Contacts of the helix formed by residues 228 - 242 (chain A) in PDB entry 1QAN
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 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A THR* 4.2 2.5 - - - -
227A ILE* 1.3 76.6 - - - +
229A PHE* 1.3 66.3 + - - +
230A GLU* 3.6 9.5 + - - +
231A GLN* 2.6 42.5 + - - +
232A PHE* 3.0 19.9 + - - +
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Residues in contact with PHE 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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138A THR* 3.9 9.0 - - - +
144A LEU* 3.5 30.7 - - + -
147A MET* 3.2 70.2 - - + -
148A ALA* 3.5 9.6 - - - -
179A LYS* 4.8 5.4 - - - -
182A ARG* 4.4 9.0 - - + -
191A TYR* 3.6 15.7 - - - -
228A SER* 1.3 73.8 - - - +
230A GLU* 1.3 58.8 + - + +
232A PHE* 3.0 11.3 + + - +
233A LEU* 2.9 55.7 + - + +
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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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182A ARG* 2.6 43.8 + - - -
228A SER* 3.1 8.8 + - - +
229A PHE* 1.3 81.2 - - + +
231A GLN* 1.3 62.7 + - + +
233A LEU* 3.3 8.6 + - - +
234A SER* 3.1 21.0 + - - -
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Residues in contact with GLN 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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219A ALA* 3.9 15.5 - - - +
220A GLY 3.3 22.7 - - - +
221A ILE* 3.8 26.3 - - + +
222A ASP* 5.4 1.6 - - - +
226A ASN 4.0 5.9 + - - +
227A ILE* 3.1 12.8 - - + +
228A SER* 2.6 45.9 + - - +
230A GLU* 1.3 77.8 - - + +
232A PHE* 1.3 61.9 + - - +
234A SER* 3.2 9.8 - - - -
235A LEU* 3.1 25.4 + - - +
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Residues in contact with PHE 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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144A LEU* 3.6 41.3 - - + -
191A TYR* 3.7 36.6 - + - -
194A PHE* 3.6 34.5 - + - -
195A VAL* 3.8 12.1 - - + -
198A TRP* 3.7 26.0 - + + -
227A ILE* 4.1 16.3 - - + +
228A SER 3.0 10.7 + - - +
229A PHE* 3.0 17.4 + + - +
231A GLN* 1.3 75.8 - - - +
233A LEU* 1.3 67.8 + - + +
235A LEU* 3.0 13.4 + - + +
236A PHE* 2.9 19.3 + - + +
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Residues in contact with LEU 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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182A ARG* 3.3 56.8 - - + +
183A ILE* 4.0 26.5 - - + -
191A TYR* 4.5 7.2 - - + -
229A PHE* 2.9 46.4 + - + +
230A GLU* 3.3 12.3 + - - +
232A PHE* 1.3 76.5 - - + +
234A SER* 1.3 63.9 + - - +
236A PHE* 3.3 8.0 + - + +
237A ASN* 2.9 24.0 + - - +
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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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215A SER 4.9 0.4 + - - -
218A HIS* 4.0 16.3 + - - -
219A ALA* 3.4 27.2 - - - +
230A GLU 3.1 12.4 + - - -
231A GLN* 3.2 12.3 - - - -
233A LEU* 1.3 77.6 - - - +
235A LEU* 1.3 64.5 + - - +
237A ASN* 2.9 8.4 + - - +
238A SER* 2.9 26.0 + - - -
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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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194A PHE* 3.8 14.4 - - + -
198A TRP* 3.4 43.3 - - + -
207A PHE* 3.8 6.4 - - + -
215A SER* 3.8 37.9 - - - +
216A LEU* 4.0 13.5 - - + -
219A ALA* 4.3 1.1 - - + -
221A ILE* 3.8 19.1 - - + -
227A ILE* 4.3 1.8 - - + -
231A GLN 3.1 11.0 + - - +
232A PHE* 3.0 16.0 + - + +
234A SER* 1.3 79.6 - - - +
236A PHE* 1.3 57.3 + - - +
238A SER* 3.2 7.2 + - - -
239A TYR* 2.9 29.1 + - - +
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Residues in contact with PHE 236 (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 ILE* 3.8 22.2 - - + -
187A ASP* 4.0 20.0 - - + -
190A LYS* 3.5 18.6 - - + -
191A TYR* 3.3 52.5 - + + -
194A PHE* 3.6 34.7 - + + -
232A PHE* 2.9 12.5 + - + +
233A LEU* 3.7 11.9 - - + +
235A LEU* 1.3 75.8 - - - +
237A ASN* 1.3 64.4 + - - +
239A TYR* 3.4 4.7 - + - +
240A LYS* 3.1 46.9 + - + +
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Residues in contact with ASN 237 (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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233A LEU 2.9 13.1 + - - +
234A SER* 3.2 12.6 - - - +
236A PHE* 1.3 78.0 - - - +
238A SER* 1.3 65.4 + - - +
240A LYS* 3.1 26.7 + - - +
241A LEU* 3.0 22.5 + - - +
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Residues in contact with SER 238 (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* 3.6 31.3 + - - -
218A HIS* 3.9 21.8 - - - +
234A SER* 2.9 13.8 + - - -
235A LEU* 3.7 6.5 - - - -
237A ASN* 1.3 75.8 - - - +
239A TYR* 1.3 57.1 + - - +
241A LEU* 3.1 11.8 + - - +
242A PHE* 2.9 43.7 + - - -
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Residues in contact with TYR 239 (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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190A LYS* 3.6 38.2 + - + +
193A TYR* 3.6 23.9 - + - -
194A PHE* 3.5 33.2 - + + -
205A LYS 5.2 0.6 + - - -
206A ILE* 3.4 43.7 - - + +
207A PHE* 4.0 9.3 - + + -
235A LEU 2.9 17.7 + - - +
236A PHE* 3.4 14.6 - + - +
238A SER* 1.3 79.1 - - - +
240A LYS* 1.3 62.3 + - - +
242A PHE* 3.4 4.7 + - - +
243A ASN* 3.3 42.7 + - + +
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Residues in contact with LYS 240 (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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187A ASP* 3.0 38.2 + - - +
190A LYS* 3.9 23.3 - - + -
236A PHE* 3.1 28.8 + - + +
237A ASN* 3.1 28.8 + - - +
239A TYR* 1.3 82.4 - - + +
241A LEU* 1.3 58.0 + - - +
243A ASN* 2.8 21.3 + - - -
244A LYS* 3.0 38.6 + - + +
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Residues in contact with LEU 241 (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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237A ASN* 3.0 14.3 + - - +
238A SER* 3.1 13.7 + - - +
240A LYS* 1.3 76.1 - - - +
242A PHE* 1.3 72.8 + - + +
243A ASN 3.2 1.6 + - - -
244A LYS* 3.8 17.1 + - + +
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Residues in contact with PHE 242 (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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207A PHE* 4.2 7.2 - + - -
211A GLN* 3.7 59.4 - - + +
214A ASN* 4.8 12.3 - - + -
215A SER* 3.5 22.7 - - - -
238A SER* 2.9 32.1 + - - +
239A TYR* 3.8 5.8 - - + +
240A LYS 3.1 0.2 - - - -
241A LEU* 1.3 85.9 - - + +
243A ASN* 1.3 74.9 + - - +
244A LYS 4.0 0.2 - - - -
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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