Contacts of the helix formed by residues 219 - 235 (chain A) in PDB entry 2I91
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 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A GLU* 6.3 0.2 - - - +
220A PRO* 1.3 74.2 - - - +
221A GLU* 3.2 8.2 + - - +
222A THR* 3.5 24.6 + - - -
223A GLU* 2.9 32.9 + - - +
274B GLN* 4.0 7.6 - - - +
275B ASP* 3.0 22.7 + - - -
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Residues in contact with PRO 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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219A SER* 1.3 90.6 - - - +
221A GLU* 1.3 61.8 + - + +
223A GLU* 3.6 7.8 + - + +
224A LYS* 3.3 24.9 + - - +
249B ASP* 4.0 42.5 - - + +
274B GLN* 3.4 37.2 - - + +
275B ASP* 4.7 4.5 - - + +
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Residues in contact with GLU 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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160A ASP* 6.2 0.3 - - - +
161A ALA* 5.5 2.1 - - - +
162A LEU* 4.6 17.9 + - - +
219A SER* 3.2 3.2 + - - +
220A PRO* 1.3 80.1 - - + +
222A THR* 1.3 65.1 + - - +
224A LYS* 3.3 32.7 + - - +
225A VAL* 3.5 12.3 + - - +
252B ARG* 3.1 46.2 + - + +
275B ASP* 2.5 32.5 - - - +
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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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193A GLU* 3.9 33.5 - - + +
194A GLY* 4.4 15.6 + - - -
197A MET* 3.5 27.4 - - + +
213A TYR* 5.0 1.3 - - + -
219A SER* 3.2 27.6 + - - -
221A GLU* 1.3 76.1 - - - +
223A GLU* 1.3 66.8 + - - +
224A LYS 3.1 0.2 - - - -
225A VAL* 3.0 16.7 + - - +
226A LEU 3.1 10.0 + - - -
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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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197A MET* 5.6 0.6 - - - +
219A SER 2.9 18.8 + - - +
220A PRO* 3.7 8.7 - - + +
222A THR* 1.3 75.5 - - - +
224A LYS* 1.3 55.1 + - - +
226A LEU* 3.0 30.5 + - - +
227A LYS* 2.8 51.9 + - + +
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Residues in contact with LYS 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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162A LEU* 4.0 26.6 - - + +
220A PRO 3.3 15.7 + - - +
221A GLU* 3.3 27.4 + - - +
223A GLU* 1.3 79.7 - - - +
225A VAL* 1.3 60.8 + - + +
227A LYS* 3.4 10.6 - - + +
228A TYR* 3.2 22.9 + - - +
251A TYR* 5.5 1.6 - - + -
249B ASP 5.8 2.9 + - - +
250B GLU* 4.1 19.6 + - - +
251B TYR* 5.8 1.4 - - - +
252B ARG* 5.8 4.8 - - - +
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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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161A ALA* 3.4 29.8 - - + +
162A LEU* 3.5 23.1 - - + +
165A ALA* 4.5 4.3 - - + -
194A GLY* 4.1 6.3 - - - +
197A MET* 4.0 13.5 - - - -
198A VAL* 3.6 30.7 - - + -
221A GLU* 3.6 15.7 - - - +
222A THR* 3.0 11.8 + - - +
224A LYS* 1.3 75.2 - - - +
226A LEU* 1.3 64.8 + - - +
228A TYR* 3.5 3.1 + - - +
229A LEU* 3.1 24.9 + - + +
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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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197A MET* 3.6 31.6 - - + -
206A TRP* 3.5 33.4 - - + -
209A VAL* 4.5 8.3 - - + +
210A GLN* 5.4 3.1 - - + -
213A TYR* 4.8 23.3 - - + +
222A THR 3.1 5.2 + - - +
223A GLU* 3.0 29.2 + - - +
225A VAL* 1.3 73.4 - - - +
227A LYS* 1.3 68.6 + - - +
229A LEU* 3.0 4.8 + - - +
230A GLU* 2.8 24.4 + - + +
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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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223A GLU* 2.8 34.0 + - + +
224A LYS* 3.4 14.6 - - + +
226A LEU* 1.3 73.1 - - - +
228A TYR* 1.3 52.6 - - - +
230A GLU* 3.1 26.0 + - - +
231A ALA* 2.8 32.2 + - - +
250A GLU* 5.4 1.4 + - - -
251A TYR* 3.6 32.0 + - + +
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Residues in contact with TYR 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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162A LEU* 4.1 17.3 - - + -
165A ALA* 3.6 22.4 - - + -
166A MET* 3.1 54.6 - - + +
169A THR* 3.7 8.3 - - + -
224A LYS 3.2 13.8 + - - +
225A VAL 3.6 4.0 - - - +
227A LYS* 1.3 77.3 - - - +
229A LEU* 1.3 72.1 + - + +
231A ALA* 2.8 18.4 + - - +
232A THR* 2.8 18.4 + - + -
251A TYR* 3.5 45.2 + + + -
252A ARG 5.1 2.1 + - - -
253A LEU* 3.8 13.1 - - + +
257A HIS* 3.4 19.4 + - - -
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Residues in contact with LEU 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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165A ALA* 4.7 17.0 - - + -
168A VAL* 5.4 0.9 - - + -
169A THR* 4.3 11.7 - - + -
197A MET* 4.1 27.6 - - + +
198A VAL* 4.5 5.4 - - + -
201A TYR* 3.4 56.4 - - + -
206A TRP* 3.7 17.5 - - + -
209A VAL* 5.2 0.2 - - + -
225A VAL* 3.1 20.4 + - + +
226A LEU 3.0 7.3 + - - +
228A TYR* 1.3 78.9 - - - +
230A GLU* 1.3 61.9 + - - +
232A THR* 2.5 20.4 + - - -
233A GLU* 3.0 14.7 + - - +
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Residues in contact with GLU 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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206A TRP* 3.4 29.9 - - + +
210A GLN* 5.4 2.6 - - - +
226A LEU* 2.8 14.1 + - + +
227A LYS* 3.1 31.1 + - - +
229A LEU* 1.3 77.7 - - - +
231A ALA* 1.3 57.0 + - - +
233A GLU* 3.1 3.1 + - - +
234A ARG* 2.8 36.4 + - + +
251A TYR* 5.4 0.5 + - - -
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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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227A LYS 2.8 8.9 + - - +
228A TYR* 2.8 14.3 + - - +
230A GLU* 1.3 72.4 + - - +
232A THR* 1.3 60.3 + - - +
234A ARG* 3.0 15.6 + - - +
235A VAL* 2.8 23.7 + - - +
247A LEU* 4.0 9.3 - - + +
251A TYR* 3.3 46.4 - - + -
253A LEU* 4.5 5.2 - - + -
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Residues in contact with THR 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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169A THR* 3.9 22.0 - - - +
201A TYR* 4.4 6.9 + - - -
228A TYR* 2.8 19.3 + - + +
229A LEU* 2.5 30.7 + - - -
231A ALA* 1.3 71.7 - - - +
233A GLU* 1.3 61.5 + - - +
235A VAL* 3.4 17.4 - - - +
236A LYS* 3.6 19.5 - - - +
253A LEU* 3.6 16.4 - - + -
257A HIS* 3.6 34.0 - - + +
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Residues in contact with GLU 233 (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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172A LYS* 5.1 3.3 + - - -
201A TYR* 2.7 31.5 + - + -
206A TRP* 3.3 51.9 - - + +
207A LYS* 5.6 2.4 + - - -
229A LEU 3.0 12.2 + - - +
230A GLU 3.6 7.0 - - - +
232A THR* 1.3 77.4 - - - +
234A ARG* 1.3 64.3 + - - +
236A LYS* 3.1 25.8 + - - +
237A ARG* 3.6 33.5 + - + +
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Residues in contact with ARG 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 GLU* 2.8 19.7 + - + +
231A ALA* 3.0 11.2 + - - +
233A GLU* 1.3 73.0 - - - +
235A VAL* 1.3 57.4 + - - +
236A LYS 2.9 10.5 + - - -
237A ARG* 3.1 21.8 + - - +
238A THR* 3.2 19.5 + - - +
243A GLU* 3.3 33.0 + - - +
247A LEU* 3.8 14.6 - - + -
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Residues in contact with VAL 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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231A ALA 2.8 19.8 + - - +
232A THR* 3.4 13.9 - - - +
234A ARG* 1.3 72.4 - - - +
236A LYS* 1.3 57.1 + - - +
237A ARG 3.6 0.2 - - - -
238A THR* 4.0 14.3 - - - +
244A ILE* 4.4 14.4 - - + +
247A LEU* 4.1 12.3 - - + -
253A LEU* 3.4 25.6 - - + -
257A HIS* 3.6 21.5 - - + +
258A LEU* 3.7 24.9 - - + -
259A LEU* 4.5 0.9 - - - +
262A HIS* 3.9 18.9 - - - -
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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