Contacts of the helix formed by residues 230 - 245 (chain A) in PDB entry 4YVG
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 THR 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A ALA 3.6 3.3 + - - +
229A LEU* 1.3 76.5 - - - +
231A ASP* 1.3 67.1 + - - +
232A GLU* 3.5 8.9 + - - +
233A GLN* 2.9 45.3 + - - +
234A ARG* 2.9 21.6 + - - +
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Residues in contact with ASP 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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229A LEU 5.2 0.5 - - - +
230A THR* 1.3 75.0 - - - +
232A GLU* 1.3 63.3 + - - +
234A ARG* 2.8 40.7 + - - +
235A LYS* 3.0 24.1 + - - +
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Residues in contact with GLU 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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205A ARG* 2.7 45.0 + - - -
206A LYS* 3.7 13.0 - - - +
209A LEU* 3.8 11.5 - - + +
230A THR* 3.2 7.7 + - - +
231A ASP* 1.3 78.2 - - - +
233A GLN* 1.3 59.1 + - - +
235A LYS* 3.3 21.5 + - - +
236A LEU* 2.9 44.5 + - + +
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Residues in contact with GLN 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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173A ASP* 4.3 12.3 + - - +
175A LEU* 4.2 11.5 - - - +
209A LEU* 4.1 34.8 - - + +
213A LEU* 3.5 19.6 - - + +
228A ALA 4.3 1.4 - - - +
229A LEU* 3.3 23.9 - - + +
230A THR* 2.9 48.0 + - - +
232A GLU* 1.3 77.7 - - - +
234A ARG* 1.3 61.7 + - - +
236A LEU* 4.7 0.7 - - - -
237A LEU* 2.9 27.3 + - - +
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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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229A LEU* 3.7 30.1 + - + -
230A THR 2.9 14.4 + - - +
231A ASP* 2.8 47.1 + - - +
233A GLN* 1.3 76.2 - - - +
235A LYS* 1.3 57.8 + - - +
237A LEU* 3.8 3.1 - - - +
238A LYS* 2.9 60.9 + - - +
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Residues in contact with LYS 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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206A LYS* 5.6 5.8 - - - +
231A ASP 3.0 11.9 + - - +
232A GLU* 3.5 30.8 + - - +
234A ARG* 1.3 74.6 - - - +
236A LEU* 1.3 67.9 - - - +
238A LYS* 3.1 10.7 + - - +
239A GLU* 2.9 46.1 + - + +
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Residues in contact with LEU 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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206A LYS* 3.8 37.5 - - + +
209A LEU* 4.0 21.1 - - + -
210A LYS* 3.7 23.4 - - + +
213A LEU* 4.0 11.2 - - + -
232A GLU* 2.9 40.6 + - + +
235A LYS* 1.3 84.8 - - - +
237A LEU* 1.3 57.7 + - - +
239A GLU* 3.3 26.2 + - - +
240A ALA* 3.0 29.1 + - - +
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Residues in contact with LEU 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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213A LEU* 4.0 29.0 - - + +
214A GLN* 4.7 1.8 - - - +
217A TRP* 3.9 23.3 - - + -
224A LEU* 4.2 16.6 - - + -
229A LEU* 3.9 23.6 - - + -
233A GLN 2.9 19.1 + - - +
234A ARG* 3.8 4.5 - - - +
236A LEU* 1.3 73.5 - - - +
238A LYS* 1.3 65.6 + - + +
240A ALA* 3.2 4.1 + - + +
241A GLN* 2.9 58.5 + - + +
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Residues in contact with LYS 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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234A ARG* 2.9 48.9 + - - +
235A LYS* 3.1 9.2 + - - +
237A LEU* 1.3 75.7 - - + +
239A GLU* 1.3 57.7 + - - +
241A GLN* 3.3 14.2 + - - +
242A ALA* 2.9 30.0 + - - +
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Residues in contact with GLU 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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210A LYS* 3.1 25.8 + - - +
235A LYS* 2.9 38.1 + - + +
236A LEU* 3.6 23.1 - - - +
237A LEU 3.2 0.2 - - - -
238A LYS* 1.3 77.6 - - + +
240A ALA* 1.3 62.5 + - - +
242A ALA* 3.3 6.7 + - - +
243A GLU* 3.0 32.1 + - - +
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Residues in contact with ALA 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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210A LYS* 3.9 18.8 - - + +
214A GLN* 3.7 45.0 - - + +
217A TRP* 4.5 2.4 - - + -
236A LEU 3.0 17.4 + - - +
237A LEU* 3.2 7.6 + - + +
239A GLU* 1.3 77.5 - - - +
241A GLN* 1.3 58.0 + - + +
243A GLU* 3.2 7.1 + - - +
244A HIS* 3.0 26.9 + - - +
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Residues in contact with GLN 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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217A TRP* 3.4 61.1 - - + +
224A LEU* 5.5 0.2 - - - +
237A LEU* 2.9 43.0 + - + +
238A LYS* 3.7 15.1 - - - +
240A ALA* 1.3 74.4 - - - +
242A ALA* 1.3 63.8 + - - +
244A HIS* 3.2 3.3 + - - +
245A ASN* 3.1 34.1 + - - +
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Residues in contact with ALA 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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238A LYS 2.9 17.5 + - - +
239A GLU* 3.3 7.4 + - - +
241A GLN* 1.3 73.2 - - - +
243A GLU* 1.3 61.6 + - + +
245A ASN* 3.2 15.7 + - - +
246A SER* 2.6 29.5 + - - +
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Residues in contact with GLU 243 (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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210A LYS* 2.6 37.6 + - - -
214A GLN* 5.0 5.5 - - - +
239A GLU* 3.0 17.9 + - - +
240A ALA* 3.2 7.9 + - - +
242A ALA* 1.3 78.3 - - + +
244A HIS* 1.3 62.3 + - - +
246A SER* 3.4 21.9 + - - +
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Residues in contact with HIS 244 (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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214A GLN* 5.4 4.6 + - - +
217A TRP* 3.8 27.7 - + + -
218A LEU* 3.7 33.0 - - + +
240A ALA 3.0 13.5 + - - +
241A GLN 3.4 9.6 - - - +
242A ALA 3.2 0.4 - - - -
243A GLU* 1.3 78.7 - - - +
245A ASN* 1.4 61.7 + - - +
246A SER* 3.2 8.3 + - - +
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Residues in contact with ASN 245 (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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217A TRP* 5.3 3.8 - - - -
241A GLN* 3.1 25.1 + - - +
242A ALA* 3.2 7.8 + - - +
244A HIS* 1.4 82.0 - - - +
246A SER* 1.3 61.2 + - - +
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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