Contacts of the helix formed by residues 261 - 271 (chain C) in PDB entry 5JHQ
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 261 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224C ALA 3.3 7.9 - - - +
225C GLY 2.9 28.6 + - - -
226C PHE* 3.5 6.1 - - - -
227C GLY* 3.3 30.3 + - - -
256C ALA* 3.1 13.4 + - + +
259C PHE* 3.4 26.2 + - + +
260C GLY* 1.3 74.7 + - - +
262C ALA* 1.3 51.7 + - - +
263C GLU* 3.1 4.5 - - + -
264C VAL* 2.7 41.0 + - + -
265C VAL* 2.8 18.3 + - - +
297C VAL* 4.1 0.4 - - - +
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Residues in contact with ALA 262 (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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260C GLY 3.2 7.0 + - - +
261C HIS* 1.3 73.7 - - - +
263C GLU* 1.3 58.1 + - + +
265C VAL* 3.7 11.4 - - - +
266C SER* 3.0 34.1 + - - -
296C ASP* 4.0 34.5 - - + +
297C VAL* 4.0 11.4 - - + -
300C VAL* 4.7 6.8 - - + +
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Residues in contact with GLU 263 (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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229C LYS* 4.0 31.1 - - + +
261C HIS* 4.6 2.0 - - - +
262C ALA* 1.3 78.8 - - + +
264C VAL* 1.3 61.3 + - + +
266C SER* 3.5 6.7 + - - -
267C LEU* 3.2 21.5 + - - +
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Residues in contact with VAL 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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224C ALA* 3.9 29.2 - - + -
227C GLY* 4.0 19.3 - - - -
228C ARG 4.2 0.7 - - - +
229C LYS* 3.7 38.4 - - + +
232C VAL* 4.0 15.7 - - + -
256C ALA* 4.1 8.1 - - + -
261C HIS* 2.7 19.5 + - + +
263C GLU* 1.3 71.1 - - + +
265C VAL* 1.3 62.9 + - - +
267C LEU* 3.4 7.0 + - - +
268C LEU* 3.0 28.3 + - + +
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Residues in contact with VAL 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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253C LEU* 3.8 15.4 - - + +
256C ALA* 4.0 15.9 - - + -
257C CYS* 3.8 21.1 - - - -
261C HIS 2.8 21.4 + - - +
262C ALA* 3.7 9.4 - - - +
263C GLU 3.3 0.2 - - - -
264C VAL* 1.3 75.4 - - - +
266C SER* 1.3 63.9 + - - +
268C LEU* 3.2 3.5 + - - +
269C LEU* 3.0 43.4 + - + +
297C VAL* 4.0 15.3 - - + -
300C VAL* 3.8 12.8 - - + -
301C LEU* 4.2 12.6 - - + -
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Residues in contact with SER 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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262C ALA 3.0 18.0 + - - -
263C GLU* 3.7 7.8 - - - -
265C VAL* 1.3 76.1 - - - +
267C LEU* 1.3 56.6 + - - +
269C LEU* 3.8 5.1 - - - +
270C CYS* 3.2 27.5 + - - +
300C VAL* 3.5 24.9 - - - +
304C HIS* 4.8 8.0 + - - -
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Residues in contact with LEU 267 (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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229C LYS* 4.0 12.1 - - + +
232C VAL* 3.8 21.3 - - + -
233C GLU* 3.8 33.9 - - + +
236C LEU* 4.2 13.6 - - + +
263C GLU 3.2 14.1 + - - +
264C VAL* 3.6 7.6 - - - +
265C VAL 3.2 0.8 - - - -
266C SER* 1.3 78.7 - - - +
268C LEU* 1.3 61.7 + - - +
270C CYS* 3.6 14.2 - - - +
271C GLN* 3.4 25.7 + - + +
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Residues in contact with LEU 268 (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 LEU* 4.2 24.7 - - + -
224C ALA* 4.1 11.4 - - + -
232C VAL* 4.4 9.4 - - + -
236C LEU* 4.7 3.6 - - + -
242C VAL* 3.4 26.7 - - + +
252C PRO* 3.7 12.3 - - + +
253C LEU* 3.6 41.1 - - + +
256C ALA* 4.2 3.8 - - + -
264C VAL* 3.0 26.4 + - + +
265C VAL 3.2 2.9 + - - +
267C LEU* 1.3 72.7 - - - +
269C LEU* 1.3 67.2 + - - +
271C GLN* 3.2 6.5 + - - +
272C GLY 3.2 5.9 + - - -
273C ALA* 3.1 24.8 + - + +
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Residues in contact with LEU 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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445B LYS 5.0 0.2 - - - +
447B ARG* 4.1 7.3 + - - -
253C LEU* 3.7 20.4 - - + -
265C VAL* 3.0 39.7 + - + +
266C SER* 3.8 3.6 - - - +
268C LEU* 1.3 75.1 - - - +
270C CYS* 1.3 58.8 + - - +
272C GLY* 2.9 21.1 + - - -
273C ALA 3.5 20.7 - - - +
275C PRO* 3.9 23.3 - - + -
300C VAL* 3.7 16.6 - - + +
301C LEU* 4.3 4.7 - - + -
304C HIS* 3.5 40.8 + - + +
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Residues in contact with CYS 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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412B TYR* 5.2 11.5 - - - -
445B LYS* 5.0 1.9 + - - -
447B ARG* 2.6 38.6 + - - +
266C SER 3.2 17.9 + - - +
267C LEU* 3.6 16.6 - - - +
269C LEU* 1.3 79.6 - - - +
271C GLN* 1.3 68.5 + - - +
304C HIS* 4.8 5.2 - - + -
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Residues in contact with GLN 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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412B TYR* 5.1 10.5 - - - -
444B SER 4.9 1.2 - - - +
445B LYS* 3.4 42.2 + - - +
236C LEU* 3.9 41.0 - - + +
242C VAL* 3.9 15.7 - - + +
243C HIS* 5.1 0.9 + - - -
267C LEU* 3.4 18.0 + - + +
268C LEU 3.2 9.9 + - - +
269C LEU 3.2 0.6 - - - -
270C CYS* 1.3 88.0 + - - +
272C GLY* 1.3 57.1 - - - +
273C ALA 3.7 0.9 - - - -
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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