Contacts of the helix formed by residues 236 - 253 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351E LYS* 5.1 4.7 + - - -
154G GLN* 5.6 1.6 - - - +
231G HIS* 2.9 17.9 + - + +
234G ARG* 3.4 24.2 + - - +
235G ALA* 1.3 75.2 - - - +
237G PHE* 1.3 57.6 + - - +
238G VAL* 3.8 6.9 + - - +
239G LEU* 3.2 42.3 + - - +
240G ALA* 3.1 26.5 + - - +
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Residues in contact with PHE 237 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232G TYR* 3.5 52.9 - + - -
235G ALA* 3.5 40.4 + - + -
236G ASP* 1.3 71.7 - - - +
238G VAL* 1.3 61.2 + - - +
239G LEU 3.4 0.4 - - - -
240G ALA* 3.9 4.0 - - - +
241G ALA* 3.0 30.5 + - - +
281G SER* 3.8 18.5 - - - +
284G LYS* 3.6 46.4 - - + -
285G LEU* 3.7 18.2 - - + +
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Residues in contact with VAL 238 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351E LYS* 3.9 37.0 - - + +
354E ALA* 6.4 0.4 - - + -
355E ALA* 4.3 18.4 - - + -
236G ASP* 3.4 3.7 + - - +
237G PHE* 1.3 78.9 - - - +
239G LEU* 1.3 66.2 + - + +
241G ALA* 3.9 3.0 - - - +
242G ASN* 3.2 21.5 + - + +
285G LEU* 3.7 30.0 - - + +
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Residues in contact with LEU 239 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150G CYS* 3.6 35.2 - - + +
152G VAL 5.0 1.3 - - - +
153G ILE* 5.4 0.7 - - - -
154G GLN* 5.0 27.4 - - + +
231G HIS* 3.6 33.6 - - + +
234G ARG* 4.5 2.5 - - - +
236G ASP* 3.2 34.6 + - - +
238G VAL* 1.3 81.0 - - + +
240G ALA* 1.4 64.6 + - - +
242G ASN* 3.2 11.8 + - + +
243G SER* 3.0 27.0 + - - -
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Residues in contact with ALA 240 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228G GLY* 3.4 27.6 - - - +
231G HIS* 3.6 3.9 - - - +
232G TYR* 3.7 12.8 - - + +
236G ASP 3.1 19.3 + - - +
237G PHE* 3.9 5.2 - - - +
238G VAL 3.5 0.2 - - - -
239G LEU* 1.4 76.3 - - - +
241G ALA* 1.4 62.3 + - - +
243G SER* 3.3 2.8 + - - -
244G TYR* 3.0 32.0 + - + -
281G SER* 3.7 15.7 - - - +
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Residues in contact with ALA 241 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237G PHE 3.0 19.2 + - - +
238G VAL* 3.9 5.2 - - - +
240G ALA* 1.4 75.6 - - - +
242G ASN* 1.4 57.8 + - - +
244G TYR* 3.4 4.2 + - - -
245G ASP* 2.9 28.1 + - - +
278G LEU* 3.4 27.2 - - + +
281G SER* 4.0 10.4 + - - -
282G GLN* 5.0 5.8 - - + -
285G LEU* 4.9 7.6 - - + -
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Residues in contact with ASN 242 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149G ASP 3.0 30.7 + - - -
150G CYS* 4.4 9.3 - - - +
238G VAL 3.2 12.7 + - - +
239G LEU* 3.2 16.4 + - + +
241G ALA* 1.4 78.7 - - - +
243G SER* 1.3 58.4 + - - +
245G ASP* 3.3 8.7 + - - +
246G LEU* 3.1 43.8 + - - +
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Residues in contact with SER 243 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149G ASP 4.6 1.9 + - - -
150G CYS 4.1 5.4 + - - -
151G ASP* 4.9 3.0 + - - -
224G LYS* 3.5 22.3 - - - +
227G CYS* 4.1 5.5 - - - +
228G GLY* 3.4 29.5 + - - -
231G HIS* 3.4 19.4 + - - -
239G LEU 3.0 12.4 + - - -
240G ALA 3.3 1.5 + - - -
242G ASN* 1.3 77.3 + - - +
244G TYR* 1.4 56.1 + - - +
246G LEU* 3.4 10.5 + - - +
247G ALA* 3.1 22.3 + - - +
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Residues in contact with TYR 244 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708B VAL* 3.2 14.9 - - + +
225G ARG* 3.6 23.6 - - + -
228G GLY* 3.2 14.4 + - - -
229G ASN* 2.8 38.6 + - - -
232G TYR* 3.7 2.7 - + - +
240G ALA* 3.0 29.7 + - + +
241G ALA* 3.8 4.3 - - - +
242G ASN 3.3 0.2 - - - -
243G SER* 1.4 71.0 - - - +
245G ASP* 1.3 64.9 + - - +
247G ALA* 3.4 7.8 - - - +
248G ILE* 3.0 28.0 + - - +
274G CYS* 3.8 17.2 - - + +
277G ASN* 3.4 40.8 - - + -
278G LEU* 3.8 10.5 - - + -
281G SER* 3.4 20.0 - - - -
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Residues in contact with ASP 245 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241G ALA 2.9 17.4 + - - +
242G ASN* 3.6 8.7 - - - +
244G TYR* 1.3 76.0 - - - +
246G LEU* 1.3 59.9 + - - +
248G ILE* 3.3 14.1 + - - +
249G LYS* 2.9 62.6 + - - +
278G LEU* 4.4 12.3 - - + +
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Residues in contact with LEU 246 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149G ASP* 3.6 52.0 - - + +
151G ASP* 5.0 0.4 - - - +
209G LEU* 5.7 0.7 - - - +
224G LYS* 4.4 20.6 - - + +
242G ASN* 3.1 31.1 + - - +
243G SER* 3.7 10.5 - - - +
244G TYR 3.3 0.2 - - - -
245G ASP* 1.3 76.2 - - - +
247G ALA* 1.3 63.5 + - - +
249G LYS* 3.4 20.4 + - + +
250G ALA* 3.0 24.8 + - - +
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Residues in contact with ALA 247 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221G ALA* 3.6 27.6 - - - +
224G LYS* 3.7 12.2 - - + +
225G ARG* 4.1 4.0 - - - +
243G SER 3.1 13.2 + - - +
244G TYR* 3.4 11.7 - - - +
246G LEU* 1.3 75.2 - - - +
248G ILE* 1.3 60.7 + - - +
250G ALA* 3.4 5.6 + - - +
251G ILE* 3.2 27.6 + - - +
274G CYS* 3.8 19.1 - - - -
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Residues in contact with ILE 248 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244G TYR 3.0 23.8 + - - +
245G ASP* 3.7 11.2 - - - +
246G LEU 3.3 0.4 - - - -
247G ALA* 1.3 74.8 - - - +
249G LYS* 1.4 58.4 + - + +
251G ILE* 3.0 23.0 + - - +
252G THR* 3.0 33.0 + - + +
271G LYS* 4.6 12.3 - - + +
274G CYS* 3.8 15.9 - - + -
275G LEU* 3.9 34.1 - - + +
278G LEU* 3.8 28.5 - - + -
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Residues in contact with LYS 249 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209G LEU* 4.2 10.5 - - + +
245G ASP* 2.9 47.4 + - - +
246G LEU* 3.7 19.7 - - + +
248G ILE* 1.4 75.7 - - + +
250G ALA* 1.3 51.4 + - - +
252G THR* 3.6 8.7 + - - +
253G SER* 2.7 37.9 + - - -
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Residues in contact with ALA 250 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209G LEU* 4.4 11.8 - - + +
212G LEU* 4.9 1.3 - - + +
217G ARG* 2.9 38.9 + - - +
220G LEU* 4.0 31.0 - - + -
221G ALA* 4.7 7.9 - - + +
224G LYS* 5.7 0.9 - - + -
246G LEU 3.0 17.4 + - - +
247G ALA* 3.5 8.5 - - - +
248G ILE 3.2 0.2 - - - -
249G LYS* 1.3 75.6 - - - +
251G ILE* 1.4 58.3 + - - +
253G SER* 3.9 4.5 - - - -
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Residues in contact with ILE 251 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217G ARG* 3.6 19.9 - - - +
221G ALA* 3.6 17.9 - - + -
247G ALA 3.2 18.1 + - - +
248G ILE* 3.0 10.8 + - - +
250G ALA* 1.4 76.6 - - - +
252G THR* 1.3 62.7 + - + +
253G SER 3.5 1.0 + - - -
254G SER* 3.8 9.0 + - - -
259G MET* 5.6 0.3 - - - +
267G LEU* 3.6 44.2 - - + +
270G LEU* 4.0 10.3 - - + +
271G LYS* 3.7 46.7 - - + +
274G CYS* 4.5 4.0 - - - -
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Residues in contact with THR 252 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248G ILE* 3.0 26.8 + - + +
249G LYS* 3.6 11.4 + - - +
251G ILE* 1.3 72.7 - - - +
253G SER* 1.3 56.3 + - - +
254G SER* 3.2 14.4 + - - -
255G ALA* 4.8 1.9 + - - +
271G LYS* 3.9 34.1 - - + +
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Residues in contact with SER 253 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209G LEU* 3.2 36.4 - - - +
210G GLU* 3.5 22.4 - - - -
217G ARG* 2.8 25.7 + - - -
249G LYS 2.7 23.1 + - - -
250G ALA 3.7 1.0 + - - -
251G ILE 3.4 1.6 - - - -
252G THR* 1.3 75.1 - - - +
254G SER* 1.4 52.1 + - - +
255G ALA 3.7 2.5 - - - +
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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