Contacts of the helix formed by residues 245 - 257 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196D GLY 3.4 21.9 - - - +
197D LYS* 3.4 15.4 + - - +
198D ALA* 2.8 35.4 + - + +
238D MET* 5.5 3.0 + - - +
240D THR* 4.9 2.2 + - - -
243D PRO 3.6 1.0 + - - -
244D MET* 1.3 72.8 - - - +
246D MET* 1.3 61.2 + - - +
247D GLU* 3.6 10.7 + - - +
248D THR* 2.8 36.9 + - - -
249D ILE* 3.7 19.2 + - - +
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Residues in contact with MET 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D MET* 3.1 20.8 + - + +
245D ASP* 1.3 72.2 - - - +
247D GLU* 1.3 64.7 + - - +
249D ILE* 3.1 31.1 + - + +
250D GLU* 2.9 45.5 + - + +
275D ILE* 3.8 14.8 - - + +
278D ARG* 3.5 51.1 - - + +
279D ILE* 3.4 41.3 - - + +
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Residues in contact with GLU 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D LYS* 5.8 2.5 - - - +
245D ASP* 3.8 9.4 - - - +
246D MET* 1.3 79.1 - - + +
248D THR* 1.3 58.6 + - - +
250D GLU* 3.4 14.7 + - - +
251D ALA* 2.9 31.6 + - - +
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Residues in contact with THR 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D LYS* 4.1 14.2 + - - +
198D ALA* 4.2 18.8 - - + +
200D ILE* 4.6 19.5 - - + +
236D ILE* 4.4 15.0 - - + -
245D ASP* 2.8 32.3 + - - +
247D GLU* 1.3 78.1 - - - +
249D ILE* 1.3 62.9 + - - +
251D ALA* 3.7 5.6 + - - +
252D SER* 3.2 22.5 + - - -
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Residues in contact with ILE 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D ALA* 5.6 1.1 - - + -
208D THR* 4.9 1.3 - - + -
210D VAL* 3.7 45.3 - - + -
236D ILE* 4.3 16.6 - - + -
238D MET* 4.8 9.6 - - + -
244D MET* 5.3 3.4 - - + -
245D ASP 3.7 17.5 - - - +
246D MET* 3.1 35.5 + - + +
248D THR* 1.3 74.8 - - - +
250D GLU* 1.3 62.0 + - - +
252D SER* 3.6 2.8 + - - -
253D VAL* 2.9 28.2 + - + +
259D LEU* 4.6 10.8 - - + -
275D ILE* 4.5 10.8 - - + -
279D ILE* 4.6 6.5 - - + -
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Residues in contact with GLU 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D MET* 2.9 45.3 + - + +
247D GLU* 3.8 14.9 - - - +
249D ILE* 1.3 74.7 - - - +
251D ALA* 1.3 54.7 + - - +
253D VAL* 2.7 7.2 + - - +
254D MET* 2.7 44.4 + - + +
278D ARG* 4.4 9.9 + - - +
279D ILE* 4.6 1.1 - - - +
282D GLY* 4.4 1.6 - - - -
283D PRO* 3.8 33.0 - - + +
284D ALA* 3.7 24.7 - - + +
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Residues in contact with ALA 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D GLU 2.9 19.4 + - - +
248D THR* 3.9 6.3 - - - +
249D ILE 3.4 0.2 - - - -
250D GLU* 1.3 77.0 - - - +
252D SER* 1.3 62.4 + - - +
254D MET* 3.2 29.5 + - + +
255D LYS* 3.4 12.0 + - - +
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Residues in contact with SER 252 (chain D).
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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200D ILE* 5.7 1.6 - - - -
208D THR* 2.6 35.0 + - - +
234D GLU* 2.7 35.9 + - - +
236D ILE* 4.1 6.5 - - - -
248D THR 3.2 15.9 + - - -
249D ILE 3.7 3.4 - - - -
251D ALA* 1.3 79.2 - - - +
253D VAL* 1.3 60.5 + - - +
255D LYS* 3.0 14.5 + - - +
256D THR* 2.8 17.8 + - - +
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Residues in contact with VAL 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D THR* 4.0 11.9 - - - +
249D ILE* 2.9 20.9 + - + +
250D GLU* 2.7 17.4 + - - +
252D SER* 1.3 71.0 - - - +
254D MET* 1.3 60.1 + - - +
255D LYS 2.9 0.3 + - - -
256D THR* 3.3 4.7 - - - -
257D ASN* 2.7 35.9 + - - -
258D HIS 4.1 1.8 - - - +
259D LEU* 4.1 25.8 - - + -
279D ILE* 4.5 11.0 - - + -
284D ALA* 4.0 24.7 - - + +
287D PHE* 4.4 4.7 - - + -
288D LEU* 4.0 20.0 - - + -
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Residues in contact with MET 254 (chain D).
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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250D GLU* 2.7 24.2 + - + +
251D ALA* 3.2 29.4 + - + +
253D VAL* 1.3 71.4 - - - +
255D LYS* 1.3 56.8 + - - +
257D ASN* 4.1 6.3 + - - -
283D PRO* 4.6 12.6 - - - +
284D ALA* 4.6 6.7 - - - -
287D PHE* 3.8 59.5 - - + -
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Residues in contact with LYS 255 (chain D).
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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203D GLN* 3.8 12.1 + - - -
204D GLY 3.0 18.2 + - - +
205D THR* 3.6 23.8 - - + +
234D GLU* 2.5 40.4 + - - -
251D ALA 3.4 7.3 + - - +
252D SER* 3.0 7.4 + - - +
253D VAL 3.0 0.8 - - - -
254D MET* 1.3 80.7 - - - +
256D THR* 1.3 61.4 + - + +
257D ASN* 3.7 6.5 - - - +
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Residues in contact with THR 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D GLY 4.3 6.7 - - - +
205D THR* 3.3 29.2 - - - +
206D HIS* 3.3 7.8 - - - +
207D ILE* 3.5 34.8 - - - +
208D THR* 2.7 24.6 + - - +
234D GLU* 4.5 1.8 - - + -
252D SER* 2.8 18.4 + - - +
253D VAL* 3.3 5.2 - - - -
255D LYS* 1.3 75.4 - - + +
257D ASN* 1.3 62.6 + - - +
258D HIS* 2.8 30.6 + - - -
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Residues in contact with ASN 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D VAL* 2.7 19.4 + - - -
254D MET 4.1 9.7 + - - -
255D LYS 4.1 6.3 - - - +
256D THR* 1.3 73.9 + - - +
258D HIS* 1.3 68.6 + - + +
287D PHE* 2.7 41.9 + - - +
288D LEU* 3.5 7.4 - - - +
289D ASP* 2.9 46.9 + - - +
290D ALA 4.3 0.5 + - - -
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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
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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