Contacts of the helix formed by residues 208 - 226 (chain O) in PDB entry 5G04
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 SER 208 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28O ASP* 5.2 2.6 + - - -
29O TRP* 6.1 6.7 - - - +
31O THR* 6.0 5.6 - - - -
34O LYS* 5.8 1.3 - - - -
72O ASP* 5.6 0.9 - - - -
207O LEU* 1.3 78.2 - - - +
209O GLN* 1.3 58.1 + - - +
210O LYS* 3.1 19.1 + - - +
211O GLN* 3.2 33.9 + - - -
212O ALA* 2.9 37.2 + - - +
247O ASN* 6.1 0.4 - - - -
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Residues in contact with GLN 209 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27O LYS* 3.6 41.5 - - + +
28O ASP* 5.7 0.2 - - - -
207O LEU 4.3 0.6 + - - -
208O SER* 1.3 72.5 + - - +
210O LYS* 1.3 70.5 + - + +
212O ALA* 4.2 4.9 - - - +
213O GLU* 3.0 33.9 + - - +
247O ASN* 3.8 24.1 + - - +
250O PHE* 3.8 28.7 - - - +
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Residues in contact with LYS 210 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D GLU* 4.8 11.6 + - - +
27O LYS* 3.6 21.0 - - - +
28O ASP* 3.4 52.9 - - - +
69O GLN 5.6 0.3 - - - +
208O SER* 3.1 8.1 + - - +
209O GLN* 1.3 82.0 + - + +
211O GLN* 1.3 64.3 + - + +
213O GLU* 3.9 22.5 + - - +
214O PHE* 3.5 18.2 + - - +
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Residues in contact with GLN 211 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31O THR* 6.2 0.2 - - - +
34O LYS* 3.0 17.2 - - - +
69O GLN 4.7 7.0 - - - +
70O GLY 4.3 5.4 - - - +
71O PRO* 3.9 20.0 - - + +
72O ASP* 2.7 42.3 + - - +
207O LEU* 3.5 32.2 - - + +
208O SER* 3.2 25.2 + - - +
210O LYS* 1.3 80.6 - - + +
212O ALA* 1.3 53.0 + - - +
214O PHE* 3.2 11.3 + - + +
215O PHE* 2.7 34.3 + - - +
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Residues in contact with ALA 212 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207O LEU* 3.5 5.8 - - + +
208O SER 2.9 18.1 + - - +
209O GLN* 4.4 4.5 - - - +
211O GLN* 1.3 72.3 - - - +
213O GLU* 1.3 66.7 + - - +
215O PHE* 3.6 6.1 - - - +
216O LEU* 2.9 30.0 + - - +
243O LEU* 3.5 28.5 - - + -
247O ASN* 6.1 1.3 - - - +
250O PHE* 4.1 20.2 - - + -
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Residues in contact with GLU 213 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LEU* 4.1 29.0 - - + +
22D ARG* 5.1 10.2 + - - +
209O GLN* 3.0 26.9 + - - +
210O LYS* 3.9 29.2 + - - +
211O GLN 3.4 0.4 - - - -
212O ALA* 1.3 76.7 - - - +
214O PHE* 1.3 55.4 + - - +
216O LEU* 4.0 1.7 - - - +
217O SER* 3.0 33.3 + - - -
250O PHE* 3.8 25.7 - - + -
252O GLU* 5.5 0.4 - - - +
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Residues in contact with PHE 214 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446I THR* 6.4 2.5 - - + -
69O GLN* 4.7 22.7 - - + +
70O GLY* 5.4 2.5 - - - -
71O PRO* 5.2 15.7 - - + -
210O LYS 3.5 12.2 + - - +
211O GLN* 3.2 14.0 + - + +
212O ALA 3.2 0.4 - - - -
213O GLU* 1.3 76.4 - - - +
215O PHE* 1.3 69.8 + + + +
217O SER* 3.4 7.6 + - - -
218O GLN* 3.0 57.5 + - + +
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Residues in contact with PHE 215 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207O LEU* 5.4 7.9 - - + -
211O GLN 2.7 20.5 + - - +
212O ALA* 3.2 8.7 + - - +
214O PHE* 1.3 80.5 - + + +
216O LEU* 1.3 79.9 + - + +
218O GLN* 3.6 11.1 - - + +
219O GLN* 3.1 41.3 + - + +
231O LEU* 4.4 18.4 - - + -
236O LEU* 4.5 13.2 - - + -
239O GLU* 3.5 39.0 - - + -
240O LEU* 5.1 2.0 - - + -
243O LEU* 4.8 11.2 - - + -
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Residues in contact with LEU 216 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D PHE* 4.7 3.4 - - + -
20D LEU* 4.5 9.2 - - + -
212O ALA 2.9 17.1 + - - +
213O GLU* 4.1 3.6 - - - +
215O PHE* 1.3 99.2 - - + +
217O SER* 1.3 65.6 + - - +
219O GLN* 3.9 2.4 - - - +
220O ALA* 2.9 29.7 + - - +
240O LEU* 3.9 14.4 - - + -
243O LEU* 4.0 7.2 - - + -
250O PHE* 3.6 20.2 - - + -
252O GLU* 3.5 42.0 - - + +
253O ALA* 3.7 3.4 - - - +
256O LEU* 3.7 24.0 - - + -
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Residues in contact with SER 217 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LEU* 3.1 40.7 + - - +
213O GLU 3.0 16.7 + - - -
214O PHE* 3.4 11.2 - - - -
216O LEU* 1.3 78.8 - - - +
218O GLN* 1.3 58.0 + - - -
220O ALA* 4.0 0.9 - - - +
221O SER* 3.1 27.3 + - - -
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Residues in contact with GLN 218 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214O PHE* 3.0 47.3 + - + +
215O PHE* 3.6 17.4 + - + +
217O SER* 1.3 76.6 - - - +
219O GLN* 1.3 78.2 + - - +
221O SER* 2.6 23.0 + - - +
222O LEU* 3.3 26.4 + - - +
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Residues in contact with GLN 219 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215O PHE* 3.1 32.0 + - + +
216O LEU 3.9 0.7 - - - +
217O SER 3.3 0.2 - - - -
218O GLN* 1.3 91.8 + - - +
220O ALA* 1.3 51.6 + - - +
222O LEU* 3.0 13.1 - - - +
223O LEU* 2.7 36.7 + - + +
230O ALA* 3.8 11.3 - - + +
231O LEU* 3.1 54.6 + - - +
236O LEU* 3.7 12.3 - - + +
256O LEU* 3.7 26.5 - - + -
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Residues in contact with ALA 220 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D THR* 5.9 1.8 - - + +
18D PHE* 4.0 21.1 - - + -
20D LEU* 5.7 0.7 - - + -
216O LEU 2.9 18.0 + - - +
217O SER* 4.2 2.0 - - - +
219O GLN* 1.3 73.4 - - - +
221O SER* 1.3 65.2 + - - +
222O LEU 3.1 1.1 - - - -
223O LEU* 3.6 8.8 - - - +
224O LYS* 3.1 25.5 + - - +
256O LEU* 3.6 23.1 - - + -
259O LEU* 4.3 7.2 - - + +
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Residues in contact with SER 221 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217O SER 3.1 12.9 + - - -
218O GLN* 2.6 28.3 + - - -
220O ALA* 1.3 78.3 - - - +
222O LEU* 1.3 62.1 + - - +
224O LYS* 3.9 4.6 - - - +
225O ASN* 3.2 36.8 + - - +
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Residues in contact with LEU 222 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218O GLN* 3.4 26.0 - - - +
219O GLN* 3.0 20.3 + - - +
221O SER* 1.3 83.6 + - - +
223O LEU* 1.3 52.4 + - - +
225O ASN* 2.9 1.9 + - + -
226O ASP* 2.5 49.4 + - + +
229O LYS* 3.8 33.9 - - + +
230O ALA* 3.5 31.4 - - + +
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Residues in contact with LEU 223 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219O GLN* 2.7 21.6 + - + +
220O ALA* 4.0 5.6 - - - +
221O SER 3.4 0.6 - - - -
222O LEU* 1.3 72.3 - - - +
224O LYS* 1.3 59.4 + - - +
226O ASP 3.5 11.2 + - - +
227O GLU* 5.2 4.3 - - - +
230O ALA* 5.3 2.7 - - + -
236O LEU* 3.8 19.3 - - + -
256O LEU* 3.6 33.9 - - + +
259O LEU* 4.0 37.9 - - + +
260O ASN* 4.2 1.3 - - - -
263O ARG* 3.6 41.1 - - + +
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Residues in contact with LYS 224 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ARG* 3.1 54.5 - - - +
12D VAL* 5.4 9.0 - - + +
13D THR* 3.7 26.5 + - + +
220O ALA 3.1 18.1 + - - +
221O SER* 3.9 4.5 - - - +
223O LEU* 1.3 78.5 - - - +
225O ASN* 1.3 69.5 + - - +
259O LEU* 5.9 1.5 - - + +
416O GLU* 4.7 9.2 - - - -
463O THR* 3.3 17.2 - - - +
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Residues in contact with ASN 225 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221O SER* 3.2 22.8 + - - +
222O LEU* 2.9 3.3 + - + -
223O LEU 5.0 0.2 - - - -
224O LYS* 1.3 99.5 - - - +
226O ASP* 1.3 57.3 + - + +
415O SER* 5.5 6.5 + - - -
450O SER* 4.8 3.6 + - - -
461O ASN* 2.4 59.4 + - - +
462O ASN* 3.5 2.8 - - - +
463O THR* 3.4 17.0 - - - +
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Residues in contact with ASP 226 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222O LEU* 2.5 49.1 + - + +
223O LEU* 3.5 10.5 + - - +
224O LYS 3.9 0.6 - - - -
225O ASN* 1.3 76.3 - - + +
227O GLU* 1.3 79.5 + - - +
228O THR* 2.7 26.8 + - - -
229O LYS* 2.9 29.6 + - - +
230O ALA* 4.6 1.6 - - - +
459O GLN* 5.0 4.7 + - - -
461O ASN 3.9 3.8 - - - +
462O ASN* 3.8 23.7 + - - +
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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
------------------------------------------------------------
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