Contacts of the helix formed by residues 235 - 250 (chain A) in PDB entry 3V30
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 TYR 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A VAL 3.3 27.6 - - - -
199A ARG* 3.4 31.1 + - - -
200A GLY 5.3 0.3 - - - -
201A ASN* 3.5 47.0 - - + +
230A ALA* 3.0 17.7 + - - +
233A LEU* 3.5 41.7 - - + +
234A GLY* 1.3 74.8 - - - +
236A ARG* 1.3 58.5 + - - +
237A LYS 3.4 2.5 - - - -
238A VAL* 3.3 10.6 + - + +
239A GLN* 2.9 27.3 + - - +
17B SER* 4.0 9.8 + - - -
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Residues in contact with ARG 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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234A GLY* 3.1 19.6 + - - +
235A TYR* 1.3 69.8 - - - +
237A LYS* 1.3 61.3 - - - +
239A GLN* 3.3 35.8 + - - +
240A GLN* 2.9 27.0 + - - +
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Residues in contact with LYS 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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201A ASN* 5.9 0.9 - - - +
203A VAL* 3.7 30.7 - - + -
207A GLU* 5.6 2.8 + - - -
235A TYR 3.4 0.2 - - - -
236A ARG* 1.3 74.8 - - - +
238A VAL* 1.3 67.0 + - - +
240A GLN* 2.7 32.0 + - - +
241A VAL* 2.9 38.8 + - - +
244A ASN* 5.6 1.4 + - - -
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Residues in contact with VAL 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A VAL* 3.9 28.3 - - + +
201A ASN* 3.4 37.9 + - - +
202A HIS 4.5 0.7 - - - +
203A VAL* 3.7 22.4 - - + +
206A VAL* 4.3 11.0 - - + -
230A ALA* 3.8 17.5 - - + -
235A TYR* 3.3 13.3 + - + +
237A LYS* 1.3 76.1 - - - +
239A GLN* 1.3 64.5 + - - +
241A VAL* 3.2 7.3 + - - +
242A ILE* 3.0 27.8 + - + +
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Residues in contact with GLN 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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227A MET* 3.4 30.6 - - + +
230A ALA* 4.2 8.0 - - + +
231A VAL* 3.8 25.9 - - - +
234A GLY* 6.0 0.3 - - - -
235A TYR 2.9 13.8 + - - +
236A ARG* 3.4 44.3 + - - +
237A LYS 3.2 0.2 - - - -
238A VAL* 1.3 76.2 - - - +
240A GLN* 1.3 57.5 + - - +
242A ILE* 3.2 4.4 + - - +
243A GLU* 2.8 52.8 + - - +
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Residues in contact with GLN 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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236A ARG 2.9 14.2 + - - +
237A LYS* 2.7 44.4 + - - +
239A GLN* 1.3 76.8 - - - +
241A VAL* 1.3 57.7 + - - +
243A GLU* 3.1 14.5 + - - +
244A ASN* 2.8 51.1 + - - +
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Residues in contact with VAL 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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203A VAL* 3.9 17.5 - - + +
206A VAL* 3.9 16.8 - - + -
207A GLU* 3.3 51.1 - - + +
210A LEU* 4.1 4.9 - - + -
237A LYS* 2.9 30.2 + - - +
238A VAL* 3.6 9.0 - - - +
240A GLN* 1.3 75.0 - - - +
242A ILE* 1.3 61.8 + - - +
244A ASN* 3.4 8.2 + - - +
245A HIS* 3.1 22.0 + - - +
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Residues in contact with ILE 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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194A LEU* 5.9 0.2 - - + -
198A VAL* 4.3 7.6 - - + -
206A VAL* 4.3 5.8 - - + -
210A LEU* 4.0 19.7 - - + -
216A LEU* 3.8 24.0 - - + -
226A PRO 4.2 6.1 - - - +
227A MET* 3.8 43.3 - - + +
230A ALA* 4.3 1.6 - - + -
238A VAL* 3.0 33.6 + - + +
239A GLN 3.5 7.0 - - - +
241A VAL* 1.3 73.7 - - - +
243A GLU* 1.3 59.4 + - - +
245A HIS* 3.1 4.0 + - - +
246A ILE* 2.9 47.0 + - + +
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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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227A MET* 3.6 15.5 - - + +
239A GLN* 2.8 46.2 + - - +
240A GLN* 3.4 19.7 + - - +
242A ILE* 1.3 76.7 - - - +
244A ASN* 1.3 62.1 + - - +
246A ILE* 3.3 12.3 + - + +
247A LEU* 3.0 32.0 + - + +
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Residues in contact with ASN 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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237A LYS* 5.6 1.2 + - - -
240A GLN* 2.8 41.7 + - - +
241A VAL* 3.8 7.2 - - - +
243A GLU* 1.3 75.6 - - - +
245A HIS* 1.3 60.0 + - - +
247A LEU* 3.4 25.9 - - + +
248A LYS* 3.4 19.2 + - - +
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Residues in contact with HIS 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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210A LEU* 3.0 57.2 + - + +
211A ALA* 5.2 1.0 - - - -
213A GLY* 5.1 4.4 - - - -
214A ALA 4.6 6.5 + - - -
216A LEU* 3.7 26.8 - - + +
241A VAL 3.1 12.7 + - - +
242A ILE 3.1 7.5 + - - +
244A ASN* 1.3 75.8 - - - +
246A ILE* 1.3 64.7 - - - +
248A LYS* 3.1 19.2 + - + +
249A LEU* 3.1 40.7 + - + +
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Residues in contact with ILE 246 (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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216A LEU* 3.7 18.6 - - + -
227A MET* 5.3 11.2 - - + -
242A ILE* 2.9 39.6 + - + +
243A GLU* 3.3 10.7 + - + +
245A HIS* 1.3 76.8 - - - +
247A LEU* 1.3 61.8 + - - +
249A LEU* 3.1 19.2 + - + +
250A PHE* 3.2 33.4 - - + -
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Residues in contact with LEU 247 (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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243A GLU* 3.0 14.2 + - + +
244A ASN* 3.4 34.8 - - - +
245A HIS 3.2 0.2 - - - -
246A ILE* 1.3 77.6 - - - +
248A LYS* 1.3 61.2 + - - +
250A PHE* 3.2 14.1 + - - +
251A GLN* 3.3 42.7 + - - +
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Residues in contact with LYS 248 (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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244A ASN 3.4 7.9 + - - +
245A HIS* 3.1 14.8 + - + +
247A LEU* 1.3 74.1 - - - +
249A LEU* 1.3 64.8 + - + +
250A PHE 3.1 2.0 - - - -
251A GLN* 3.1 22.7 - - - +
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Residues in contact with LEU 249 (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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216A LEU* 5.0 5.8 - - + -
245A HIS* 3.1 48.4 + - + +
246A ILE* 3.1 23.1 + - + +
248A LYS* 1.3 77.6 - - + +
250A PHE* 1.3 82.3 + - + +
251A GLN 3.7 0.2 - - - -
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Residues in contact with PHE 250 (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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246A ILE* 3.2 39.0 - - + -
247A LEU* 3.2 5.8 + - - +
248A LYS 3.1 0.4 - - - -
249A LEU* 1.3 101.6 - - + +
251A GLN* 1.3 65.6 + - + +
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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