Contacts of the helix formed by residues 270 - 281 (chain F) in PDB entry 5MG3
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 270 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449D ASN* 4.5 14.6 - - + +
452D GLN* 3.8 26.2 - - + +
453D GLY 4.8 2.2 - - - +
504D MET* 4.1 32.1 - - + -
262F LEU* 5.0 6.1 - - + +
266F GLY* 3.1 34.1 + - - +
267F GLY 3.9 1.8 - - - -
269F VAL* 1.4 81.9 - - + +
271F GLU* 1.3 57.3 + - - +
272F GLY 3.6 2.2 - - - -
273F PHE* 3.5 30.0 + - + -
274F SER* 2.8 32.8 + - - +
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Residues in contact with GLU 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368C ILE* 5.8 4.5 - - - +
88F PHE* 3.7 23.6 - - + -
89F GLY 4.8 0.9 - - - +
90F SER* 2.6 32.3 + - - -
191F PHE* 5.6 2.4 - - - -
263F TYR* 4.9 17.3 + - + +
267F GLY 3.2 13.7 + - - +
268F PRO 3.1 16.6 + - - +
269F VAL 3.6 0.8 + - - -
270F LEU* 1.3 75.3 - - - +
272F GLY* 1.4 60.3 + - - +
274F SER* 3.4 7.2 + - - -
275F LEU* 2.8 36.2 + - + +
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Residues in contact with GLY 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F PHE* 5.6 4.5 - - - -
188F LEU* 5.9 3.4 - - - -
193F ILE* 5.8 7.9 - - - -
199F ILE* 4.6 8.3 - - - -
270F LEU 3.6 0.4 - - - -
271F GLU* 1.4 80.9 - - - +
273F PHE* 1.3 55.6 + - - +
275F LEU* 3.5 13.5 - - - +
276F THR* 2.9 35.7 + - - +
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Residues in contact with PHE 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504D MET* 3.8 24.2 - - + -
508D ALA* 3.8 25.6 - - + -
198F THR* 3.3 48.5 - - + -
199F ILE* 4.6 6.5 - - + +
201F ALA* 5.1 2.9 - - + -
202F SER* 3.7 16.2 + - - -
262F LEU* 4.2 19.1 - - + -
270F LEU* 3.6 34.0 - - + +
272F GLY* 1.3 74.9 - - - +
274F SER* 1.3 59.2 + - - +
276F THR* 3.0 17.5 + - - -
277F MET* 3.3 29.6 + - + +
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Residues in contact with SER 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259F ILE* 4.0 3.3 - - - +
262F LEU* 4.0 12.7 + - - +
263F TYR* 3.5 48.3 + - - -
266F GLY* 5.2 0.3 - - - -
270F LEU* 2.8 25.7 + - - +
271F GLU 3.6 3.8 - - - -
273F PHE* 1.3 77.7 - - - +
275F LEU* 1.4 49.5 + - - +
277F MET* 3.4 7.9 + - - +
278F LEU* 2.7 38.4 + - - +
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Residues in contact with LEU 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C ILE* 3.9 43.5 - - + -
188F LEU* 3.9 29.6 - - + -
263F TYR* 5.1 6.7 - - + -
271F GLU* 2.8 26.8 + - + +
272F GLY* 3.5 11.2 - - - +
274F SER* 1.4 66.3 - - - +
276F THR* 1.4 62.1 + - + +
278F LEU* 4.2 10.5 - - + -
279F ILE* 3.0 51.9 + - + +
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Residues in contact with THR 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185F LEU* 5.0 11.0 - - + -
188F LEU* 4.0 24.9 - - + -
199F ILE* 4.1 15.7 - - + +
202F SER* 2.9 29.1 + - - -
203F LEU* 5.1 10.5 - - + -
206F VAL* 4.2 3.3 - - - +
272F GLY 2.9 21.9 + - - +
273F PHE* 3.0 12.0 + - - -
275F LEU* 1.4 70.8 - - + +
277F MET* 1.3 47.3 + - - -
279F ILE* 4.1 3.9 - - - +
280F GLY* 2.8 32.9 + - - -
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Residues in contact with MET 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508D ALA* 5.6 2.2 - - + +
511D VAL* 5.0 16.8 - - + -
512D LEU 6.2 0.2 - - - +
202F SER* 3.4 12.6 + - - +
205F SER* 3.5 31.2 - - - +
206F VAL* 3.7 23.7 - - - +
259F ILE* 3.3 43.6 - - + +
262F LEU* 5.0 9.0 - - + -
273F PHE* 3.3 38.0 + - + +
274F SER* 3.4 7.8 + - - +
276F THR* 1.3 73.4 + - - +
278F LEU* 1.4 56.0 + - - +
280F GLY* 3.2 13.3 + - - -
281F VAL* 3.2 12.6 + - - +
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Residues in contact with LEU 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256F LEU* 4.2 11.7 - - + +
259F ILE* 3.4 10.7 - - + +
260F LEU* 3.7 23.3 - - + -
263F TYR* 3.7 44.2 - - + -
274F SER 2.7 20.6 + - - +
275F LEU* 4.0 9.9 - - + +
277F MET* 1.4 69.7 - - - +
279F ILE* 1.3 73.7 + - + +
281F VAL* 3.7 11.3 - - - +
282F SER* 3.5 14.5 - - - -
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Residues in contact with ILE 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368C ILE* 4.5 15.5 - - - +
370C TYR* 6.1 0.2 - - + -
371C PRO* 4.6 18.4 - - + -
372C LEU* 6.0 0.9 - - + -
180F ASP* 4.9 1.3 - - + +
181F VAL* 5.9 1.8 - - + -
184F THR* 3.5 43.3 - - + +
275F LEU* 3.0 37.0 + - + +
276F THR* 4.1 3.8 - - - +
278F LEU* 1.3 81.2 - - + +
280F GLY* 1.3 58.7 + - - +
282F SER* 2.6 32.9 + - - +
283F ILE* 3.5 15.9 - - + +
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Residues in contact with GLY 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181F VAL* 5.6 2.9 - - - -
206F VAL* 3.8 29.4 - - - +
209F TYR 4.1 0.3 - - - +
210F SER* 3.4 6.1 + - - -
276F THR 2.8 20.5 + - - -
277F MET 3.2 3.7 + - - -
279F ILE* 1.3 78.2 - - - +
281F VAL* 1.4 53.8 + - - +
282F SER 3.2 1.3 - - - -
283F ILE* 3.3 30.0 - - - +
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Residues in contact with VAL 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206F VAL* 5.3 1.8 - - + -
209F TYR* 3.1 26.4 - - + +
210F SER* 3.1 16.7 + - - -
213F ASP* 5.7 0.2 - - - +
252F SER* 4.1 12.6 - - - +
255F THR* 3.6 33.2 - - - +
256F LEU* 3.4 42.8 - - + -
259F ILE* 3.9 9.4 - - + -
277F MET 3.2 12.1 + - - +
278F LEU 3.7 6.7 - - - +
280F GLY* 1.4 71.9 - - - +
282F SER* 1.4 58.7 + - - +
284F GLY* 5.5 0.3 - - - -
285F THR* 5.3 1.7 + - - -
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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
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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