Contacts of the helix formed by residues 236 - 253 (chain H) in PDB entry 5MGX
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 ASP 236 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231H HIS* 2.8 21.2 + - + +
234H ARG* 3.4 31.9 + - - +
235H ALA* 1.3 70.8 - - - +
237H PHE* 1.3 57.9 + - - +
238H VAL* 3.8 5.7 + - - +
239H LEU* 3.2 41.8 + - - +
240H ALA* 3.0 26.7 + - - +
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Residues in contact with PHE 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232H TYR* 3.6 53.4 - + - -
235H ALA* 3.5 41.2 + - + -
236H ASP* 1.3 73.2 - - - +
238H VAL* 1.3 60.8 + - - +
240H ALA* 3.9 3.3 - - - +
241H ALA* 3.0 30.7 + - - +
281H SER* 3.8 17.9 - - - +
284H LYS* 3.6 48.5 - - + -
285H LEU* 3.7 18.1 - - + +
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Residues in contact with VAL 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236H ASP* 3.4 6.7 + - - +
237H PHE* 1.3 78.1 - - - +
239H LEU* 1.4 69.6 + - + +
241H ALA* 3.8 3.2 - - - +
242H ASN* 3.3 21.2 + - + +
285H LEU* 3.7 29.6 - - + -
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Residues in contact with LEU 239 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150H CYS* 4.3 26.0 - - + +
152H VAL 5.0 2.2 - - - +
153H ILE* 5.3 0.4 - - - -
154H GLN* 5.0 23.3 - - + +
231H HIS* 3.4 33.6 - - + +
234H ARG* 4.0 3.8 - - - +
236H ASP* 3.2 36.0 + - - +
238H VAL* 1.4 85.6 - - + +
240H ALA* 1.4 65.5 + - - +
242H ASN* 3.2 9.4 + - - +
243H SER* 3.0 25.6 + - - -
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Residues in contact with ALA 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228H GLY* 3.4 27.8 - - - +
231H HIS* 3.5 4.1 - - - +
232H TYR* 3.7 12.6 - - + +
236H ASP 3.0 20.9 + - - +
237H PHE* 3.9 4.7 - - - +
238H VAL 3.5 0.2 - - - -
239H LEU* 1.4 76.0 - - - +
241H ALA* 1.4 62.2 + - - +
243H SER* 3.3 2.8 + - - -
244H TYR* 3.0 31.5 + - + -
281H SER* 3.7 15.7 - - - +
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Residues in contact with ALA 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237H PHE 3.0 19.5 + - - +
238H VAL* 3.8 5.4 - - - +
240H ALA* 1.4 75.4 - - - +
242H ASN* 1.3 56.5 + - - +
244H TYR* 3.4 4.6 + - - -
245H ASP* 3.0 25.8 + - - +
278H LEU* 3.4 28.3 - - + +
281H SER* 4.0 10.6 + - - -
282H GLN* 5.1 5.4 - - + -
285H LEU* 4.8 8.1 - - + -
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Residues in contact with ASN 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149H ASP* 3.0 30.5 + - - +
150H CYS* 4.4 9.5 + - - +
238H VAL 3.3 12.3 + - - +
239H LEU* 3.2 14.0 + - + +
241H ALA* 1.3 78.7 - - - +
243H SER* 1.4 58.4 + - - +
245H ASP* 3.3 7.2 + - - +
246H LEU* 3.1 44.1 + - - +
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Residues in contact with SER 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149H ASP 5.0 1.4 + - - -
150H CYS 4.3 4.7 + - - -
151H ASP* 5.2 2.7 + - - -
224H LYS* 3.4 17.8 - - - +
227H CYS* 4.0 5.7 - - - +
228H GLY* 3.4 27.9 + - - -
231H HIS* 3.3 20.3 + - - -
239H LEU 3.0 13.9 + - - -
240H ALA 3.3 0.9 + - - -
242H ASN* 1.4 76.6 + - - +
244H TYR* 1.4 55.5 + - - +
246H LEU* 3.4 10.6 + - - +
247H ALA* 3.0 27.9 + - - +
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Residues in contact with TYR 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707D GLU* 5.7 1.4 - - - +
225H ARG* 3.6 23.8 - - + -
228H GLY* 3.2 14.7 + - - -
229H ASN* 2.7 40.5 + - - -
232H TYR* 3.8 11.2 - + - +
240H ALA* 3.0 30.6 + - + +
241H ALA 3.8 4.7 - - - +
242H ASN 3.3 0.2 - - - -
243H SER* 1.4 74.0 - - - +
245H ASP* 1.3 57.6 + - - +
247H ALA* 3.3 6.2 + - - +
248H ILE* 3.0 33.8 + - - +
274H CYS* 3.8 16.7 - - + +
277H ASN* 3.4 42.9 + - + +
278H LEU* 3.8 9.6 - - + -
281H SER* 3.3 20.0 - - - -
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Residues in contact with ASP 245 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241H ALA 3.0 16.9 + - - +
242H ASN* 3.3 6.9 + - - +
244H TYR* 1.3 75.5 - - - +
246H LEU* 1.4 58.7 + - + +
248H ILE* 3.5 13.0 + - - +
249H LYS* 3.0 59.4 + - - +
278H LEU* 4.3 17.0 - - + +
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Residues in contact with LEU 246 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149H ASP* 3.6 53.4 - - + +
151H ASP* 5.0 4.0 - - - +
209H LEU* 5.9 0.3 - - - +
224H LYS* 4.5 8.5 - - + -
242H ASN* 3.1 34.1 + - - +
243H SER* 3.7 8.5 - - - +
244H TYR 3.3 0.2 - - - -
245H ASP* 1.4 73.9 - - + +
247H ALA* 1.4 59.9 + - - +
249H LYS* 3.4 21.8 + - + +
250H ALA* 3.1 29.3 + - - +
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Residues in contact with ALA 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221H ALA* 3.6 27.7 - - - +
224H LYS* 3.7 11.6 - - + +
225H ARG* 4.0 4.5 - - - +
243H SER 3.0 14.8 + - - +
244H TYR* 3.4 10.8 - - - +
246H LEU* 1.4 76.8 - - - +
248H ILE* 1.4 58.7 + - - +
250H ALA* 3.5 5.4 - - - +
251H ILE* 3.3 28.2 + - - +
274H CYS* 3.7 17.9 - - - -
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Residues in contact with ILE 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244H TYR 3.0 23.7 + - - +
245H ASP* 3.7 10.5 - - - +
246H LEU 3.3 0.2 - - - -
247H ALA* 1.4 74.2 - - - +
249H LYS* 1.4 60.9 + - + +
251H ILE* 3.0 10.2 + - - +
252H THR* 3.0 45.8 + - + +
271H LYS* 4.6 12.3 - - + +
274H CYS* 3.8 15.3 - - + -
275H LEU* 3.9 33.7 - - + +
278H LEU* 3.8 28.5 - - + -
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Residues in contact with LYS 249 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209H LEU* 4.2 11.8 - - + +
245H ASP* 3.0 41.2 + - - +
246H LEU* 3.4 21.0 + - + +
248H ILE* 1.4 75.7 - - + +
250H ALA* 1.4 59.3 + - - +
252H THR* 3.6 8.9 + - - +
253H SER* 3.3 28.2 + - - -
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Residues in contact with ALA 250 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209H LEU* 4.5 14.1 - - + +
212H LEU* 5.0 1.0 - - - +
217H ARG* 2.9 39.4 + - + +
220H LEU* 4.1 29.4 - - + -
221H ALA* 4.5 9.6 - - + +
246H LEU 3.1 16.5 + - - +
247H ALA* 3.5 10.3 - - - +
248H ILE 3.2 0.2 - - - -
249H LYS* 1.4 75.7 - - - +
251H ILE* 1.3 56.6 + - - +
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Residues in contact with ILE 251 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F LEU 5.0 3.2 - - - +
99F ASN* 4.9 1.0 + - - -
217H ARG* 3.6 14.4 - - - -
221H ALA* 3.6 21.8 - - + -
247H ALA 3.3 19.0 + - - +
248H ILE* 3.0 9.9 + - - +
250H ALA* 1.3 76.4 - - - +
252H THR* 1.3 62.5 + - + +
253H SER 3.5 1.0 + - - -
254H SER* 4.0 8.0 - - - -
267H LEU* 3.6 43.0 - - + +
270H LEU* 4.0 12.3 - - + +
271H LYS* 3.7 46.7 - - + +
274H CYS* 4.5 3.6 - - - -
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Residues in contact with THR 252 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F LEU 3.7 11.7 - - - +
98F GLY* 3.7 34.5 + - - +
99F ASN* 3.3 23.9 - - - +
248H ILE* 3.0 26.6 + - + +
249H LYS* 3.6 11.6 + - - +
251H ILE* 1.3 72.1 - - - +
253H SER* 1.3 56.7 + - - +
254H SER 3.2 10.5 + - - -
255H ALA* 5.9 0.2 - - - +
271H LYS* 3.9 19.7 - - + +
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Residues in contact with SER 253 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209H LEU* 3.2 32.3 - - - +
210H GLU* 3.4 13.2 - - - -
217H ARG* 2.8 21.7 + - - -
249H LYS 3.3 18.8 + - - -
250H ALA 4.1 0.4 + - - -
251H ILE 3.4 2.0 - - - -
252H THR* 1.3 75.1 - - - +
254H SER* 1.3 52.5 + - - +
255H ALA* 3.7 2.7 - - - +
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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
------------------------------------------------------------
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