Contacts of the helix formed by residues 228 - 239 (chain A) in PDB entry 3QPV
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 ASP 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ASN* 4.6 5.2 + - - +
33A SER 5.3 0.3 - - - +
35A THR* 4.6 1.6 + - - -
146A LYS* 2.9 35.1 + - - +
226A VAL* 3.7 3.0 - - - +
227A GLN* 1.3 83.7 - - - +
229A HIS* 1.3 66.3 + - - +
230A ILE* 4.0 16.1 - - - +
231A GLN* 2.9 34.7 + - - +
232A SER* 3.1 22.1 + - - -
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Residues in contact with HIS 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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228A ASP* 1.3 74.2 - - - +
230A ILE* 1.3 75.3 + - + +
232A SER* 3.0 25.1 + - - -
233A ARG* 3.1 53.8 + - + +
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Residues in contact with ILE 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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35A THR* 4.5 9.6 - - + +
58A LEU* 4.0 27.8 - - + -
61A ILE* 4.5 6.1 - - + -
63A VAL* 4.0 22.7 - - + -
119A GLN* 5.6 7.4 - - + +
120A ILE* 4.0 27.1 - - + -
228A ASP* 3.3 15.9 + - - +
229A HIS* 1.3 89.8 - - + +
231A GLN* 1.3 64.9 + - + +
233A ARG* 3.6 18.6 + - + +
234A ILE* 3.2 30.9 + - + +
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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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35A THR* 4.9 6.5 + - + +
146A LYS* 4.6 8.3 - - - +
147A ALA 4.7 0.6 + - - -
148A PHE* 3.3 49.0 - - + +
210A SER* 3.3 5.9 - - - -
226A VAL* 3.4 15.3 - - + -
227A GLN* 3.2 50.0 + - - +
228A ASP* 2.9 26.9 + - - +
230A ILE* 1.3 79.1 - - + +
232A SER* 1.3 62.9 + - - +
234A ILE* 3.3 10.0 + - + +
235A VAL* 3.0 28.1 + - - +
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Residues in contact with SER 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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226A VAL* 3.7 20.2 - - - -
228A ASP 3.1 9.7 + - - -
229A HIS* 3.0 17.0 + - - -
231A GLN* 1.3 75.4 - - - +
233A ARG* 1.3 67.7 + - - +
235A VAL* 3.3 6.9 + - - +
236A TYR* 2.9 23.4 + - - +
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Residues in contact with ARG 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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57A TYR* 3.3 21.1 + - + +
58A LEU* 5.9 0.2 - - + -
61A ILE* 4.0 21.6 - - - +
229A HIS* 3.2 52.8 + - + +
230A ILE* 3.7 19.9 - - + +
232A SER* 1.3 79.2 + - - +
234A ILE* 1.3 63.3 + - - +
236A TYR* 2.9 20.0 + - - +
237A TYR* 2.8 24.8 + - - +
370A GLU* 3.3 34.1 + - - +
374A MET* 5.0 1.2 - - - +
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Residues in contact with ILE 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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35A THR* 6.2 1.3 - - + -
37A ILE* 3.6 24.2 - - + -
54A LEU* 3.9 30.5 - - + -
57A TYR* 5.8 1.1 - - - -
58A LEU* 4.4 15.3 - - + -
120A ILE* 4.8 5.2 - - + -
148A PHE* 4.0 21.5 - - + -
150A ILE* 4.1 1.1 - - + -
230A ILE* 3.2 33.6 + - + +
231A GLN* 3.3 11.4 + - + +
233A ARG* 1.3 74.5 - - - +
235A VAL* 1.3 53.0 + - - +
237A TYR* 3.2 7.8 + - - +
238A LEU* 2.7 58.3 + - + +
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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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148A PHE* 4.0 22.4 - - + -
212A ILE* 3.9 17.5 - - + -
223A VAL* 4.0 26.9 - - + -
226A VAL* 4.7 5.8 - - + -
231A GLN 3.0 18.2 - - - +
232A SER* 3.6 9.2 - - - +
233A ARG 3.1 0.6 - - - -
234A ILE* 1.3 77.9 - - - +
236A TYR* 1.3 58.4 + - - +
238A LEU* 3.2 5.9 + - - -
239A MET* 2.6 55.0 + - - +
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Residues in contact with TYR 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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232A SER 2.9 14.3 + - - +
233A ARG* 3.2 19.7 - - - +
235A VAL* 1.3 80.3 - - - +
237A TYR* 1.3 59.4 + - - +
239A MET* 3.2 16.0 + - + +
240A ASN* 2.6 50.3 + - - -
370A GLU* 4.9 5.4 - - - -
374A MET* 3.4 38.1 - - + +
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Residues in contact with TYR 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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53A LYS* 3.3 25.5 + - + +
54A LEU* 3.9 29.8 - - + -
57A TYR* 3.3 53.2 - + + +
233A ARG 2.8 15.3 + - - +
234A ILE* 3.3 10.8 - - - +
236A TYR* 1.3 73.9 - - - +
238A LEU* 1.3 63.9 + - + +
240A ASN* 2.8 21.1 + - - +
241A ILE* 3.3 40.5 + - + +
373A ILE* 5.3 0.4 - - + -
374A MET* 3.7 25.5 - - + +
377A GLU* 4.2 6.7 - - + -
397A TYR* 2.8 24.2 + + - -
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Residues in contact with LEU 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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50A ILE* 3.9 26.5 - - + -
54A LEU* 4.6 7.2 - - + -
150A ILE* 3.8 34.8 - - + -
212A ILE* 4.2 25.6 - - + -
214A VAL* 4.8 7.2 - - + +
221A PHE* 3.9 14.0 - - + -
234A ILE* 2.7 32.3 + - + +
235A VAL* 3.8 4.5 - - - +
237A TYR* 1.3 81.0 - - + +
239A MET* 1.3 60.2 + - - +
240A ASN 3.4 0.3 + - - -
241A ILE* 3.8 33.0 + - + +
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Residues in contact with MET 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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212A ILE* 4.5 1.1 - - + -
221A PHE* 3.7 49.8 - - + -
223A VAL* 5.0 3.6 - - - -
235A VAL* 2.6 45.4 + - + +
236A TYR* 3.6 11.4 - - + +
237A TYR 3.0 0.6 + - - -
238A LEU* 1.3 77.7 - - - +
240A ASN* 1.3 61.0 + - - +
241A ILE 3.8 2.5 - - - +
378A ARG* 3.8 11.3 + - - -
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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