Contacts of the helix formed by residues 214 - 228 (chain R) 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 ARG 214 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120R ALA 5.2 2.2 + - - -
148R TRP* 3.9 6.5 + - - -
172R ASN* 3.6 21.4 + - - +
174R LEU* 3.8 45.4 - - - +
175R MET* 3.9 26.5 - - + +
213R SER* 1.3 82.5 + - - +
215R PRO* 1.3 67.7 - - + +
216R VAL 2.7 7.3 + - - -
217R GLY* 2.9 15.8 + - - -
218R HIS* 3.3 35.3 + - + +
313R ILE* 4.6 24.4 - - - +
315R GLN* 6.0 1.8 + - - +
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Residues in contact with PRO 215 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172R ASN* 5.5 0.7 - - - +
211R SER* 3.7 6.1 - - - +
212R HIS* 3.7 12.1 - - + +
213R SER* 2.8 5.5 - - - +
214R ARG* 1.3 94.0 - - + +
216R VAL* 1.3 61.1 + - - -
217R GLY 3.2 0.4 - - - -
218R HIS* 3.7 20.4 - - + +
219R CYS* 3.3 25.1 + - - -
262R VAL* 3.9 19.5 - - + +
263R GLU 4.4 2.5 - - - -
264R GLY* 4.0 27.4 - - - +
313R ILE* 6.3 3.8 - - + -
314R PRO* 4.9 9.4 - - + -
319R ILE* 5.5 0.4 - - + -
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Residues in contact with VAL 216 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148R TRP* 3.5 35.4 - - + -
201R GLU* 4.5 5.4 - - + -
211R SER* 3.6 36.3 - - - +
212R HIS* 3.8 1.3 - - - +
213R SER 2.6 22.9 + - - +
214R ARG 2.7 1.6 + - - -
215R PRO* 1.3 72.8 - - - +
217R GLY* 1.3 62.9 + - - +
219R CYS* 3.1 14.9 + - - +
220R LEU* 3.1 15.3 + - + +
235R VAL* 5.0 6.7 - - + -
236R ILE 4.7 1.1 - - - +
237R ASN* 3.8 29.2 - - + +
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Residues in contact with GLY 217 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148R TRP* 3.5 24.0 - - - +
214R ARG 2.9 10.1 + - - -
216R VAL* 1.3 80.0 - - - +
218R HIS* 1.3 58.3 + - - +
220R LEU* 3.2 7.6 + - - +
221R GLU* 2.9 31.3 + - - +
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Residues in contact with HIS 218 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214R ARG* 3.3 49.1 + - + +
215R PRO* 3.4 19.4 + - + +
216R VAL 3.2 1.0 - - - -
217R GLY* 1.3 77.2 - - - +
219R CYS* 1.3 58.3 + - - +
221R GLU* 3.2 25.1 + - - +
222R ALA* 3.0 27.9 + - - +
313R ILE* 5.6 3.0 - - + +
314R PRO 4.3 14.7 + - - -
315R GLN* 5.6 6.1 + - - -
316R VAL* 3.7 21.3 - - + +
319R ILE* 3.7 21.6 - - + +
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Residues in contact with CYS 219 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209R VAL* 3.7 26.9 - - + +
211R SER* 3.8 10.5 - - - -
215R PRO 3.3 15.6 + - - -
216R VAL* 3.1 9.2 + - - +
218R HIS* 1.3 75.0 - - - +
220R LEU* 1.3 60.6 + - - +
222R ALA* 3.5 4.1 + - - +
223R ALA* 3.0 28.1 + - - +
233R CYS* 5.7 0.5 - - - +
235R VAL* 3.8 23.6 - - + +
262R VAL* 3.8 25.8 - - - -
319R ILE* 4.5 7.4 - - - -
323R ILE* 6.1 0.5 - - - +
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Residues in contact with LEU 220 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148R TRP* 3.4 38.4 - - + -
201R GLU* 4.2 18.8 - - + +
202R ARG* 4.1 29.3 + - + -
216R VAL* 3.1 11.5 + - + +
217R GLY* 3.4 7.0 - - - +
219R CYS* 1.3 75.6 - - - +
221R GLU* 1.3 65.5 + - - +
223R ALA* 3.4 4.0 + - - +
224R ALA* 3.1 21.3 + - - +
235R VAL* 4.1 11.9 - - + -
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Residues in contact with GLU 221 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217R GLY 2.9 13.5 + - - +
218R HIS* 3.2 27.8 - - - +
219R CYS 3.3 0.2 - - - -
220R LEU* 1.3 79.0 - - - +
222R ALA* 1.3 60.5 + - - +
224R ALA* 3.5 7.2 + - - +
225R VAL* 3.2 25.4 + - - +
316R VAL* 3.6 23.5 - - + +
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Residues in contact with ALA 222 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218R HIS 3.0 17.4 + - - +
219R CYS 4.0 3.4 - - - +
220R LEU 3.3 0.2 - - - -
221R GLU* 1.3 73.6 - - - +
223R ALA* 1.3 61.1 + - - +
224R ALA 3.2 0.4 - - - -
225R VAL* 3.3 1.9 + - - +
226R LEU* 2.9 34.8 + - - +
233R CYS* 5.5 0.2 - - - -
316R VAL* 3.8 17.2 - - + +
319R ILE* 4.1 15.5 - - + -
320R ILE* 3.6 25.8 - - + -
323R ILE* 5.2 4.3 - - + -
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Residues in contact with ALA 223 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202R ARG* 3.5 35.2 + - - +
219R CYS 3.0 19.2 + - - +
220R LEU* 3.7 6.1 - - - +
221R GLU 3.3 0.2 - - - -
222R ALA* 1.3 78.3 - - - +
224R ALA* 1.3 60.6 + - - +
226R LEU* 4.0 1.2 - - - +
227R SER* 3.1 26.0 + - - -
231R VAL 4.7 0.9 - - - +
233R CYS* 4.0 27.5 - - + -
235R VAL* 4.4 1.6 - - + -
323R ILE* 5.9 0.2 - - - +
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Residues in contact with ALA 224 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202R ARG* 5.2 2.7 - - - +
220R LEU 3.1 13.5 + - - +
221R GLU* 3.7 11.0 - - - +
222R ALA 3.2 0.2 - - - -
223R ALA* 1.3 76.9 - - - +
225R VAL* 1.3 69.0 + - + +
226R LEU 3.2 0.7 + - - -
227R SER* 3.5 10.7 + - - -
228R LYS* 3.7 25.1 + - - +
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Residues in contact with VAL 225 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221R GLU* 3.2 16.8 - - + +
222R ALA* 3.3 2.6 + - - +
224R ALA* 1.3 78.0 - - + +
226R LEU* 1.3 63.7 + - - +
228R LYS* 3.5 26.2 + - + +
229R GLU* 4.3 13.5 - - - +
316R VAL* 4.8 5.6 - - + -
320R ILE* 3.6 32.5 - - + -
324R LYS* 6.1 0.4 - - - +
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Residues in contact with LEU 226 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222R ALA 2.9 20.1 + - - +
223R ALA* 4.0 4.9 - - - +
225R VAL* 1.3 73.9 - - + +
227R SER* 1.3 57.6 + - - +
228R LYS 3.0 4.9 - - - -
229R GLU* 2.7 47.4 + - - +
231R VAL* 3.5 29.6 + - + +
233R CYS* 4.0 9.4 - - - -
320R ILE* 4.2 22.4 - - + -
323R ILE* 3.6 45.1 - - + -
324R LYS* 4.1 20.4 - - + -
329R ILE* 5.7 0.2 - - + -
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Residues in contact with SER 227 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202R ARG* 3.4 24.6 + - - -
223R ALA 3.1 7.3 + - - -
224R ALA* 3.5 8.5 + - - -
226R LEU* 1.3 76.2 - - - +
228R LYS* 1.3 58.3 + - - +
229R GLU 3.0 1.8 - - - -
230R GLY* 3.2 13.8 + - - -
231R VAL 3.1 16.3 + - - +
232R GLU* 3.1 23.9 - - - +
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Residues in contact with LYS 228 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224R ALA* 3.7 23.9 + - - +
225R VAL* 3.5 16.8 + - + +
226R LEU 2.9 1.2 + - - -
227R SER* 1.3 78.4 + - - +
229R GLU* 1.3 60.2 + - + +
230R GLY 3.4 0.9 - - - -
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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