Contacts of the helix formed by residues 203 - 220 (chain A) in PDB entry 5UNH
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 LYS 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A PRO* 3.2 7.6 + - + +
202A GLU* 1.4 79.1 - - + +
204A TYR* 1.4 60.3 + - - +
205A ALA 3.5 2.2 - - - +
206A GLN* 3.9 31.6 - - + +
207A TRP* 3.2 31.5 + - + +
1008A GLU* 5.8 1.6 - - - +
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Residues in contact with TYR 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ILE* 4.4 11.7 - - + +
197A MET 3.3 16.0 + - - -
198A ALA* 4.7 1.6 - - - -
199A PHE* 3.4 49.9 - + + -
200A PRO 3.2 7.8 + - - +
201A PRO* 3.9 17.7 + - + +
203A LYS* 1.4 72.8 - - - +
205A ALA* 1.4 63.1 + - - +
207A TRP* 3.5 2.8 + - - +
208A SER* 3.1 43.2 + - - -
283A TRP* 3.8 25.8 - + - -
1102A ILE* 4.4 22.9 - - + -
1106A LEU* 5.6 6.3 - - + -
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Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LYS 3.5 0.6 - - - -
204A TYR* 1.4 75.3 - - - +
206A GLN* 1.4 64.0 + - - +
208A SER* 3.5 0.9 + - - -
209A ALA* 3.2 24.3 + - - +
283A TRP* 3.6 47.2 - - + +
1004A GLU* 5.9 2.7 - - - +
1106A LEU* 4.2 14.3 - - + +
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Residues in contact with GLN 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A LYS* 3.7 31.0 + - + +
205A ALA* 1.4 78.0 - - - +
207A TRP* 1.3 63.7 + - + +
209A ALA* 3.5 5.5 + - - +
210A GLY* 2.9 26.3 + - - -
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Residues in contact with TRP 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A PRO* 5.7 0.7 - - + -
181A PHE* 3.8 29.8 - + - -
199A PHE* 3.6 31.6 - + + -
200A PRO* 3.7 27.2 - - + +
203A LYS* 3.2 27.5 + - + +
204A TYR 3.8 2.0 - - - +
205A ALA 3.4 0.2 - - - -
206A GLN* 1.3 84.8 + - - +
208A SER* 1.3 58.9 + - - +
210A GLY* 3.8 1.7 - - - -
211A ILE* 2.9 72.6 + - + +
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Residues in contact with SER 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A PHE* 3.6 23.5 - - - -
204A TYR* 3.1 30.1 + - - -
205A ALA 3.9 0.4 - - - -
206A GLN 3.4 0.2 - - - -
207A TRP* 1.3 73.8 - - - +
209A ALA* 1.4 56.3 + - - +
211A ILE* 3.8 1.9 + - - +
212A ALA* 3.1 29.1 + - - +
279A ASP* 5.1 0.7 - - - +
283A TRP* 3.6 37.9 - - - -
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Residues in contact with ALA 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A ALA 3.2 16.7 + - - +
206A GLN* 3.8 6.1 - - - +
208A SER* 1.4 74.8 - - - +
210A GLY* 1.3 62.7 + - - +
212A ALA* 3.5 5.3 + - - +
213A LEU* 3.2 32.5 + - - +
280A ALA* 3.8 22.9 - - - +
283A TRP* 4.1 6.2 - - + +
284A MET* 3.9 21.1 - - + +
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Residues in contact with GLY 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A GLN 2.9 16.8 + - - -
207A TRP* 3.9 2.9 - - - -
209A ALA* 1.3 76.4 - - - +
211A ILE* 1.4 61.2 + - - +
213A LEU* 3.5 9.7 + - - +
214A MET* 3.3 19.9 + - - +
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Residues in contact with ILE 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A PRO* 4.1 23.3 - - + -
181A PHE* 5.5 0.2 - - + -
197A MET* 4.4 4.9 - - + -
199A PHE* 3.7 23.3 - - + -
207A TRP* 2.9 51.2 + - + +
208A SER* 4.3 1.8 - - - +
210A GLY* 1.4 74.6 - - - +
212A ALA* 1.4 64.5 + - - +
214A MET* 3.2 19.0 + - + +
215A LYS* 3.1 41.6 + - - +
1501A 8EM 4.2 16.2 - - + -
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Residues in contact with ALA 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A SER 3.1 20.9 + - - +
209A ALA 3.7 5.6 - - - +
210A GLY 3.4 0.4 - - - -
211A ILE* 1.4 75.5 - - - +
213A LEU* 1.3 60.1 + - - +
215A LYS* 3.3 23.7 + - - +
216A ASN* 3.4 14.8 - - - +
276A THR* 3.4 22.2 - - + +
279A ASP* 4.5 7.9 - - - +
280A ALA* 3.7 21.8 - - + -
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Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ALA 3.2 22.4 + - - +
210A GLY* 3.7 11.7 - - - +
211A ILE 3.3 0.2 - - - -
212A ALA* 1.3 74.4 - - - +
214A MET* 1.4 60.9 + - - +
216A ASN* 3.2 9.8 + - - +
217A ILE* 3.1 34.2 + - + +
277A PHE* 4.6 19.1 - - + -
280A ALA* 3.7 12.6 - - + -
284A MET* 3.7 26.2 - - + -
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Residues in contact with MET 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A PHE* 5.2 0.5 - - - -
173A LEU 5.4 0.2 - - - +
174A SER* 3.4 28.9 - - - +
177A PRO* 3.7 25.8 - - + -
210A GLY 3.3 10.0 + - - +
211A ILE* 3.2 24.7 + - + +
213A LEU* 1.4 73.9 - - - +
215A LYS* 1.3 65.6 + - - +
217A ILE* 4.7 5.6 - - - +
218A LEU* 3.2 50.4 + - + +
1501A 8EM 3.8 16.6 - - + -
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Residues in contact with LYS 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A PHE* 5.2 1.8 - - - -
211A ILE* 3.1 32.1 + - - +
212A ALA* 3.3 11.2 - - + +
213A LEU 3.2 0.2 - - - -
214A MET* 1.3 77.7 - - - +
216A ASN* 1.4 55.7 + - - +
219A GLY* 3.2 18.1 + - - +
272A PHE* 4.8 6.8 - - + -
273A HIS* 3.1 20.3 - - + -
276A THR* 4.2 21.2 + - + +
1501A 8EM 2.9 86.7 + - + -
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Residues in contact with ASN 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A ALA 3.4 15.5 - - - +
213A LEU* 3.2 9.6 + - - +
215A LYS* 1.4 75.1 - - - +
217A ILE* 1.3 57.7 + - + +
220A PHE* 2.9 11.3 + - + +
221A ILE* 2.8 42.6 + - + +
273A HIS* 2.9 54.3 + - + +
276A THR* 3.7 9.5 - - - +
277A PHE* 3.9 31.3 + - + +
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Residues in contact with ILE 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A LEU* 3.1 23.4 + - + +
214A MET* 4.4 5.2 - - - +
216A ASN* 1.3 80.2 - - + +
218A LEU* 1.3 64.4 + - + +
221A ILE* 3.5 26.1 + - + -
222A ILE* 3.0 50.8 + - + +
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Residues in contact with LEU 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A PHE* 3.9 11.4 - - + -
133A PHE* 3.7 27.8 - - + -
174A SER* 4.1 22.9 - - - +
214A MET* 3.2 47.2 + - + +
217A ILE* 1.3 81.9 - - + +
219A GLY* 1.3 57.6 + - - +
220A PHE 3.7 0.2 - - - -
222A ILE* 4.9 13.5 - - + +
223A PRO* 3.4 17.0 - - - +
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Residues in contact with GLY 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A MET* 5.5 1.6 - - - -
129A PHE* 3.9 13.9 - - - -
132A ILE* 3.9 21.5 - - - +
215A LYS 3.2 18.2 + - - -
218A LEU* 1.3 79.5 - - - +
220A PHE* 1.4 59.6 + - - +
223A PRO* 3.8 6.3 - - - +
265A PHE* 3.9 12.6 - - - -
269A TRP* 5.3 1.0 - - - -
273A HIS* 3.8 12.2 + - - -
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Residues in contact with PHE 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ASN* 2.9 12.6 + - + +
219A GLY* 1.4 77.4 - - - +
221A ILE* 1.3 72.0 + - + +
223A PRO* 3.5 5.4 - - - +
224A LEU* 2.8 50.2 + - + +
265A PHE* 3.7 25.5 - + - -
266A ILE* 3.9 19.5 - - + -
269A TRP* 3.7 18.6 - - + -
270A LEU* 3.6 55.4 - - + -
273A HIS* 3.6 29.2 - + + +
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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