Contacts of the helix formed by residues 232 - 251 (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 THR 232 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228F ILE* 3.6 11.2 - - - +
231F GLY* 1.4 72.8 - - - -
233F PRO* 1.3 72.3 - - - +
234F TYR* 3.8 13.5 + - - +
235F GLU* 3.7 35.9 - - + +
236F ILE* 3.9 10.6 - - + +
301F MET* 5.1 4.3 - - - +
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Residues in contact with PRO 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225F PHE* 3.7 26.9 - - + -
228F ILE* 4.3 9.9 - - + -
231F GLY 4.1 4.5 - - - +
232F THR* 1.3 91.5 - - - +
234F TYR* 1.3 81.1 + - + +
236F ILE* 3.0 8.9 + - + +
237F PHE* 3.0 54.0 + - + -
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Residues in contact with TYR 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168F ARG* 5.9 0.7 + - - -
232F THR* 3.5 10.5 + - - +
233F PRO* 1.3 98.1 - - + +
235F GLU* 1.4 59.8 + - - +
237F PHE* 3.4 40.4 + + - +
238F ASN* 3.6 7.0 + - - +
296F ALA 5.0 0.4 - - - -
297F LEU* 3.5 46.1 - - + +
300F GLY* 2.8 42.1 + - - -
301F MET* 3.4 36.6 - - + -
302F LYS 5.4 0.2 - - - -
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Residues in contact with GLU 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232F THR* 3.7 26.5 - - + +
234F TYR* 1.4 73.8 - - - +
236F ILE* 1.4 69.9 + - + +
238F ASN* 3.3 13.0 + - - +
239F VAL* 3.3 29.2 + - + +
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Residues in contact with ILE 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224F ASN* 3.5 40.6 - - + +
225F PHE* 5.1 1.1 - - - +
228F ILE* 4.5 20.9 - - + -
232F THR 3.9 14.8 - - - +
233F PRO 3.0 8.6 + - - +
235F GLU* 1.4 82.0 - - + +
237F PHE* 1.4 66.7 + - + +
239F VAL* 3.4 17.2 + - + +
240F SER* 2.8 29.4 + - - +
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Residues in contact with PHE 237 (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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166F GLU* 5.0 8.7 - - - -
221F ILE* 3.8 35.6 - - + +
222F ARG* 3.9 22.7 - - - -
225F PHE* 4.2 20.6 - + + -
233F PRO* 3.0 37.0 + - + -
234F TYR* 3.6 40.2 - + - +
235F GLU 3.3 0.4 - - - -
236F ILE* 1.4 81.8 - - + +
238F ASN* 1.3 60.3 + - - +
240F SER* 3.4 14.6 - - - -
241F LEU* 3.4 20.1 - - - +
293F SER* 4.8 7.2 - - - +
296F ALA 5.8 1.8 - - - -
297F LEU* 4.4 18.4 - - + -
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Residues in contact with ASN 238 (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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20F MET* 5.6 0.2 - - - +
234F TYR 3.6 8.9 + - - -
235F GLU* 3.3 11.9 + - - +
237F PHE* 1.3 75.7 - - - +
239F VAL* 1.4 63.0 + - + +
241F LEU* 3.0 35.8 + - + +
242F THR* 3.4 9.9 + - - +
293F SER* 5.8 0.2 + - - -
297F LEU* 3.5 22.6 - - - +
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Residues in contact with VAL 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235F GLU* 3.3 23.7 + - + +
236F ILE* 3.4 21.0 + - + +
238F ASN* 1.4 76.7 - - + +
240F SER* 1.3 56.2 + - - +
242F THR* 3.1 11.6 + - - +
243F GLN* 2.9 51.2 + - + +
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Residues in contact with SER 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217F VAL* 4.2 7.0 - - - +
220F ARG* 4.8 2.7 - - - -
221F ILE* 3.3 38.2 - - - +
224F ASN* 2.8 26.7 + - - +
236F ILE* 2.8 17.1 + - - +
237F PHE 3.4 4.3 - - - -
239F VAL* 1.3 75.5 - - - +
241F LEU* 1.4 59.3 + - - +
243F GLN* 3.6 9.9 + - - +
244F THR* 2.9 29.3 + - - -
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Residues in contact with LEU 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F MET* 4.4 21.3 - - + -
217F VAL* 3.7 22.7 - - + -
221F ILE* 4.2 1.3 - - + -
237F PHE 3.4 14.1 - - - +
238F ASN* 3.0 23.5 + - + +
240F SER* 1.4 77.3 - - - +
242F THR* 1.3 57.8 + - - +
244F THR 3.2 2.4 + - - -
245F LEU* 2.9 34.2 + - - +
289F ILE* 5.0 0.9 - - + -
290F TYR* 3.7 45.3 - - + +
293F SER* 3.5 31.2 - - - +
294F ALA* 5.7 1.6 - - + +
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Residues in contact with THR 242 (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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16F VAL 6.3 0.2 - - - -
17F TYR* 4.2 29.9 + - + +
20F MET* 4.0 25.8 - - + -
238F ASN 3.4 10.4 + - - +
239F VAL* 3.1 19.8 + - - +
241F LEU* 1.3 77.3 - - - +
243F GLN* 1.3 60.0 + - - +
244F THR 3.5 0.2 - - - -
245F LEU* 4.1 15.5 + - + +
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Residues in contact with GLN 243 (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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530D GLU* 4.7 12.3 - - - +
534D ASN* 3.8 38.9 + - - +
220F ARG* 3.5 31.2 + - + +
224F ASN* 3.5 22.5 + - - -
239F VAL* 2.9 36.6 + - + +
240F SER* 3.6 8.2 - - - +
242F THR* 1.3 77.2 - - - +
244F THR* 1.3 59.5 + - - +
245F LEU 3.5 1.8 + - - -
246F HIS 5.4 0.7 + - - -
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Residues in contact with THR 244 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216F VAL* 3.8 26.7 - - + +
217F VAL* 4.0 15.9 - - + +
220F ARG* 4.3 18.0 - - + +
240F SER 2.9 17.2 + - - -
241F LEU 3.2 4.1 + - - -
243F GLN* 1.3 79.0 - - - +
245F LEU* 1.4 64.1 + - - +
246F HIS 3.6 1.8 - - - -
247F ARG* 3.5 34.2 - - + +
248F THR* 3.2 19.1 + - - +
290F TYR* 4.4 1.6 - - - -
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Residues in contact with LEU 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F TYR* 3.5 52.0 - - + +
19F PHE* 4.0 15.3 - - + -
20F MET* 3.8 26.7 - - + -
241F LEU 2.9 17.2 + - - +
242F THR* 4.1 8.9 + - + +
243F GLN 3.5 3.4 + - - -
244F THR* 1.4 76.2 - - - +
246F HIS* 1.4 65.2 + - - +
248F THR* 3.0 22.2 + - - -
249F LEU* 3.5 21.3 + - + +
290F TYR* 3.7 28.3 - - + -
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Residues in contact with HIS 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C TYR 4.9 2.8 + - - -
413C LYS* 3.0 50.9 + - + +
416C LYS* 4.3 11.8 + - - -
526D GLU* 5.3 4.2 + - - -
530D GLU* 4.4 13.9 + - - +
17F TYR* 4.0 12.3 + - - +
242F THR 5.6 0.2 + - - -
243F GLN 5.4 0.6 + - - -
244F THR 3.6 0.4 - - - -
245F LEU* 1.4 75.1 - - - +
247F ARG* 1.3 60.2 + - - +
249F LEU* 3.0 23.4 + - + +
250F ILE* 2.9 60.0 + - + +
512G SER* 6.3 0.4 - - - -
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Residues in contact with ARG 247 (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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523D LEU* 3.1 39.2 + - - +
526D GLU* 3.9 33.6 - - + +
527D ARG* 3.9 34.6 - - - +
530D GLU* 4.3 15.2 + - + +
531D GLU* 5.9 1.2 + - - +
549D ALA 5.8 0.2 + - - -
552D SER* 4.4 7.5 + - - -
553D ILE* 5.7 1.0 - - - +
216F VAL* 3.3 39.2 + - + +
244F THR* 3.5 31.0 - - + +
246F HIS* 1.3 72.7 + - - +
248F THR* 1.3 57.2 + - - +
250F ILE* 3.5 1.9 + - - +
251F THR* 2.5 47.2 + - - +
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Residues in contact with THR 248 (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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213F ASP* 3.6 46.5 - - + +
216F VAL* 4.1 5.4 - - + -
217F VAL* 3.7 8.7 - - + -
244F THR 3.2 8.9 + - - +
245F LEU 3.0 12.0 + - - -
247F ARG* 1.3 79.6 - - - +
249F LEU* 1.3 61.6 + - - +
251F THR* 3.2 19.5 - - - +
284F GLY 5.2 0.7 + - - -
285F THR* 3.7 17.9 - - - +
289F ILE* 4.7 2.7 - - + -
290F TYR* 3.0 36.6 + - + +
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Residues in contact with LEU 249 (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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413C LYS 5.6 0.2 - - - +
416C LYS* 5.5 8.7 - - - +
17F TYR* 5.2 6.5 - - + -
245F LEU* 3.7 24.5 - - + +
246F HIS* 3.0 35.5 + - + +
248F THR* 1.3 77.1 + - - +
250F ILE* 1.3 66.4 + - + +
251F THR 3.5 5.0 - - - +
253F GLY* 4.5 4.9 + - - -
285F THR* 3.9 30.1 - - + +
290F TYR* 6.1 1.6 - - + -
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Residues in contact with ILE 250 (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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467D PHE* 3.5 23.8 - - + -
471D PHE* 4.4 31.0 - - + -
472D TYR* 4.0 12.1 - - + +
522D VAL* 4.3 9.4 - - + +
526D GLU* 3.8 26.5 - - + +
246F HIS* 2.9 48.7 + - + +
247F ARG* 3.9 5.2 - - - +
249F LEU* 1.3 70.9 - - + +
251F THR* 1.4 65.3 + - - +
252F SER 3.4 0.3 + - - -
253F GLY* 3.0 18.2 + - - -
254F THR 4.5 0.2 + - - -
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Residues in contact with THR 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519D ASP* 5.2 2.0 - - - +
522D VAL* 4.1 17.2 + - + +
523D LEU* 4.0 21.4 - - + +
526D GLU* 5.2 1.4 - - - +
212F ASN* 3.7 28.5 - - - +
213F ASP* 4.7 10.7 - - + +
216F VAL* 5.8 1.3 - - + +
247F ARG* 2.5 41.1 + - - +
248F THR* 3.2 20.0 - - - +
249F LEU 3.5 3.5 - - - +
250F ILE* 1.4 71.7 - - - +
252F SER* 1.4 65.3 + - - +
253F GLY 3.3 2.8 + - - -
285F THR* 5.6 0.5 - - - +
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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
------------------------------------------------------------
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