Contacts of the helix formed by residues 270 - 282 (chain B) in PDB entry 5LCM
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 ARG 270 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221B PRO* 3.1 28.4 + - - +
222B GLU* 3.3 26.7 - - - +
223B LYS 3.8 7.2 - - - +
225B ALA* 2.8 32.4 + - - +
227B LEU* 3.7 36.1 - - + +
235B ASP* 4.4 9.9 + - - -
236B TYR* 3.1 29.6 + - + +
268B PHE 3.9 0.4 + - - -
269B VAL* 1.3 73.8 - - - +
271B CYS* 1.3 54.4 + - - +
272B GLU 3.2 0.2 + - - -
273B VAL* 4.5 0.4 - - - -
274B GLU* 2.8 41.2 + - + +
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Residues in contact with CYS 271 (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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210B LEU* 3.9 23.6 - - - -
222B GLU 5.2 0.9 - - - -
223B LYS* 2.9 38.4 + - + +
224B TYR* 4.7 4.5 - - - -
269B VAL* 3.9 16.2 - - - -
270B ARG* 1.3 74.4 - - - +
272B GLU* 1.3 67.9 + - - +
274B GLU* 4.4 5.1 - - - +
275B ALA* 3.3 23.2 + - - +
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Residues in contact with GLU 272 (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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208B PHE* 4.2 8.0 - - - +
210B LEU* 6.0 0.6 - - + +
248B LEU 5.3 1.6 - - - +
249B PHE* 3.5 18.8 - - + +
250B HIS* 2.7 60.5 + - - +
268B PHE* 6.2 0.4 - - + +
269B VAL* 3.1 26.5 + - + +
271B CYS* 1.3 80.0 - - - +
273B VAL* 1.3 65.6 + - + +
275B ALA* 3.4 4.8 + - - +
276B PHE* 3.1 22.9 + - - +
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Residues in contact with VAL 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B LEU* 4.4 4.7 - - + -
232B CYS* 3.5 16.2 - - - -
236B TYR* 3.3 32.1 - - + -
238B LEU* 3.5 22.0 - - + +
243B LEU* 5.4 0.4 - - + -
249B PHE* 4.0 12.3 - - + -
268B PHE* 3.5 30.3 - - + -
269B VAL 3.2 16.6 + - - +
270B ARG 3.7 4.3 - - - +
272B GLU* 1.3 75.3 - - + +
274B GLU* 1.4 58.2 + - - +
276B PHE* 3.3 4.0 + - - +
277B ALA* 2.9 27.4 + - - +
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Residues in contact with GLU 274 (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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222B GLU 4.4 7.8 - - - +
236B TYR* 3.2 35.4 + - + +
270B ARG* 2.8 33.6 + - - +
271B CYS* 4.4 4.4 - - - +
273B VAL* 1.4 73.2 - - - +
275B ALA* 1.3 59.3 + - - +
277B ALA* 3.3 0.9 + - - +
278B PHE* 2.9 67.6 + - + -
284B GLU* 5.7 0.5 - - - +
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Residues in contact with ALA 275 (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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271B CYS 3.3 18.9 + - - +
272B GLU* 3.8 4.3 - - - +
273B VAL 3.4 0.2 - - - -
274B GLU* 1.3 78.9 - - - +
276B PHE* 1.3 65.3 + - - +
278B PHE* 3.5 8.0 + - - +
279B LYS* 3.1 23.4 + - - +
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Residues in contact with PHE 276 (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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238B LEU* 3.7 20.4 - - + -
242B GLU* 3.7 38.8 - - + -
248B LEU* 3.6 42.6 - - + -
249B PHE* 3.6 29.8 - + + -
272B GLU 3.1 7.1 + - - +
273B VAL 3.6 3.4 - - - +
275B ALA* 1.3 78.4 - - - +
277B ALA* 1.3 55.2 + - - +
279B LYS* 3.1 31.5 + - + +
280B LYS* 2.9 32.0 + - + +
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Residues in contact with ALA 277 (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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236B TYR* 3.8 42.2 - - + +
238B LEU* 4.2 6.7 - - + -
273B VAL 2.9 17.2 + - - +
274B GLU 3.6 3.8 - - - +
276B PHE* 1.3 75.1 - - - +
278B PHE* 1.3 63.4 + - + +
280B LYS* 4.2 5.8 - - - -
281B TRP* 2.9 38.3 + - + +
287B LEU* 4.7 2.2 - - + -
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Residues in contact with PHE 278 (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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236B TYR* 5.1 0.7 - + - -
274B GLU* 2.9 54.7 + - + +
275B ALA* 3.8 7.4 - - - +
277B ALA* 1.3 78.5 - - + +
279B LYS* 1.3 56.8 + - - +
282B GLY* 3.0 12.1 + - - -
283B GLY* 2.8 42.5 + - - +
284B GLU* 3.7 43.1 - - + -
287B LEU* 3.9 17.9 - - + -
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Residues in contact with LYS 279 (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 LEU* 5.8 2.0 - - - +
275B ALA 3.1 14.2 + - - +
276B PHE* 3.2 37.6 - - + +
278B PHE* 1.3 78.0 - - - +
280B LYS* 1.3 63.2 + - - +
281B TRP 3.6 0.2 + - - -
282B GLY* 4.2 3.1 + - - -
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Residues in contact with LYS 280 (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 PHE 3.0 22.8 + - - -
238B LEU* 4.0 9.4 - - + -
239B THR* 4.0 12.1 - - - +
242B GLU* 3.0 39.6 + - - +
276B PHE* 2.9 22.7 + - + +
277B ALA* 3.7 5.6 - - - +
279B LYS* 1.3 80.7 - - - +
281B TRP* 1.3 95.3 + - + +
282B GLY 3.6 0.4 + - - -
8C 6TW 4.6 4.2 + - - -
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Residues in contact with TRP 281 (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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236B TYR 3.0 27.6 + - - -
237B PHE* 3.6 21.3 + - + +
277B ALA* 2.9 25.9 + - - +
280B LYS* 1.3 108.0 - - + +
282B GLY* 1.3 59.7 + - - +
283B GLY 4.5 1.3 - - - +
286B GLY* 3.1 18.9 - - - +
287B LEU* 4.0 31.6 - - + +
289B GLU* 5.2 0.9 - - - +
290B GLU* 3.2 43.1 - - + -
294B ARG* 3.5 21.5 - - - -
8C 6TW 4.1 12.8 - - - -
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Residues in contact with GLY 282 (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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278B PHE 3.0 8.5 + - - -
279B LYS 4.2 3.2 + - - -
280B LYS 3.6 2.0 - - - -
281B TRP* 1.3 73.3 - - - +
283B GLY* 1.3 59.3 + - - -
285B GLU* 4.2 2.6 + - - +
286B GLY* 2.9 24.9 + - - -
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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