Contacts of the helix formed by residues 221 - 235 (chain A) in PDB entry 2XAR
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 221 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A SER* 3.0 15.3 + - - -
220A GLY* 1.3 79.7 - - - +
222A LYS* 1.3 62.9 + - - +
223A GLU* 3.0 20.3 + - - -
224A ARG* 3.3 22.9 + - - +
225A VAL* 2.9 26.2 + - - +
296A TYR* 4.1 1.8 - - - -
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Residues in contact with LYS 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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221A SER* 1.3 73.3 + - - +
223A GLU* 1.3 64.0 + - + +
225A VAL* 3.4 4.3 + - - +
226A LEU* 3.3 21.8 + - - +
289A GLN* 3.9 11.1 - - - +
292A SER* 4.1 4.8 + - - +
293A ASP* 2.8 30.5 + - - -
296A TYR* 3.7 49.2 + - + +
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Residues in contact with GLU 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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221A SER* 3.0 17.8 + - - -
222A LYS* 1.3 77.9 + - + +
224A ARG* 1.3 62.7 + - + +
225A VAL 3.2 1.1 - - - -
226A LEU* 3.4 16.6 + - + +
227A GLU* 3.0 31.0 + - - +
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Residues in contact with ARG 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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213A ASP* 5.1 2.0 + - - -
215A LEU* 3.5 29.7 + - - +
216A ASP* 2.7 45.0 + - - +
219A SER* 3.3 34.6 - - - +
221A SER* 3.3 18.5 + - - +
223A GLU* 1.3 77.5 - - + +
225A VAL* 1.3 63.9 + - - +
227A GLU* 3.5 12.4 - - - +
228A ALA 3.1 15.9 + - - -
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Residues in contact with VAL 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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216A ASP 3.9 5.4 - - - +
217A LEU* 3.6 26.9 - - + +
219A SER* 4.7 1.8 - - - +
220A GLY* 4.9 2.7 - - - +
221A SER 2.9 25.2 + - - +
222A LYS* 3.6 7.0 - - - +
223A GLU 3.2 0.2 - - - -
224A ARG* 1.3 77.9 - - - +
226A LEU* 1.3 57.3 + - - +
228A ALA* 3.1 7.6 + - - +
229A ILE* 3.0 26.5 + - + +
292A SER* 3.7 22.2 - - - +
295A VAL* 3.7 29.4 - - + -
296A TYR* 4.5 15.7 - - + +
301A LEU* 5.7 0.2 - - + -
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Residues in contact with LEU 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 LYS 3.3 8.9 + - - +
223A GLU* 3.6 17.5 - - + +
224A ARG 3.3 0.2 - - - -
225A VAL* 1.3 78.5 - - - +
227A GLU* 1.3 56.2 + - - +
229A ILE* 3.2 1.7 + - + +
230A LYS* 2.9 69.5 + - + +
285A GLU 5.8 0.7 - - - +
288A LEU* 4.4 6.1 - - + +
289A GLN* 4.1 37.2 - - + +
292A SER* 3.3 29.3 + - - +
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Residues in contact with GLU 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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216A ASP* 5.0 14.8 - - - +
223A GLU* 3.0 19.7 + - - +
224A ARG* 3.5 17.0 - - - +
226A LEU* 1.3 76.9 - - - +
228A ALA* 1.3 56.3 + - - +
230A LYS* 3.5 9.7 + - - +
231A ALA* 2.9 29.4 + - + +
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Residues in contact with ALA 228 (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* 4.2 11.8 - - + -
213A ASP 4.8 1.1 - - - +
216A ASP* 4.0 6.8 - - + +
217A LEU* 3.7 37.0 - - + +
224A ARG 3.1 10.3 + - - +
225A VAL 3.1 10.0 + - - +
227A GLU* 1.3 76.6 - - - +
229A ILE* 1.3 59.2 + - - +
231A ALA* 3.1 8.2 + - - +
232A LEU* 2.8 35.2 + - - +
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Residues in contact with ILE 229 (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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167A ILE* 4.2 10.3 - - + -
217A LEU* 3.8 23.6 - - + -
225A VAL* 3.0 15.6 + - + +
226A LEU* 3.8 5.6 - - + +
228A ALA* 1.3 74.4 - - - +
230A LYS* 1.3 60.9 + - - +
232A LEU* 3.3 14.7 + - + +
233A TYR* 3.0 23.0 + - - +
240A PHE* 4.3 9.5 - - + -
288A LEU* 3.8 37.2 - - + +
291A VAL* 4.0 25.8 - - + -
292A SER* 4.0 20.4 - - - -
295A VAL* 4.4 5.2 - - + -
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Residues in contact with LYS 230 (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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226A LEU* 2.9 56.4 + - + +
227A GLU* 3.6 8.0 - - - +
229A ILE* 1.3 77.2 - - - +
231A ALA* 1.3 62.4 + - - +
233A TYR* 3.3 9.9 + - - +
234A SER* 3.1 25.4 + - - -
285A GLU* 6.4 1.8 - - - -
288A LEU* 4.5 18.6 - - + -
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Residues in contact with ALA 231 (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 GLU* 3.6 43.3 - - + +
212A TYR* 3.7 8.5 - - - -
213A ASP 5.2 0.2 - - - +
227A GLU 2.9 16.7 + - - +
228A ALA* 3.3 10.8 - - - +
230A LYS* 1.3 73.4 - - - +
232A LEU* 1.3 64.9 + - - +
234A SER* 3.0 4.9 + - - -
235A THR* 3.0 27.2 + - - -
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Residues in contact with LEU 232 (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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167A ILE* 4.3 13.7 - - + -
212A TYR* 3.7 35.0 - - + +
217A LEU* 4.7 2.9 - - + -
228A ALA 2.8 29.9 + - - +
229A ILE* 3.5 20.4 - - + +
231A ALA* 1.3 71.9 - - - +
233A TYR* 1.3 62.0 + - - +
235A THR 4.5 4.0 - - - +
236A PRO* 3.0 31.4 - - - +
239A ASN* 3.7 41.7 - - + +
240A PHE* 3.3 24.7 - - + +
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Residues in contact with TYR 233 (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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229A ILE 3.0 13.4 + - - +
230A LYS* 3.5 9.4 - - - +
232A LEU* 1.3 78.6 - - - +
234A SER* 1.3 63.5 + - - +
236A PRO* 3.4 4.9 - - - +
240A PHE* 4.5 11.3 - - + -
250A LEU* 3.7 21.0 - - + +
260A THR* 2.7 48.3 + - + +
265A GLY* 3.5 25.1 + - - -
268A PHE* 4.1 16.2 - + - -
284A THR* 3.9 26.7 - - + +
287A PHE* 6.3 0.2 - + - -
288A LEU* 3.8 30.5 - - + -
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Residues in contact with SER 234 (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 GLU* 3.5 23.5 + - - -
230A LYS 3.1 12.4 + - - -
231A ALA 3.0 9.0 + - - -
233A TYR* 1.3 86.6 - - - +
235A THR* 1.3 59.4 + - - +
236A PRO* 3.5 0.2 - - - +
259A ARG* 3.5 18.2 - - - +
260A THR* 2.7 34.5 + - - -
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Residues in contact with THR 235 (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 GLU* 4.8 6.7 - - + +
209A GLU 4.3 3.1 - - - +
210A SER* 3.0 24.7 + - - -
211A GLU* 2.8 31.5 + - - +
212A TYR* 5.2 0.7 - - - +
231A ALA 3.0 10.6 + - - +
232A LEU* 3.3 7.9 - - - +
234A SER* 1.3 83.2 - - - +
236A PRO* 1.4 65.1 - - - +
237A GLN* 3.3 10.8 + - - +
239A ASN* 5.1 1.6 - - - +
257A THR 5.8 0.2 - - - -
258A GLY 5.5 0.2 - - - -
259A ARG* 3.6 41.7 - - + +
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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
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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