Contacts of the helix formed by residues 245 - 257 (chain P) in PDB entry 3EXG
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 245 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196P GLY 3.2 21.0 + - - +
197P LYS* 3.4 15.4 + - - +
198P ALA* 2.8 36.5 + - + +
238P MET 5.2 1.7 + - - +
240P THR* 4.6 2.8 + - - -
243P PRO 3.6 2.2 + - - -
244P MET* 1.3 68.1 - - - +
246P MET* 1.3 59.4 + - - +
247P GLU* 3.3 12.1 + - - +
248P THR* 2.6 40.5 + - - -
249P ILE* 3.9 16.0 + - - +
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Residues in contact with MET 246 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244P MET* 2.8 27.1 + - - +
245P ASP* 1.3 73.2 - - - +
247P GLU* 1.3 64.4 + - - +
249P ILE* 3.2 25.4 + - + +
250P GLU* 3.1 43.5 + - + +
275P ILE* 4.0 6.5 - - + +
278P ARG* 3.6 58.1 - - + +
279P ILE* 3.7 36.6 - - + +
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Residues in contact with GLU 247 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197P LYS* 5.7 2.4 + - - -
245P ASP* 3.4 9.0 - - - +
246P MET* 1.3 75.3 - - + +
248P THR* 1.3 68.9 + - - +
249P ILE 3.0 2.0 - - - -
250P GLU* 3.3 13.0 + - - +
251P ALA* 2.9 26.8 + - - +
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Residues in contact with THR 248 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197P LYS* 4.6 9.7 + - - +
198P ALA* 4.6 15.9 - - + +
200P ILE* 4.3 29.5 - - + +
236P ILE* 4.2 8.6 - - + +
245P ASP* 2.6 32.8 + - - -
247P GLU* 1.3 81.8 - - - +
249P ILE* 1.3 56.1 + - - +
251P ALA* 3.6 6.8 - - - +
252P SER* 3.1 25.5 + - - -
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Residues in contact with ILE 249 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208P THR* 4.9 1.1 - - + -
210P VAL* 3.8 45.3 - - + -
236P ILE* 4.3 15.5 - - + -
238P MET* 5.3 4.9 - - + -
244P MET* 5.7 1.8 - - - -
245P ASP 3.9 12.6 - - - +
246P MET* 3.2 31.4 + - + +
247P GLU 3.0 0.6 - - - -
248P THR* 1.3 76.0 - - - +
250P GLU* 1.3 67.8 + - - +
252P SER* 2.9 3.3 + - - -
253P VAL* 2.8 30.1 + - + +
259P LEU* 4.5 4.3 - - + -
275P ILE* 4.0 20.4 - - + -
279P ILE* 4.3 10.5 - - + -
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Residues in contact with GLU 250 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246P MET* 3.1 36.5 + - + +
247P GLU* 3.7 12.6 - - - +
249P ILE* 1.3 74.2 - - - +
251P ALA* 1.3 53.8 + - - +
253P VAL* 3.0 4.2 + - - +
254P MET* 2.7 43.9 + - + +
278P ARG 3.7 17.8 - - - +
279P ILE* 4.5 2.3 - - + -
282P GLY* 3.8 2.3 - - - -
283P PRO* 3.4 36.4 - - + +
284P ALA* 3.7 21.9 + - + +
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Residues in contact with ALA 251 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247P GLU 2.9 17.8 + - - +
248P THR* 3.6 10.1 - - + +
250P GLU* 1.3 74.9 - - - +
252P SER* 1.3 64.3 + - - +
254P MET* 3.2 33.2 + - + +
255P LYS* 3.5 8.1 + - - +
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Residues in contact with SER 252 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200P ILE* 5.9 1.3 - - - -
208P THR* 2.6 26.4 + - - +
234P GLU* 2.7 34.3 + - - +
236P ILE* 3.7 14.5 - - - +
248P THR 3.1 11.4 + - - -
249P ILE 2.9 11.1 + - - -
251P ALA* 1.3 74.5 - - - +
253P VAL* 1.3 55.0 + - - +
255P LYS* 2.7 29.8 + - - +
256P THR* 3.0 12.5 + - - +
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Residues in contact with VAL 253 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208P THR* 4.0 9.0 - - - +
249P ILE* 2.8 23.4 + - + +
250P GLU* 3.3 8.5 - - - +
252P SER* 1.3 71.3 - - - +
254P MET* 1.3 58.7 + - - +
255P LYS 2.8 2.3 + - - -
256P THR* 3.4 8.1 - - - -
257P ASN* 2.7 34.6 + - - -
258P HIS 4.7 0.2 - - - +
259P LEU* 4.1 23.6 - - + -
279P ILE* 4.0 20.0 - - + -
284P ALA* 4.2 19.5 - - + +
287P PHE* 4.2 5.0 - - + +
288P LEU* 3.7 25.6 - - + -
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Residues in contact with MET 254 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A VAL* 4.1 13.1 - - - +
314A ARG* 5.6 1.0 - - - +
315A LYS* 4.0 31.0 + - - +
250P GLU* 2.7 23.2 + - + +
251P ALA* 3.4 30.1 - - + +
252P SER 3.1 0.4 - - - -
253P VAL* 1.3 71.5 - - - +
255P LYS* 1.3 57.0 + - - +
257P ASN* 4.4 3.7 + - - -
283P PRO* 5.1 6.3 - - - +
284P ALA* 4.1 12.1 - - + -
287P PHE* 3.5 54.8 - - + -
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Residues in contact with LYS 255 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A LYS* 4.8 3.8 + - - +
308A GLU* 6.2 3.6 - - + -
311A VAL* 3.6 36.8 - - + +
203P GLN* 4.5 5.3 + - - -
204P GLY 3.2 17.7 + - - +
205P THR* 3.7 20.6 - - + +
234P GLU* 2.5 38.4 + - - -
251P ALA 3.5 6.7 + - - +
252P SER* 2.7 9.9 + - - +
254P MET* 1.3 77.9 - - + +
256P THR* 1.3 63.4 - - + +
257P ASN* 3.9 5.8 - - - +
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Residues in contact with THR 256 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A LYS* 5.5 2.0 + - - +
204P GLY 4.2 7.2 - - - +
205P THR* 3.2 29.5 - - - +
206P HIS* 3.5 5.0 - - - +
207P ILE* 3.4 35.9 - - - +
208P THR* 2.8 22.8 + - - +
234P GLU* 4.9 0.7 - - + +
252P SER* 3.0 10.7 + - - +
253P VAL* 3.4 2.8 - - - -
255P LYS* 1.3 80.6 - - + +
257P ASN* 1.3 71.2 + - - +
258P HIS* 2.9 23.6 + - - -
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Residues in contact with ASN 257 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A LYS* 4.6 10.0 + - - -
311A VAL* 5.6 2.3 - - - +
314A ARG* 3.3 20.3 + - - +
253P VAL* 2.7 23.4 + - - -
254P MET 4.4 8.1 + - - -
255P LYS 4.1 5.6 - - - +
256P THR* 1.3 77.7 + - - +
258P HIS* 1.3 69.7 + - + +
287P PHE* 2.7 35.7 + - - +
288P LEU* 3.5 7.5 - - - +
289P ASP* 2.7 49.3 + - - +
290P ALA 3.9 0.7 + - - -
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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