Contacts of the helix formed by residues 213 - 227 (chain A) in PDB entry 6F3T
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 MET 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A ASP* 3.0 25.3 + - + +
212A THR* 1.3 111.8 + - - +
214A TYR* 1.3 63.9 + - - +
215A GLU 3.2 3.4 - - - -
216A GLU* 3.2 35.4 + - + +
217A TYR* 2.9 50.3 + - + +
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Residues in contact with TYR 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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207A GLN 5.0 0.3 + - - -
209A GLY* 4.2 14.8 + - - -
210A ASP 3.3 27.6 - - - -
211A PRO* 3.4 17.5 + - + +
212A THR 3.4 3.2 - - - -
213A MET* 1.3 78.3 - - - +
215A GLU* 1.3 62.7 + - + +
217A TYR* 3.9 19.7 - + - -
218A TYR* 3.1 20.1 + - - +
247A MET* 3.4 63.5 - - + +
250A GLU* 3.0 36.5 + - + +
251A LEU* 3.9 23.1 - - + -
263A PHE* 3.6 6.6 - - + -
332A ILE* 4.4 11.3 - - + +
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Residues in contact with GLU 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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211A PRO 5.2 0.2 + - - -
212A THR 5.3 3.1 - - - +
213A MET 3.2 1.0 - - - -
214A TYR* 1.3 78.6 - - + +
216A GLU* 1.3 67.3 + - - +
218A TYR 3.4 0.7 + - - -
219A SER* 2.9 31.6 + - - -
259A GLU 4.6 1.5 - - - +
262A SER* 2.5 48.3 + - - +
263A PHE* 3.3 18.1 + - + -
266A LYS* 4.1 24.8 + - - +
267A PHE* 3.6 18.0 - - + -
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Residues in contact with GLU 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 THR 3.0 21.1 - - - +
213A MET* 3.2 48.5 - - + +
215A GLU* 1.3 82.0 - - - +
217A TYR* 1.3 66.8 + - + +
219A SER* 3.3 7.0 + - - -
220A GLY* 2.8 22.0 + - - -
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Residues in contact with TYR 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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209A GLY* 4.7 2.5 - - - -
210A ASP* 3.6 35.5 + - - +
213A MET* 2.9 39.3 + - + +
214A TYR* 3.8 26.0 - + - +
216A GLU* 1.3 79.5 - - + +
218A TYR* 1.3 62.4 + - - +
220A GLY* 3.3 7.7 + - - -
221A LEU* 3.3 10.0 + - - +
247A MET* 4.2 4.5 - - + -
328A GLN* 3.7 42.5 - - + +
329A ILE* 3.9 30.6 - - + +
332A ILE* 4.9 5.8 - - + -
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Residues in contact with TYR 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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214A TYR 3.1 14.2 + - - +
215A GLU 3.7 4.5 - - - +
216A GLU 3.2 0.2 - - - -
217A TYR* 1.3 77.1 - - - +
219A SER* 1.3 60.4 + - - +
221A LEU* 3.1 7.5 + - + +
222A LYS* 2.8 35.0 + - + +
240A PHE* 3.0 47.4 + + - -
243A LEU* 4.2 10.1 - - + -
244A PHE* 3.8 24.9 - - + -
247A MET* 3.9 13.9 - - + +
263A PHE* 3.9 14.8 - + + -
267A PHE* 3.6 46.7 - + + -
270A ASP* 5.3 2.4 - - + +
271A GLN* 3.1 20.4 + - - -
329A ILE* 4.6 6.3 - - + -
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Residues in contact with SER 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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215A GLU 2.9 19.1 + - - -
216A GLU* 3.8 7.9 - - - -
218A TYR* 1.3 76.5 - - - +
220A GLY* 1.3 57.6 + - - +
222A LYS* 3.6 10.5 - - - +
223A HIS* 2.9 31.9 + - - +
266A LYS* 3.9 11.4 + - - -
267A PHE* 3.5 18.3 - - - -
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Residues in contact with GLY 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 GLU 2.8 15.9 + - - -
217A TYR* 3.3 3.3 + - - -
218A TYR 3.1 0.4 - - - -
219A SER* 1.3 78.3 - - - +
221A LEU* 1.3 60.3 + - - +
223A HIS* 3.9 4.5 - - - +
224A PHE* 3.4 18.4 + - - +
320A HIS* 4.0 9.3 + - - -
326A ASN* 5.0 7.9 - - - -
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Residues in contact with LEU 221 (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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217A TYR 3.3 10.0 + - - +
218A TYR* 3.1 10.5 + - + +
220A GLY* 1.3 73.7 - - - +
222A LYS* 1.3 64.8 + - - +
224A PHE* 3.3 7.4 + - + +
225A ILE* 3.0 34.7 + - + +
239A LEU* 4.2 13.7 - - + -
240A PHE* 5.9 3.4 - - + -
243A LEU* 3.2 34.5 - - + -
317A LEU* 4.0 21.1 - - + -
320A HIS* 3.8 28.9 - - + +
321A LEU* 4.0 10.1 - - + -
329A ILE* 4.4 14.7 - - + +
333A VAL* 5.4 2.7 - - + -
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Residues in contact with LYS 222 (chain A).
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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218A TYR* 2.8 24.6 + - + +
219A SER* 3.3 9.4 + - - +
221A LEU* 1.3 76.5 - - - +
223A HIS* 1.3 62.5 + - - +
225A ILE* 3.2 2.6 + - - +
226A GLU* 2.9 53.9 + - - +
240A PHE* 3.8 31.3 - - + -
266A LYS* 5.5 1.0 + - - +
267A PHE* 4.4 19.4 - - + -
270A ASP* 2.8 36.5 + - + +
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Residues in contact with HIS 223 (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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219A SER 2.9 18.5 + - - +
220A GLY* 3.9 5.8 - - - +
222A LYS* 1.3 77.0 - - - +
224A PHE* 1.3 67.1 + - - +
226A GLU* 3.3 5.4 + - - +
227A CYS* 3.1 52.1 + - - -
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Residues in contact with PHE 224 (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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220A GLY 3.4 4.8 + - - +
221A LEU* 3.3 11.8 + - + +
223A HIS* 1.3 83.9 - - - +
225A ILE* 1.3 72.8 + - + +
227A CYS* 3.3 5.4 + - - +
228A SER* 3.1 34.9 + - - -
236A LEU* 3.8 22.7 - - + -
316A LEU* 3.5 31.4 - - + -
317A LEU* 4.1 13.9 - - + -
320A HIS* 3.4 54.5 - + + +
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Residues in contact with ILE 225 (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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221A LEU* 3.0 38.5 + - + +
222A LYS 3.2 3.8 + - - +
224A PHE* 1.3 85.3 - - + +
226A GLU* 1.3 60.1 + - + +
228A SER* 2.9 29.7 + - - -
233A ARG* 3.5 21.7 - - + +
236A LEU* 3.3 45.1 - - + +
237A SER* 4.0 6.7 - - - +
239A LEU* 4.3 7.6 - - + -
240A PHE* 3.8 37.9 - - + -
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Residues in contact with GLU 226 (chain A).
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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222A LYS* 2.9 51.2 + - + +
223A HIS* 4.0 6.3 - - - +
225A ILE* 1.3 77.2 - - + +
227A CYS* 1.3 61.2 + - - +
228A SER 3.4 2.6 + - - +
233A ARG* 4.1 24.3 + - - +
240A PHE* 4.7 11.1 - - + -
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Residues in contact with CYS 227 (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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223A HIS* 3.1 50.5 + - + +
224A PHE* 3.8 5.6 - - - +
225A ILE 3.1 0.4 - - - -
226A GLU* 1.3 77.9 - - - +
228A SER* 1.3 65.2 + - - +
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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