Contacts of the helix formed by residues 245 - 257 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196N GLY 3.4 16.9 + - - +
197N LYS* 3.3 19.4 - - - +
198N ALA* 2.8 37.5 + - + +
238N MET* 5.3 3.6 + - + +
240N THR* 4.5 3.0 + - - -
243N PRO 3.7 1.2 + - - -
244N MET* 1.3 73.3 - - - +
246N MET* 1.3 57.6 + - - +
247N GLU* 3.4 8.8 + - - +
248N THR* 2.8 39.4 + - - -
249N ILE* 3.5 21.8 + - - +
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Residues in contact with MET 246 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244N MET* 3.0 20.7 + - + +
245N ASP* 1.3 71.0 - - - +
247N GLU* 1.3 66.9 + - - +
249N ILE* 3.0 24.7 + - + +
250N GLU* 2.9 46.1 + - + +
275N ILE* 3.9 13.5 - - + +
278N ARG* 3.7 49.4 - - + +
279N ILE* 3.3 51.4 - - + +
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Residues in contact with GLU 247 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197N LYS* 5.5 5.7 + - - -
245N ASP* 3.7 6.4 - - - +
246N MET* 1.3 78.8 - - - +
248N THR* 1.3 63.8 + - - +
250N GLU* 3.6 12.5 + - - +
251N ALA* 3.0 24.3 + - - +
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Residues in contact with THR 248 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198N ALA* 4.4 13.6 + - + +
200N ILE* 4.1 31.6 - - + +
236N ILE* 4.5 16.4 - - + -
245N ASP* 2.8 39.7 + - - -
247N GLU* 1.3 73.7 + - - +
249N ILE* 1.3 65.7 + - - +
251N ALA* 3.4 7.8 - - + +
252N SER* 3.2 17.7 + - - -
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Residues in contact with ILE 249 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208N THR* 4.7 1.8 - - + -
210N VAL* 3.7 45.5 - - + -
236N ILE* 4.3 15.0 - - + -
238N MET* 4.8 7.6 - - + -
244N MET* 5.4 3.4 - - + -
245N ASP 3.5 15.7 + - - +
246N MET* 3.0 27.6 + - + +
248N THR* 1.3 74.2 - - - +
250N GLU* 1.3 56.7 + - - +
252N SER* 2.9 19.9 + - - -
253N VAL* 2.9 24.1 + - + +
259N LEU* 4.5 12.3 - - + -
275N ILE* 4.2 19.3 - - + -
279N ILE* 4.9 0.7 - - + -
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Residues in contact with GLU 250 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246N MET* 2.9 39.9 + - + +
247N GLU* 3.9 11.4 + - - +
249N ILE* 1.3 68.1 - - - +
251N ALA* 1.3 66.9 + - - +
253N VAL* 3.2 2.9 + - - +
254N MET* 2.8 45.1 + - + +
278N ARG* 4.6 1.4 - - - +
279N ILE* 4.1 13.0 - - + +
282N GLY* 3.9 9.1 - - - -
283N PRO* 3.3 35.7 - - - +
284N ALA* 4.0 14.0 + - + -
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Residues in contact with ALA 251 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247N GLU 3.0 14.3 + - - +
248N THR* 3.4 12.8 - - + +
250N GLU* 1.3 76.1 - - - +
252N SER* 1.3 63.4 + - - +
254N MET* 3.4 11.3 + - - +
255N LYS* 3.2 20.4 + - - +
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Residues in contact with SER 252 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200N ILE* 5.9 2.0 - - - -
208N THR* 2.6 28.4 + - - +
234N GLU* 2.9 34.5 + - - +
236N ILE* 3.5 20.6 - - - -
248N THR* 3.2 4.3 + - - -
249N ILE 2.9 12.2 + - - -
251N ALA* 1.3 76.2 - - - +
253N VAL* 1.3 59.1 + - - +
255N LYS* 3.2 5.2 + - - +
256N THR* 2.9 32.9 + - - +
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Residues in contact with VAL 253 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208N THR* 3.8 17.3 - - + +
249N ILE* 2.9 19.4 + - + +
250N GLU* 3.7 9.4 - - - +
252N SER* 1.3 71.1 - - - +
254N MET* 1.3 62.5 + - - +
255N LYS 3.0 1.6 - - - -
256N THR* 4.1 1.8 - - - -
257N ASN* 2.6 34.4 + - - +
258N HIS 4.3 2.0 - - - +
259N LEU* 3.9 31.0 - - + -
279N ILE* 4.7 4.7 - - + -
284N ALA* 4.2 20.2 - - + +
287N PHE* 4.1 1.9 - - + +
288N LEU* 3.7 27.1 - - + -
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Residues in contact with MET 254 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250N GLU* 2.8 39.3 + - + +
251N ALA* 3.4 8.7 + - - +
253N VAL* 1.3 72.8 - - - +
255N LYS* 1.3 59.7 + - - +
257N ASN* 3.6 10.9 + - - -
283N PRO* 4.0 25.4 - - + -
284N ALA* 4.2 6.7 - - + +
287N PHE* 3.7 55.4 - - + -
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Residues in contact with LYS 255 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203N GLN* 3.6 11.7 + - - +
204N GLY 3.3 20.9 + - - +
205N THR* 4.0 17.8 - - + +
234N GLU* 3.2 31.3 + - - -
251N ALA 3.2 10.7 + - - +
252N SER* 3.2 8.2 + - - +
253N VAL 3.0 0.4 - - - -
254N MET* 1.3 81.1 - - - +
256N THR* 1.3 64.8 + - + +
257N ASN* 4.1 6.5 + - - +
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Residues in contact with THR 256 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204N GLY 4.4 2.9 - - - +
205N THR* 3.6 18.4 - - - +
206N HIS 3.0 23.2 - - - +
207N ILE 3.7 8.5 - - - +
208N THR* 2.9 23.7 + - - +
234N GLU* 4.6 2.2 - - + -
252N SER* 2.9 20.4 + - - +
253N VAL* 4.1 0.9 - - - -
255N LYS* 1.3 89.9 - - + +
257N ASN* 1.3 62.7 + - - +
258N HIS* 2.7 43.8 + - - -
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Residues in contact with ASN 257 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253N VAL* 2.6 19.8 + - - -
254N MET 3.6 18.6 + - - -
255N LYS 4.1 5.1 + - - +
256N THR* 1.3 72.9 + - - +
258N HIS* 1.3 69.3 + - + +
287N PHE* 3.0 31.1 + - - +
288N LEU* 3.5 6.8 - - - -
289N ASP* 2.6 51.6 + - - +
290N ALA 3.9 1.2 + - - -
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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