Contacts of the helix formed by residues 221 - 235 (chain A) in PDB entry 2Y4U
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 ASN 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A LYS* 5.7 0.4 - - - +
215A SER 5.5 0.6 + - - +
218A LYS* 3.6 42.3 + - + +
219A ASN 3.7 1.4 - - - -
220A ASP* 1.3 77.5 + - - +
222A THR* 1.3 68.1 + - - +
223A GLU* 2.8 19.7 + - - +
224A ALA* 2.7 46.1 + - + +
225A PHE* 3.3 17.3 - - - -
251A LEU* 4.1 1.5 - - - +
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Residues in contact with THR 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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220A ASP 3.3 7.1 + - - -
221A ASN* 1.3 74.2 + - - +
223A GLU* 1.3 79.4 + - + +
224A ALA 3.1 1.7 + - - -
225A PHE* 3.1 12.4 + - - +
226A TYR* 3.5 8.0 + - - +
248A CYS* 3.5 17.3 + - - -
251A LEU* 4.5 11.2 - - - -
252A ASP* 4.6 12.8 - - - +
255A HIS* 2.7 40.1 + - + +
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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 ASN* 2.8 11.8 + - - +
222A THR* 1.3 81.4 - - + +
224A ALA* 1.3 57.3 + - - +
225A PHE 3.3 0.2 - - - -
226A TYR* 3.6 22.5 - - - +
227A LYS* 3.0 43.4 + - + +
255A HIS* 4.9 2.0 + - + -
257A ARG* 2.2 36.3 + - - -
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Residues in contact with ALA 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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192A GLU* 5.0 5.2 - - - +
211A LEU* 5.0 1.9 - - - +
214A ALA* 4.9 1.8 - - + -
215A SER* 4.0 27.6 - - - +
218A LYS* 4.6 11.2 - - - +
221A ASN* 2.7 34.5 + - + +
222A THR 3.1 0.4 + - - -
223A GLU* 1.3 74.2 - - - +
225A PHE* 1.3 62.3 + - - +
227A LYS* 3.3 16.2 + - - +
228A ILE* 3.3 15.8 + - - +
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Residues in contact with PHE 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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215A SER* 3.9 34.8 - - - -
216A LYS* 5.6 1.6 - - - -
219A ASN* 3.9 24.0 - - - -
221A ASN 3.3 21.5 - - - -
222A THR 3.1 7.4 + - - +
224A ALA* 1.3 75.8 - - + +
226A TYR* 1.3 69.5 + - - +
228A ILE* 3.3 6.6 - - + +
229A SER* 2.9 23.9 + - - -
244A GLU* 3.5 31.4 - - - +
245A VAL* 5.8 0.2 - - - -
247A GLU* 3.6 33.4 - - + -
248A CYS* 3.9 17.9 - - + -
251A LEU* 4.0 16.8 - - + -
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Residues in contact with TYR 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 THR 3.5 5.7 + - - +
223A GLU* 3.6 32.5 - - - +
225A PHE* 1.3 78.2 - - - +
227A LYS* 1.3 70.0 + - + +
229A SER* 4.5 4.0 - - - -
230A THR* 2.7 47.9 + - + -
245A VAL* 5.5 0.9 - - + -
248A CYS* 4.6 3.7 - - - +
255A HIS* 5.8 0.2 - - + -
257A ARG* 3.6 57.1 + - + +
258A CYS* 4.1 23.3 - - - -
261A HIS* 4.1 19.9 - + + +
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Residues in contact with LYS 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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196A GLU* 4.6 14.9 + - - -
199A ILE* 4.8 9.9 - - - +
211A LEU* 4.5 26.0 - - + +
223A GLU* 3.0 35.1 + - + +
224A ALA* 3.4 13.2 - - - +
225A PHE 3.2 0.6 - - - -
226A TYR* 1.3 82.1 - - + +
228A ILE* 1.3 62.4 + - - +
230A THR* 3.4 14.5 - - + +
231A LEU* 3.2 19.0 + - - +
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Residues in contact with ILE 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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208A ILE* 3.9 10.3 - - + +
211A LEU* 3.9 22.4 - - + +
212A LYS* 3.4 37.5 - - + +
215A SER* 4.6 7.9 - - - +
224A ALA 3.5 10.3 - - - +
225A PHE* 3.3 15.0 - - - +
226A TYR 2.8 2.6 + - - -
227A LYS* 1.3 74.4 - - - +
229A SER* 1.3 59.5 + - - +
231A LEU* 2.6 29.0 + - + +
232A TYR* 2.8 49.9 + - + +
244A GLU* 4.7 12.8 - - + +
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Residues in contact with SER 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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225A PHE 2.9 22.7 + - - -
226A TYR* 3.6 2.9 - - - -
228A ILE* 1.3 73.2 - - - +
230A THR* 1.3 63.8 + - - +
232A TYR* 3.3 1.9 + - - -
233A TYR* 2.9 21.5 + - - +
241A SER* 2.8 45.8 + - - +
244A GLU* 3.8 14.5 - - - +
245A VAL* 3.5 8.9 - - - +
261A HIS* 3.0 18.0 + - - -
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Residues in contact with THR 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 TYR* 2.7 52.2 + - + -
227A LYS* 3.4 15.5 - - + +
229A SER* 1.3 73.5 - - - +
231A LEU* 1.3 56.9 + - - +
233A TYR* 3.2 8.7 - - - +
234A GLN* 3.0 52.4 + - - +
261A HIS* 4.3 8.3 + - - -
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Residues in contact with LEU 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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199A ILE* 4.6 9.6 - - + -
204A PRO* 3.5 42.8 - - + +
207A ALA* 4.0 9.0 - - + -
208A ILE* 3.8 32.5 - - + +
211A LEU* 4.3 11.0 - - + -
227A LYS* 3.2 10.3 + - - +
228A ILE* 2.6 17.5 + - + +
230A THR* 1.3 71.8 - - - +
232A TYR* 1.3 67.5 + - - +
233A TYR 3.0 1.6 - - - -
234A GLN* 2.8 29.1 + - + +
235A LEU* 3.0 17.9 + - + +
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Residues in contact with TYR 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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208A ILE* 3.7 36.4 - - + +
212A LYS* 3.7 21.8 - - - +
228A ILE* 2.8 44.6 + - + +
229A SER 3.7 5.2 - - - +
231A LEU* 1.3 72.0 - - - +
233A TYR* 1.3 53.8 + - - +
235A LEU* 3.0 6.8 + - - +
236A GLY 2.9 8.5 + - - -
237A ASP* 2.8 62.3 + - + +
240A LEU* 3.8 37.4 - - + +
241A SER* 3.7 9.4 - - - -
244A GLU* 3.9 22.8 + - + -
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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 SER 2.9 13.5 + - - +
230A THR 3.2 11.7 - - - +
232A TYR* 1.3 77.2 - - - +
234A GLN* 1.3 55.7 + - + +
236A GLY 2.7 11.3 + - - -
237A ASP 4.7 1.1 - - - -
238A HIS* 5.4 2.0 - - + -
241A SER* 3.6 8.6 - - - +
261A HIS* 3.6 13.0 - + + -
264A GLN* 2.8 41.7 + - + +
265A VAL* 3.2 35.2 - - + -
268A LEU* 3.6 11.2 - - + +
298A GLU* 3.0 24.3 + - + +
301A ILE* 3.6 25.4 - - + -
304A TYR* 2.7 39.2 + + - -
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Residues in contact with GLN 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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230A THR* 3.0 39.2 + - - +
231A LEU* 2.8 26.0 + - + +
233A TYR* 1.3 72.9 - - - +
235A LEU* 1.3 71.8 + - + +
236A GLY 3.1 0.4 + - - -
301A ILE* 3.6 40.0 - - + +
303A GLU* 4.5 4.2 - - - +
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Residues in contact with LEU 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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204A PRO* 3.6 34.1 - - + +
205A ARG* 3.5 67.1 + - + +
208A ILE* 4.0 14.4 - - + -
231A LEU* 3.0 18.7 + - + +
232A TYR 3.0 8.9 + - - +
234A GLN* 1.3 85.1 - - + +
236A GLY* 1.3 59.6 + - - +
237A ASP* 3.1 6.5 + - - +
303A GLU* 3.9 17.6 - - - +
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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