
298B ILE* 4.2 18.3 - - + +
300D GLU* 3.3 26.9 + - - -
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Residues in contact with PHE 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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86B TYR* 3.7 13.5 - + - -
95B ARG* 3.5 29.2 - - - +
263B THR* 3.1 23.2 - - - +
264B ARG* 1.3 121.8 - - + +
266B GLU* 1.3 62.2 + - - +
268B GLN* 4.0 6.2 - - - +
269B GLU* 3.2 21.7 + - - +
291B GLU* 4.8 0.9 - - - -
300D GLU* 5.7 0.2 - - - -
301D HIS* 6.2 1.6 - - - -
239G ASP* 3.4 44.9 - - + -
269G GLU* 5.5 0.5 - - - +
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Residues in contact with GLU 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ARG* 3.4 24.8 + - - +
238B HIS* 5.0 2.8 - - - -
261B SER* 2.9 32.0 - - - -
262B THR* 3.2 26.7 + - - +
263B THR* 3.4 5.5 + - - +
265B PHE* 1.3 73.4 - - - +
267B ALA* 1.3 68.6 + - - +
269B GLU* 2.9 20.6 + - - +
270B TRP* 2.9 24.2 + - + -
94G MET* 5.6 1.9 - - - +
95G ARG* 3.8 29.9 + - - +
266G GLU* 4.8 0.7 - - - +
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Residues in contact with ALA 267 (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 ALA* 4.9 4.7 - - - -
261B SER* 4.7 2.0 + - - -
263B THR 3.3 11.7 + - - +
264B ARG* 3.6 9.4 - - - +
266B GLU* 1.3 79.8 - - - +
268B GLN* 1.3 62.6 + - - +
270B TRP* 3.3 10.9 + - - +
271B LEU* 3.1 29.2 + - + +
279B VAL* 4.5 6.3 - - + +
281B SER* 4.1 9.9 - - - +
295B ILE* 3.9 31.6 - - + -
298B ILE* 6.1 1.6 - - + -
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Residues in contact with GLN 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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264B ARG* 2.8 22.8 + - - +
265B PHE* 4.0 6.8 - - - +
267B ALA* 1.3 75.5 - - - +
269B GLU* 1.3 57.1 + - - +
271B LEU* 3.2 9.5 + - - +
272B GLU* 2.9 52.1 + - - +
298B ILE* 3.3 38.9 - - + +
302B HIS* 5.0 1.3 - - + -
301D HIS* 2.7 48.4 + - - +
273G LYS* 5.3 0.2 + - - -
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Residues in contact with GLU 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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241B LEU* 3.6 28.0 - - + +
265B PHE 3.2 14.1 + - - +
266B GLU* 2.9 14.0 + - - +
268B GLN* 1.3 76.9 - - - +
270B TRP* 1.3 57.7 + - + +
272B GLU* 3.8 5.6 - - + +
273B LYS* 2.9 55.8 + - + +
269G GLU* 3.4 44.1 - - - +
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Residues in contact with TRP 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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238B HIS* 3.1 48.6 + + - -
241B LEU* 3.8 22.8 - - + +
244B HIS* 3.6 44.6 - + - -
257B GLY* 3.7 9.4 - - - -
258B ALA* 3.5 37.4 - - + +
261B SER* 4.3 4.5 - - - -
266B GLU* 2.9 29.7 + - + +
267B ALA* 3.4 10.1 - - - +
269B GLU* 1.3 76.2 - - + +
271B LEU* 1.3 56.3 + - - +
274B THR* 2.5 51.5 + - + -
276B ILE* 3.5 28.5 - - + -
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Residues in contact with LEU 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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246A LYS* 6.0 0.6 + - - +
267B ALA* 3.1 19.3 + - + +
268B GLN 3.5 6.5 - - - +
270B TRP* 1.3 82.8 - - - +
272B GLU* 1.3 63.0 + - - +
274B THR* 4.8 0.2 - - - -
275B GLY* 3.4 18.1 + - - +
276B ILE* 3.6 19.3 - - + +
279B VAL* 3.7 24.5 - - + -
295B ILE* 5.6 0.2 - - + -
298B ILE* 3.9 24.9 - - + -
299B CYS* 4.1 15.3 - - - -
302B HIS* 3.9 33.7 - - + +
304B ALA* 3.6 28.5 - - + -
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Residues in contact with GLU 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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268B GLN* 2.9 42.5 + - - +
269B GLU* 3.8 8.0 - - + +
271B LEU* 1.3 77.6 - - - +
273B LYS* 1.3 62.1 + - + +
275B GLY 5.0 0.3 + - - -
302B HIS* 3.1 36.9 + - - +
301D HIS* 4.6 5.9 + - - -
273G LYS* 4.8 6.9 + - - -
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Residues in contact with LYS 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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241B LEU* 4.5 20.7 - - + +
242B ILE* 4.6 16.4 - - + +
245B GLN* 3.0 21.3 - - + +
269B GLU* 2.9 40.6 + - + +
272B GLU* 1.3 80.6 - - + +
274B THR* 1.3 64.6 + - + +
301E HIS* 4.3 21.6 + - - -
272G GLU* 4.9 7.9 + - - -
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Residues in contact with THR 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B LEU* 3.2 45.1 - - + +
244B HIS* 3.8 15.0 - - + -
245B GLN* 3.3 29.7 - - - +
248B ALA* 3.6 11.3 - - - +
270B TRP* 2.5 29.2 + - + +
273B LYS* 1.3 80.6 - - + +
275B GLY* 1.3 62.8 + - - +
276B ILE* 3.2 21.8 + - - +
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Residues in contact with GLY 275 (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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214A TRP* 5.9 1.6 - - - -
246A LYS* 5.2 18.1 + - - -
248B ALA* 4.3 9.7 - - - +
255B LEU 5.8 0.2 + - - -
271B LEU* 3.4 16.5 + - - -
272B GLU 4.9 0.4 + - - -
273B LYS 3.8 0.2 - - - -
274B THR* 1.3 77.8 + - - +
276B ILE* 1.3 68.2 + - - +
277B SER* 3.4 8.8 + - - -
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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