Contacts of the helix formed by residues 263 - 274 (chain C) in PDB entry 4J1R
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 VAL 263 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C ILE* 4.4 4.5 - - - -
261C SER* 3.1 4.0 + - - +
262C GLY* 1.3 75.5 - - - +
264C ASP* 1.3 65.1 + - - +
265C GLN 3.1 1.8 - - - -
266C LEU* 3.0 22.1 + - + +
267C VAL* 3.6 8.1 + - + +
291C PHE* 4.1 26.7 - - + -
61D VAL* 4.3 13.5 - - + +
62D ILE* 3.5 15.7 - - - +
63D GLY* 3.4 41.1 - - - +
64D ASN* 4.0 6.7 - - + +
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Residues in contact with ASP 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C PRO 4.3 0.3 - - - +
259C GLY* 3.5 3.5 - - - -
260C ASP* 2.6 40.2 + - + +
261C SER* 2.7 30.8 + - - +
263C VAL* 1.3 73.1 - - - +
265C GLN* 1.3 57.2 + - - +
267C VAL* 2.9 34.8 + - - +
268C GLU* 3.1 25.5 + - - +
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Residues in contact with GLN 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C ARG* 3.1 36.7 + - + +
221C TYR* 3.3 11.5 + - - -
223C ARG* 4.6 5.9 + - + +
228C ILE* 3.6 18.8 - - + -
257C PHE* 2.9 45.6 - - - +
259C GLY* 2.9 21.6 + - - -
261C SER 3.0 16.8 + - - +
262C GLY* 3.6 10.1 - - - +
263C VAL 3.1 0.2 - - - -
264C ASP* 1.3 77.3 - - - +
266C LEU* 1.3 60.0 + - - +
268C GLU* 3.4 2.6 + - - +
269C ILE* 3.1 31.9 + - + +
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Residues in contact with LEU 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C PRO* 4.8 10.1 - - + +
228C ILE* 3.9 27.9 - - + +
229C PHE* 3.7 37.5 - - + -
263C VAL* 3.0 14.6 + - + +
265C GLN* 1.3 75.7 - - - +
267C VAL* 1.3 62.1 + - + +
269C ILE* 3.1 12.2 + - + +
270C ILE* 2.8 48.9 + - + +
276C PRO* 6.4 1.3 - - + -
291C PHE* 4.1 33.7 - - + -
323C TYR* 5.5 4.0 - - + -
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Residues in contact with VAL 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C VAL* 3.9 13.7 - - + +
264C ASP* 2.9 25.3 + - - +
266C LEU* 1.3 77.6 - - + +
268C GLU* 1.3 59.1 + - - +
270C ILE* 3.2 12.8 + - + +
271C LYS* 2.8 44.1 + - + +
293C PHE* 5.5 10.5 - - + -
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Residues in contact with GLU 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C ILE 5.0 1.3 - - - +
257C PHE* 3.6 28.7 - - + -
258C PRO* 4.0 37.4 - - - +
259C GLY* 4.1 3.8 - - - -
260C ASP* 5.8 0.3 - - - -
264C ASP* 3.1 27.8 + - - +
265C GLN* 3.6 7.6 - - - +
266C LEU 3.2 0.2 - - - -
267C VAL* 1.3 78.3 - - - +
269C ILE* 1.3 62.3 + - - +
271C LYS* 3.5 41.2 + - - +
272C VAL* 3.7 6.9 - - - +
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Residues in contact with ILE 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C ARG 4.2 8.1 - - - +
225C PRO* 4.3 7.6 - - + -
228C ILE* 4.0 22.7 - - + -
241C TRP* 3.5 25.1 - - + -
257C PHE* 3.8 24.7 - - + -
265C GLN* 3.1 22.0 + - - +
266C LEU* 3.1 12.5 + - + +
268C GLU* 1.3 75.5 - - - +
270C ILE* 1.3 58.6 + - - +
272C VAL* 3.1 5.9 + - - +
273C LEU* 2.8 39.4 + - + +
323C TYR* 3.6 29.8 - - + +
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Residues in contact with ILE 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266C LEU* 2.8 38.4 + - + +
267C VAL* 3.4 13.7 - - + +
269C ILE* 1.3 68.0 - - - +
271C LYS* 1.3 58.0 + - + +
272C VAL 2.8 6.1 + - - -
274C GLY* 2.6 57.1 + - - +
275C THR* 3.8 26.7 - - + -
276C PRO* 4.5 8.5 - - + -
293C PHE* 4.4 19.5 - - + -
294C PRO 5.2 0.7 - - - +
296C ILE* 4.0 22.4 - - + +
297C LYS 4.8 0.2 - - - +
323C TYR* 3.6 6.3 - - + +
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Residues in contact with LYS 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C VAL* 2.8 35.6 + - + +
268C GLU* 3.6 34.5 + - - +
269C ILE 3.3 0.4 - - - -
270C ILE* 1.3 73.3 - - + +
272C VAL* 1.3 61.5 + - + +
296C ILE* 5.3 12.7 - - + +
297C LYS 5.2 2.2 - - - +
299C HIS* 4.0 23.6 + - - +
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Residues in contact with VAL 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C ILE* 4.8 10.1 - - + +
257C PHE* 3.7 26.7 - - + -
268C GLU 3.7 6.1 - - - +
269C ILE 3.1 5.3 + - - +
270C ILE 2.8 0.8 + - - -
271C LYS* 1.3 83.9 - - + +
273C LEU* 1.3 71.0 + - + +
274C GLY 3.2 4.3 - - - -
298C ALA* 3.7 1.7 - - - +
299C HIS* 3.0 33.1 + - - +
301C TRP* 4.5 15.8 - - + -
304C VAL* 4.0 30.3 - - + -
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Residues in contact with LEU 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C TRP* 3.8 26.5 - - + -
257C PHE* 4.8 4.0 - - + -
269C ILE* 2.8 16.5 + - + +
272C VAL* 1.3 80.6 - - + +
274C GLY* 1.3 60.7 + - - +
275C THR 4.7 1.6 - - - +
298C ALA* 3.6 14.9 - - - +
301C TRP* 3.5 38.4 - - + +
321C LEU* 3.7 22.0 - - + +
323C TYR* 3.4 46.1 - - + +
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Residues in contact with GLY 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C ILE* 2.6 32.3 + - - -
272C VAL 3.2 3.2 + - - -
273C LEU* 1.3 73.0 - - - +
275C THR* 1.3 59.7 - - - -
296C ILE 3.0 15.3 - - - -
297C LYS 3.8 2.9 - - - -
298C ALA* 3.8 12.9 - - - +
323C TYR* 2.6 25.6 + - - -
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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