Contacts of the helix formed by residues 207 - 221 (chain A) in PDB entry 1F9E
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 THR 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A LYS* 6.2 1.1 - - + -
206A CYS* 1.3 75.7 - - - +
208A VAL* 1.3 67.2 + - - +
209A GLU* 3.4 11.3 - - - +
210A GLN* 2.8 46.2 + - - +
211A ILE* 2.8 23.3 + - - +
245A GLY* 4.3 0.4 - - - -
246A THR* 3.3 20.0 - - + +
247A ASP* 3.0 29.2 - - + +
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Residues in contact with VAL 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A THR* 1.3 72.7 - - - +
209A GLU* 1.3 66.6 + - - +
211A ILE* 3.0 11.1 + - - +
212A TYR* 3.0 53.2 + - + -
245A GLY* 3.7 9.7 - - - +
247A ASP* 3.0 6.2 + - - +
254A GLN* 2.9 53.6 - - + +
255A GLU 3.7 15.7 - - - +
256A ALA* 4.2 8.7 - - + +
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Residues in contact with GLU 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A THR* 3.4 10.1 + - - +
208A VAL* 1.3 80.9 - - - +
210A GLN* 1.3 64.9 + - + +
212A TYR* 3.3 11.7 + - - +
213A GLU* 3.0 42.3 + - - +
247A ASP* 5.5 1.5 + - - +
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Residues in contact with GLN 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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204A HIS 5.1 1.6 - - - +
205A ASP 4.2 5.9 + - - +
206A CYS* 3.9 16.3 - - + +
207A THR* 2.8 49.4 + - - +
209A GLU* 1.3 75.8 - - + +
211A ILE* 1.3 60.8 + - - +
213A GLU* 3.3 16.2 - - - +
214A ILE* 2.8 38.3 + - + +
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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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168A ILE* 3.8 31.0 - - + -
170A ASN* 4.4 8.1 - - - +
206A CYS* 3.7 20.0 - - + +
207A THR 2.8 27.0 + - - +
208A VAL* 3.0 12.3 + - + +
210A GLN* 1.3 68.7 - - - +
212A TYR* 1.3 69.0 + - + +
214A ILE* 2.9 11.3 + - - +
215A LEU* 2.9 40.8 + - + +
234A ILE* 5.2 4.9 - - + -
243A ILE* 4.5 20.0 - - + -
245A GLY* 4.7 2.9 - - - -
256A ALA* 5.6 2.7 - - + -
261A LEU* 4.3 18.4 - - + -
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Residues in contact with TYR 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 VAL* 3.0 44.1 + - + -
209A GLU* 3.6 13.0 - - - +
211A ILE* 1.3 77.1 - - + +
213A GLU* 1.3 57.1 + - - +
215A LEU* 3.2 7.0 + - + +
216A LYS* 2.8 30.9 + - - +
255A GLU 4.5 1.2 + - - -
256A ALA* 3.9 6.0 - - + -
257A PRO* 3.6 18.5 - - - +
260A GLU* 3.5 33.3 + - + +
261A LEU* 3.6 26.9 - - + -
264A GLN* 4.8 12.1 + - - +
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Residues in contact with GLU 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 GLU* 3.0 36.9 + - + +
210A GLN* 3.3 19.1 - - - +
212A TYR* 1.3 75.8 - - - +
214A ILE* 1.3 65.0 + - + +
216A LYS* 3.2 10.1 + - - +
217A ILE* 3.1 28.3 + - + +
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Residues in contact with ILE 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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166A LEU* 4.0 19.3 - - + -
168A ILE* 4.1 9.4 - - + -
203A HIS* 3.2 56.1 - - + +
206A CYS* 3.7 20.6 - - - -
210A GLN* 2.8 25.7 + - + +
211A ILE* 2.9 6.5 + - - +
213A GLU* 1.3 75.5 - - + +
215A LEU* 1.3 63.2 + - + +
217A ILE* 3.3 12.2 + - + +
218A TYR* 3.1 34.9 + - + -
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Residues in contact with LEU 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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166A LEU* 3.7 26.7 - - + -
168A ILE* 5.7 2.9 - - + -
211A ILE* 2.9 27.6 + - + +
212A TYR* 3.7 8.3 - - + +
214A ILE* 1.3 73.4 - - + +
216A LYS* 1.3 55.2 + - - +
218A TYR* 3.1 2.5 + - - +
219A GLN* 2.6 39.1 + - - +
232A CYS* 4.1 17.3 - - - -
234A ILE* 5.6 1.3 - - + -
261A LEU* 3.7 47.8 - - + +
264A GLN* 4.5 10.3 - - + +
265A PHE* 3.8 26.1 - - + -
280A PHE* 5.2 0.9 - - + -
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Residues in contact with LYS 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 TYR 2.8 14.2 + - - +
213A GLU* 3.2 14.1 + - - +
215A LEU* 1.3 76.9 - - - +
217A ILE* 1.3 64.0 + - + +
219A GLN* 3.1 36.3 + - - +
220A LEU* 3.0 52.3 + - + +
264A GLN* 4.5 8.6 - - - +
269A LYS* 4.8 8.7 - - - +
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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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203A HIS* 6.4 1.8 - - + -
213A GLU* 3.1 15.1 + - + +
214A ILE* 3.4 16.8 - - + +
216A LYS* 1.3 77.7 - - + +
218A TYR* 1.3 78.0 + - + +
220A LEU* 3.0 9.4 + - - +
221A MET* 3.0 36.7 + - + +
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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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164A TYR* 3.7 37.7 - + + -
166A LEU* 3.4 34.8 - - + -
201A LYS* 3.3 30.5 + - + +
203A HIS* 4.4 7.4 + + - -
214A ILE* 3.1 33.4 - - + -
215A LEU 3.1 5.4 + - - +
217A ILE* 1.3 89.8 - - + +
219A GLN* 1.3 66.6 + - - +
221A MET* 3.3 22.9 + - - -
224A HIS* 2.8 27.3 + + - +
230A PHE* 4.1 18.6 - + + -
265A PHE* 3.9 9.0 - - + -
270A CYS* 4.5 0.2 - - - -
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Residues in contact with GLN 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 LEU 2.6 22.5 + - - +
216A LYS* 3.1 39.7 + - - +
217A ILE 3.1 0.2 - - - -
218A TYR* 1.3 74.9 - - - +
220A LEU* 1.3 78.9 + - - +
221A MET 4.1 0.9 - - - +
264A GLN* 3.2 40.0 + - + +
265A PHE* 3.8 14.3 - - + -
269A LYS* 3.3 35.4 + - - +
270A CYS* 3.5 21.2 - - + +
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Residues in contact with LEU 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 LYS* 3.0 44.6 + - + +
217A ILE* 3.0 6.7 + - - +
219A GLN* 1.3 100.0 - - - +
221A MET* 1.3 65.6 + - - +
269A LYS 5.3 0.7 - - - +
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Residues in contact with MET 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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164A TYR* 3.3 44.2 - - + +
217A ILE* 3.0 27.5 + - + +
218A TYR* 3.3 30.9 + - - +
219A GLN 4.1 3.3 - - - +
220A LEU* 1.3 83.4 - - - +
222A ASP* 1.3 72.4 + - - +
224A HIS* 3.7 13.1 - - - +
272A SER* 3.3 12.8 + - - -
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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