Contacts of the helix formed by residues 283 - 293 (chain B) in PDB entry 4IVR
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 HIS 283 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261B GLN* 3.3 52.8 + - - +
262B LEU* 5.1 0.9 - - + -
281B ARG 3.8 0.2 + - - -
282B PRO* 1.3 73.4 - - - +
284B ILE* 1.3 55.3 + - + +
285B GLY* 2.9 30.7 + - - -
286B ASP* 2.6 49.0 + - - +
287B THR* 3.7 2.6 + - - +
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Residues in contact with ILE 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B TYR* 3.8 18.1 - - + +
255B TRP* 3.7 26.5 - - + +
258B ASP* 3.5 47.0 + - + +
259B TRP* 3.9 3.1 - - + +
261B GLN* 4.2 6.2 + - + +
262B LEU* 3.6 33.2 - - + -
282B PRO 3.8 1.8 + - - -
283B HIS* 1.3 84.4 - - + +
285B GLY* 1.3 60.6 + - - +
287B THR* 2.8 38.4 + - - +
289B PHE* 4.1 7.6 - - + -
290B THR* 3.9 9.7 + - - -
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Residues in contact with GLY 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ARG* 5.1 2.9 + - - -
241B LEU* 4.7 1.4 - - - +
262B LEU* 3.7 18.4 - - - -
283B HIS* 2.9 19.8 + - - -
284B ILE* 1.3 79.8 - - - +
286B ASP* 1.3 64.6 + - - +
287B THR 3.4 0.7 - - - -
290B THR* 3.6 20.7 + - - +
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Residues in contact with ASP 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B LEU* 3.3 16.9 - - + +
244B ASN* 3.1 36.9 + - - +
282B PRO* 4.8 4.6 - - + +
283B HIS* 2.6 34.5 + - - +
285B GLY* 1.3 77.4 - - - +
287B THR* 1.3 58.2 + - - -
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Residues in contact with THR 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B LEU* 3.7 10.7 - - - +
244B ASN 4.1 8.5 - - - +
245B THR* 3.6 11.2 - - - -
248B TYR* 3.9 34.1 - - + -
282B PRO* 4.5 3.4 - - + -
283B HIS 3.7 12.1 - - - +
284B ILE* 2.8 20.1 + - - +
286B ASP* 1.3 84.5 - - - +
288B LEU* 1.3 64.0 + - - +
289B PHE* 3.3 27.0 + - - +
290B THR* 3.3 22.7 + - - +
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Residues in contact with LEU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B LEU* 4.1 26.9 - - + -
174B ALA* 5.3 0.4 - - + -
238B VAL* 3.7 21.3 - - + +
241B LEU* 3.6 21.5 - - + +
242B LEU* 3.8 29.6 - - + +
245B THR* 2.8 22.8 + - + +
287B THR* 1.3 72.4 - - - +
289B PHE* 1.3 65.0 + - - +
290B THR 3.1 0.2 - - - -
291B LEU* 3.1 44.1 + - + +
292B PHE* 3.4 12.5 - - + -
315B LEU* 4.5 12.3 - - + -
319B LEU* 4.2 7.9 - - + -
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Residues in contact with PHE 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B THR* 4.1 17.0 - - + -
248B TYR* 3.9 24.9 - + - -
249B LEU* 4.1 14.8 - - + -
255B TRP* 3.8 39.0 - + + -
259B TRP* 3.8 19.1 - - + -
262B LEU* 4.5 2.0 - - - -
284B ILE* 4.1 14.8 - - + -
287B THR* 3.1 22.5 - - - +
288B LEU* 1.3 78.0 - - - +
290B THR* 1.3 61.9 + - - +
292B PHE* 3.1 19.4 + - - +
312B LEU* 3.8 36.8 - - + -
315B LEU* 4.1 15.0 - - + -
316B ALA* 4.2 10.3 - - + -
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Residues in contact with THR 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B ARG* 4.2 20.4 - - - +
241B LEU* 4.8 2.2 - - + -
262B LEU* 3.3 20.3 - - - +
284B ILE 3.9 9.8 + - - -
285B GLY* 3.6 23.0 + - - +
287B THR 3.3 19.5 + - - +
288B LEU 3.1 1.4 - - - -
289B PHE* 1.3 79.3 - - - +
291B LEU* 1.3 69.0 + - + +
292B PHE 3.0 0.2 - - - -
293B ARG* 2.7 51.6 + - - +
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Residues in contact with LEU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B ALA* 4.1 22.2 - - + +
177B TYR* 3.6 32.5 + - + -
178B LEU* 3.9 20.9 - - + -
237B ARG* 3.7 27.6 - - - +
238B VAL* 4.6 7.9 - - + -
241B LEU* 4.1 17.3 - - + -
288B LEU* 3.1 36.8 + - + +
290B THR* 1.3 80.5 - - + +
292B PHE* 1.3 74.3 + - + +
293B ARG* 3.4 1.8 + - - -
294B ALA* 4.2 2.6 + - - +
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Residues in contact with PHE 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B LEU* 4.8 10.8 - - + -
174B ALA* 5.4 1.6 - - + -
177B TYR* 5.8 4.9 - + - -
184B PRO* 4.6 8.1 - - + -
187B VAL* 4.0 27.4 - - + -
188B LEU* 3.6 33.7 - - + -
191B VAL* 5.0 0.4 - - + -
259B TRP* 3.7 13.3 - - - -
288B LEU* 3.4 29.8 - - + -
289B PHE 3.1 6.8 + - - +
290B THR 3.0 1.6 - - - -
291B LEU* 1.3 95.2 - - + +
293B ARG* 1.3 55.9 + - - +
294B ALA 2.9 9.6 + - - +
297B LEU* 3.5 23.4 - - + +
304B LEU* 3.7 8.9 - - + +
312B LEU* 3.7 36.8 - - + -
315B LEU* 4.4 14.1 - - + -
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Residues in contact with ARG 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B TRP* 4.0 17.9 - - + -
262B LEU* 3.5 51.2 + - + +
290B THR* 2.7 55.8 + - - +
291B LEU 3.4 2.4 - - - -
292B PHE* 1.3 75.1 - - - +
294B ALA* 1.3 64.8 + - - +
295B PRO* 3.5 2.8 - - - +
298B LEU* 3.4 18.8 - - + +
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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