Contacts of the helix formed by residues 255 - 268 (chain M) in PDB entry 5MQF
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 LEU 255 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254M GLN* 1.3 78.0 - - + +
256M GLY* 1.3 61.3 + - - +
257M LYS 3.2 0.2 + - - -
258M LEU* 3.4 4.0 + - - +
259M TRP* 2.9 30.4 + - - +
287M MET* 4.7 19.9 - - - +
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Residues in contact with GLY 256 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254M GLN 3.1 0.8 + - - -
255M LEU* 1.3 77.9 - - - +
257M LYS* 1.3 56.9 + - - +
259M TRP* 3.8 8.7 - - - +
260M CYS* 2.9 31.0 + - - +
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Residues in contact with LYS 257 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248M LEU* 6.1 1.3 - - + -
253M ASP* 3.6 27.4 - - + -
254M GLN 3.0 14.1 + - - +
256M GLY* 1.3 77.2 - - - +
258M LEU* 1.3 60.0 + - - +
260M CYS* 3.4 3.9 + - - +
261M SER* 2.9 29.0 + - - -
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Residues in contact with LEU 258 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253M ASP* 4.9 4.0 - - - +
254M GLN* 4.0 15.6 - - - +
255M LEU 3.4 6.5 + - - +
257M LYS* 1.3 76.7 - - - +
259M TRP* 1.3 60.5 + - - +
261M SER* 4.3 5.8 - - - -
262M LEU* 2.9 33.3 + - - +
285M THR 5.3 9.2 - - - +
287M MET* 5.9 5.8 - - + +
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Residues in contact with TRP 259 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255M LEU 2.9 20.2 + - - +
256M GLY* 4.0 8.3 - - - +
258M LEU* 1.3 78.9 - - - +
260M CYS* 1.3 56.4 + - - +
262M LEU* 4.5 2.1 - - - +
263M ALA* 2.8 32.8 + - - +
291M ASP* 6.5 0.7 - - + -
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Residues in contact with CYS 260 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256M GLY 2.9 20.1 + - - +
257M LYS* 3.9 3.4 - - - +
259M TRP* 1.3 74.8 - - - +
261M SER* 1.3 60.5 + - - +
263M ALA* 4.0 3.8 - - - +
264M ASP* 2.9 31.0 + - - +
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Residues in contact with SER 261 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241M ASP* 5.5 2.1 - - - +
244M ILE* 3.8 35.5 - - - +
245M ARG* 5.4 0.7 - - - -
248M LEU* 6.0 3.6 - - - -
257M LYS 2.9 17.9 + - - -
258M LEU* 4.0 7.0 - - - -
260M CYS* 1.3 75.2 - - - +
262M LEU* 1.3 60.2 + - - +
264M ASP* 3.4 3.0 + - - +
265M TYR* 2.9 30.7 + - - +
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Residues in contact with LEU 262 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258M LEU 2.9 19.4 + - - +
259M TRP* 4.5 2.2 - - - +
261M SER* 1.3 76.8 - - - +
263M ALA* 1.3 56.4 + - - +
265M TYR* 4.0 5.1 - - - +
266M TYR* 2.9 31.7 + - - +
282M ALA* 3.8 29.5 - - + +
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Residues in contact with ALA 263 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259M TRP 2.8 23.1 + - - +
260M CYS* 4.0 5.2 - - - +
262M LEU* 1.3 77.9 - - - +
264M ASP* 1.3 57.0 + - - +
266M TYR* 4.7 2.7 - - - -
267M ILE* 2.9 34.3 + - - +
294M GLN* 5.2 15.9 - - + -
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Residues in contact with ASP 264 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240M VAL* 5.5 13.1 - - + +
241M ASP* 5.9 2.9 - - - +
260M CYS 2.9 20.5 + - - +
261M SER* 4.0 4.3 - - - +
263M ALA* 1.3 76.6 - - - +
265M TYR* 1.3 51.7 + - - +
267M ILE* 4.9 2.2 - - - -
268M ARG* 2.7 39.7 + - - +
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Residues in contact with TYR 265 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241M ASP* 4.3 22.2 - - + +
261M SER 2.9 18.6 + - - +
262M LEU* 4.0 6.3 - - - +
264M ASP* 1.3 76.3 - - - +
266M TYR* 1.3 64.2 + - - +
268M ARG* 3.6 11.0 + - - +
269M SER* 3.6 13.0 + - - -
278M VAL* 5.5 7.4 - - + +
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Residues in contact with TYR 266 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262M LEU 2.9 19.5 + - - +
263M ALA* 4.2 3.6 - - - +
265M TYR* 1.3 76.8 - - - +
267M ILE* 1.3 62.6 + - - +
269M SER* 3.4 19.1 + - - +
270M GLY 4.9 0.7 - - - +
275M ALA* 4.5 18.7 - - + +
278M VAL* 5.5 8.3 - - + +
279M TYR* 5.3 12.6 - - + +
282M ALA* 6.2 1.8 - - + -
294M GLN* 5.9 6.3 - - + +
295M VAL* 6.3 1.1 - - - -
298M SER* 5.4 14.5 - - - -
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Residues in contact with ILE 267 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263M ALA 2.9 19.5 + - - +
264M ASP* 4.7 2.5 - - - +
266M TYR* 1.3 73.8 - - - +
268M ARG* 1.3 62.7 + - - +
269M SER 3.2 8.7 - - - +
298M SER* 6.4 0.9 - - - -
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Residues in contact with ARG 268 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237M SER* 3.6 39.1 - - - +
240M VAL* 6.2 3.1 - - + -
241M ASP* 6.3 1.3 - - + -
264M ASP 2.7 23.6 + - - +
265M TYR* 3.7 8.7 - - - +
266M TYR 3.2 0.4 - - - -
267M ILE* 1.3 80.4 - - - +
269M SER* 1.3 59.5 + - - +
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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