Contacts of the helix formed by residues 287 - 301 (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 SER 287 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23F ASP* 4.7 0.8 - - - +
27F PHE* 3.8 18.6 - - - -
176F ALA* 3.4 24.0 + - - -
177F LEU* 5.3 0.2 - - - -
179F HIS* 3.5 11.8 + - - -
180F ASP* 2.5 34.4 + - - -
283F ILE 3.6 3.0 + - - -
286F ALA* 1.4 73.5 - - - +
288F SER* 1.3 80.3 + - - +
291F VAL* 3.5 23.9 - - - +
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Residues in contact with SER 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F ASP* 4.8 2.9 + - - -
176F ALA* 3.8 11.5 - - - +
177F LEU* 4.6 9.2 - - - +
283F ILE 3.3 6.4 + - - -
284F GLY* 3.0 27.1 - - - -
285F THR* 3.6 11.8 + - - -
286F ALA 3.0 12.6 + - - -
287F SER* 1.3 92.2 + - - +
289F ILE* 1.3 65.2 + - - +
290F TYR* 3.4 25.1 + - - +
292F ALA* 3.7 11.7 + - - +
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Residues in contact with ILE 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169F LEU* 4.3 18.2 - - + -
173F VAL* 4.0 24.5 - - + -
177F LEU* 5.3 0.2 - - - +
213F ASP 4.3 7.6 - - - +
214F SER* 3.8 30.9 + - - +
217F VAL* 4.1 32.8 - - + -
218F SER 5.4 0.2 - - - +
241F LEU* 5.0 0.7 - - + -
248F THR* 4.7 2.0 - - + -
284F GLY 3.8 7.1 + - - +
288F SER* 1.3 73.2 - - - +
290F TYR* 1.4 84.6 - - + +
292F ALA* 3.2 6.3 + - + +
293F SER* 2.7 41.8 + - - +
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Residues in contact with TYR 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F PHE* 4.3 19.3 - + + -
20F MET* 4.5 10.9 - - + +
23F ASP* 4.0 15.0 - - - +
217F VAL* 4.0 4.6 - - + +
241F LEU* 3.7 55.8 - - + +
245F LEU* 3.7 31.5 - - + -
248F THR* 3.0 39.6 + - - +
249F LEU* 6.1 1.3 - - + -
284F GLY 5.4 0.9 - - - -
285F THR* 5.6 4.0 - - - -
288F SER* 3.2 18.6 - - - +
289F ILE* 1.4 93.1 - - + +
291F VAL* 1.4 57.4 + - - +
293F SER* 3.8 4.8 + - - -
294F ALA* 3.2 27.5 + - - +
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Residues in contact with VAL 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F ASP* 3.4 33.0 - - - +
24F TYR* 4.1 23.1 - - + +
27F PHE* 3.6 47.1 - - + -
176F ALA* 4.8 2.5 - - + -
287F SER* 3.5 18.8 + - - +
288F SER 4.0 0.4 + - - -
289F ILE 3.5 0.2 - - - -
290F TYR* 1.4 72.1 - - - +
292F ALA* 1.4 64.0 + - - +
294F ALA* 3.4 6.6 + - - +
295F LEU* 3.1 34.0 + - + +
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Residues in contact with ALA 292 (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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169F LEU* 5.0 3.1 - - + +
172F GLY* 3.2 40.7 - - - +
173F VAL* 3.6 17.5 - - + +
176F ALA* 4.3 2.4 - - + +
288F SER 3.7 12.4 + - - +
289F ILE* 3.2 11.4 + - + +
291F VAL* 1.4 80.1 - - - +
293F SER* 1.3 62.1 + - - +
295F LEU* 3.5 5.7 + - - +
296F ALA* 3.3 22.1 + - - +
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Residues in contact with SER 293 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169F LEU* 5.5 6.9 - - - +
221F ILE* 4.0 14.2 - - - +
237F PHE* 4.6 9.9 + - - +
238F ASN* 5.8 0.3 + - - -
241F LEU* 3.5 32.3 - - - +
289F ILE* 2.7 28.4 + - - +
290F TYR 3.9 3.8 - - - -
292F ALA* 1.3 69.0 - - - +
294F ALA* 1.3 60.1 + - - +
296F ALA* 3.4 7.1 + - - +
297F LEU* 2.8 32.0 + - - +
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Residues in contact with ALA 294 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F TYR* 4.0 31.0 - - + -
241F LEU* 5.7 2.2 - - + +
290F TYR 3.2 19.3 + - - +
291F VAL* 3.4 5.8 + - - +
293F SER* 1.3 73.0 - - - +
295F LEU* 1.4 57.9 + - + +
297F LEU* 3.3 12.8 + - - +
298F LYS* 2.9 36.4 + - + +
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Residues in contact with LEU 295 (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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24F TYR* 5.9 6.1 - - + -
27F PHE* 4.7 11.2 - - + -
172F GLY* 5.6 7.9 - - - +
175F ILE* 5.3 10.1 - - + -
291F VAL* 3.1 33.6 + - + +
292F ALA* 4.0 6.1 - - - +
294F ALA* 1.4 73.3 - - + +
296F ALA* 1.3 61.0 + - - +
298F LYS* 3.4 12.6 + - + +
299F LEU* 3.2 22.9 + - - +
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Residues in contact with ALA 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166F GLU* 4.7 4.7 - - - +
168F ARG* 3.7 40.8 - - + +
169F LEU* 3.7 11.0 - - + +
172F GLY* 5.6 0.8 - - - -
234F TYR* 5.0 0.9 - - - -
237F PHE* 5.8 2.5 - - - -
292F ALA 3.3 16.7 + - - +
293F SER* 3.7 7.0 - - - +
295F LEU* 1.3 74.9 - - - +
297F LEU* 1.4 52.4 + - - +
299F LEU* 3.5 7.4 + - - +
300F GLY* 2.8 31.2 + - - -
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Residues in contact with LEU 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234F TYR* 3.5 45.3 - - + +
237F PHE* 4.4 14.8 - - + -
238F ASN* 3.5 27.4 - - - +
293F SER* 2.8 21.0 + - - +
294F ALA* 3.3 11.0 - - - +
295F LEU 3.3 0.2 - - - -
296F ALA* 1.4 73.2 - - - +
298F LYS* 1.3 86.2 + - + +
301F MET* 3.0 32.8 + - + +
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Residues in contact with LYS 298 (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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24F TYR* 5.4 14.1 + - - -
294F ALA* 2.9 21.2 + - - +
295F LEU* 3.4 15.9 + - + +
297F LEU* 1.3 91.0 - - + +
299F LEU* 1.3 62.4 + - - +
301F MET* 3.4 19.9 + - + +
302F LYS* 5.0 0.9 + - - -
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Residues in contact with LEU 299 (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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168F ARG* 4.0 34.1 + - + +
295F LEU 3.2 13.9 + - - +
296F ALA* 3.7 7.0 - - - +
297F LEU 3.3 0.2 - - - -
298F LYS* 1.3 80.7 - - - +
300F GLY* 1.4 60.6 + - - +
302F LYS* 3.2 39.7 + - - +
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Residues in contact with GLY 300 (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* 5.9 0.2 - - - -
168F ARG* 3.8 22.2 + - - +
234F TYR* 2.8 32.1 + - - -
296F ALA 2.8 20.1 + - - -
297F LEU 3.4 0.2 + - - -
299F LEU* 1.4 69.3 - - - +
301F MET* 1.3 64.1 + - - +
302F LYS* 3.1 12.7 + - - +
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Residues in contact with MET 301 (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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232F THR* 5.1 4.5 - - - +
234F TYR* 3.4 37.7 - - + -
297F LEU* 3.0 22.9 + - + +
298F LYS* 3.4 16.9 - - + +
299F LEU 3.4 0.8 - - - +
300F GLY* 1.3 75.4 - - - +
302F LYS* 1.4 83.3 + - - +
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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