Contacts of the helix formed by residues 211 - 226 (chain A) in PDB entry 2P8Q
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 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A ASN* 5.0 6.3 + - - -
207A ALA* 3.8 18.4 - - - +
208A ASN 3.2 5.6 + - - +
209A PHE 3.1 2.4 - - - -
210A ASP* 1.3 82.4 - - + +
212A GLU* 1.3 54.6 + - - +
213A SER* 3.0 5.2 - - - +
214A GLU* 2.6 62.6 + - + +
215A ARG* 2.8 12.8 + - - -
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Residues in contact with GLU 212 (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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210A ASP 3.9 1.2 + - - -
211A LYS* 1.3 69.2 - - - +
213A SER* 1.3 57.9 + - - +
215A ARG* 3.6 34.9 + - - +
216A HIS* 2.8 41.8 + - + +
255A TYR* 5.5 1.3 - - - +
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Residues in contact with SER 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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211A LYS* 2.7 8.2 + - - -
212A GLU* 1.3 79.5 + - - +
214A GLU* 1.3 65.7 + - - +
216A HIS* 4.0 5.7 - - - +
217A PHE* 3.4 19.2 + - - +
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Residues in contact with GLU 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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171A ASN* 3.7 17.5 + - - +
208A ASN* 3.5 38.8 - - + +
211A LYS* 2.6 44.9 + - + +
213A SER* 1.3 77.5 - - - +
215A ARG* 1.3 65.8 + - - +
216A HIS 3.1 1.6 - - - -
217A PHE* 2.9 11.2 + - + +
218A ILE* 2.8 32.9 + - + +
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Residues in contact with ARG 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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208A ASN 3.9 3.8 + - - -
209A PHE* 3.0 53.7 + - + +
210A ASP 3.9 7.3 + - - -
211A LYS 2.8 12.9 + - - +
212A GLU* 3.6 37.9 - - - +
214A GLU* 1.3 72.9 - - - +
216A HIS* 1.3 62.7 + - - +
218A ILE* 3.2 7.6 + - - +
219A MET* 3.0 28.9 + - + +
251A TYR* 3.5 38.9 - - + +
254A THR* 5.1 11.7 - - - +
255A TYR* 3.2 30.9 + - + +
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Residues in contact with HIS 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 GLU* 2.8 26.7 + - + +
213A SER* 4.0 5.4 - - - +
215A ARG* 1.3 78.4 - - - +
217A PHE* 1.3 63.3 + - - +
219A MET* 3.6 1.4 + - - +
220A GLN* 3.3 43.3 + - + +
255A TYR* 3.4 24.2 + + - +
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Residues in contact with PHE 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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175A THR* 6.3 2.2 - - - -
178A ILE* 3.2 39.7 - - + -
179A GLN* 6.0 3.6 - - - -
213A SER 3.4 13.6 + - - +
214A GLU* 2.9 14.2 + - + +
216A HIS* 1.3 84.4 - - - +
218A ILE* 1.3 66.9 + - + +
220A GLN* 3.6 8.3 + - + +
221A VAL* 3.3 36.1 + - + +
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Residues in contact with ILE 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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174A LEU* 4.3 18.8 - - + -
178A ILE* 3.4 37.0 - - + -
181A MET* 6.0 0.7 - - + -
198A LEU* 4.6 14.6 - - + -
208A ASN* 5.9 2.2 - - + +
209A PHE* 4.1 31.4 - - + -
214A GLU* 2.8 24.3 + - + +
215A ARG* 3.6 7.6 - - - +
217A PHE* 1.3 82.7 - - + +
219A MET* 1.3 63.8 + - - +
221A VAL* 3.2 7.5 + - - +
222A VAL* 3.0 34.5 + - + +
244A ILE* 5.4 3.4 - - + -
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Residues in contact with MET 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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209A PHE* 4.3 12.3 - - + -
215A ARG* 3.0 24.4 + - + +
216A HIS 4.1 1.3 - - - +
218A ILE* 1.3 76.8 - - - +
220A GLN* 1.3 57.1 + - - +
222A VAL* 4.1 4.9 - - - +
223A CYS* 2.9 39.5 + - - -
241A LEU* 4.1 14.1 - - + -
244A ILE* 4.1 24.0 - - + -
252A MET* 4.1 17.7 - - - -
255A TYR* 3.7 57.7 - - + -
260A LEU* 4.1 17.3 - - + -
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Residues in contact with GLN 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 HIS* 3.3 37.2 + - + +
217A PHE* 3.9 9.6 - - - +
218A ILE 3.2 0.8 - - - -
219A MET* 1.3 78.3 - - - +
221A VAL* 1.3 62.2 + - + +
223A CYS* 4.0 3.4 - - - +
224A GLU* 2.9 59.9 + - + +
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Residues in contact with VAL 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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178A ILE* 3.7 25.1 - - + +
181A MET* 3.5 52.6 - - + +
182A ARG* 4.3 7.9 - - + +
217A PHE* 3.3 24.9 + - + +
218A ILE* 3.2 7.7 + - - +
220A GLN* 1.3 78.6 - - + +
222A VAL* 1.3 60.7 + - - +
224A GLU* 3.6 7.3 + - - +
225A ALA* 3.0 26.3 + - - +
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Residues in contact with VAL 222 (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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181A MET* 4.9 5.2 - - + -
195A THR* 6.3 1.1 - - + -
198A LEU* 3.5 31.9 - - + -
218A ILE* 3.0 22.5 + - + +
219A MET* 4.1 6.5 - - - +
221A VAL* 1.3 73.7 - - - +
223A CYS* 1.3 67.2 + - - +
225A ALA* 3.0 16.3 + - - +
226A THR* 3.1 13.0 + - - +
237A ALA* 3.6 26.7 - - + +
240A ASN* 4.1 9.9 - - + -
241A LEU* 3.7 25.8 - - + -
244A ILE* 5.8 5.2 - - + -
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Residues in contact with CYS 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 MET* 2.9 30.3 + - - +
220A GLN* 4.0 4.3 - - - +
222A VAL* 1.3 76.7 - - - +
224A GLU* 1.3 61.3 + - + +
226A THR* 2.6 32.0 + - - +
227A GLN* 3.8 5.5 + - - +
241A LEU* 4.5 10.3 - - - -
255A TYR* 6.1 1.1 - - - -
259A ALA* 4.3 15.9 - - + -
260A LEU* 3.9 28.7 - - - -
263A ILE* 4.7 10.1 - - + +
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Residues in contact with GLU 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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183A LYS* 3.6 49.5 + - + +
184A GLU* 5.3 0.2 - - - +
220A GLN* 2.9 53.9 + - + +
221A VAL* 3.9 6.5 + - - +
223A CYS* 1.3 76.9 - - + +
225A ALA* 1.3 57.3 + - - +
227A GLN* 2.8 32.5 + - - +
228A CYS* 3.6 3.1 + - - -
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Residues in contact with ALA 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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181A MET* 5.2 11.0 - - + +
195A THR* 4.8 9.2 - - + +
221A VAL* 3.0 17.0 + - + +
222A VAL* 3.0 14.6 + - - +
224A GLU* 1.3 72.4 - - - +
226A THR* 1.3 59.3 + - - +
227A GLN 2.9 6.6 + - - -
228A CYS* 3.0 24.3 + - - +
233A VAL* 3.9 17.1 - - + +
234A ARG* 3.9 5.2 - - - -
237A ALA* 3.6 15.3 - - + -
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Residues in contact with THR 226 (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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222A VAL 3.1 14.6 + - - +
223A CYS* 2.6 18.8 + - - +
225A ALA* 1.3 75.2 - - - +
227A GLN* 1.3 76.5 + - - +
234A ARG* 2.8 33.6 + - - +
237A ALA* 3.7 17.7 - - + -
238A LEU* 4.0 24.0 - - + -
241A LEU* 4.0 18.8 - - + -
263A ILE* 3.5 16.9 - - + +
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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