Contacts of the helix formed by residues 270 - 282 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A PRO* 3.4 15.2 + - - +
222A GLU* 3.2 28.0 - - - +
223A LYS 3.8 7.0 - - - +
225A ALA* 2.8 27.2 + - - +
227A LEU* 3.5 39.1 - - + +
235A ASP* 4.5 8.5 + - - +
236A TYR* 2.9 40.0 + - + +
268A PHE 3.8 1.2 + - - -
269A VAL* 1.3 72.8 - - - +
271A CYS* 1.4 57.8 + - - +
272A GLU 3.1 0.3 + - - -
273A VAL* 5.1 0.7 - - - -
274A GLU* 2.7 38.5 + - + +
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Residues in contact with CYS 271 (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* 4.0 23.8 - - - -
222A GLU 5.1 0.9 - - - -
223A LYS* 2.8 38.2 + - + +
224A TYR* 4.8 3.8 - - - -
269A VAL* 3.9 16.4 - - - -
270A ARG* 1.4 72.3 - - - +
272A GLU* 1.3 62.8 + - - +
274A GLU* 4.2 5.5 - - - +
275A ALA* 3.1 28.6 + - - +
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Residues in contact with GLU 272 (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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208A PHE* 4.1 9.0 - - - +
210A LEU* 6.0 0.2 - - - +
248A LEU 5.3 1.6 - - - +
249A PHE* 3.6 19.1 - - + +
250A HIS* 2.7 60.5 + - - +
268A PHE* 6.1 0.6 - - + +
269A VAL* 3.1 27.0 + - + +
271A CYS* 1.3 79.6 - - - +
273A VAL* 1.3 65.7 + - + +
275A ALA* 3.3 5.9 + - - +
276A PHE* 3.1 23.2 + - - +
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Residues in contact with VAL 273 (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 LEU* 4.7 2.5 - - + -
232A CYS* 3.9 19.7 - - + -
236A TYR* 3.3 34.8 - - + -
238A LEU* 3.5 26.9 - - + +
243A LEU* 3.9 17.0 - - + -
249A PHE* 3.7 20.0 - - + -
268A PHE* 4.3 8.7 - - + -
269A VAL 3.2 11.2 + - - +
270A ARG 4.6 0.9 - - - +
272A GLU* 1.3 78.2 - - - +
274A GLU* 1.4 59.0 + - - +
276A PHE* 3.4 2.4 + - - +
277A ALA* 2.9 27.5 + - - +
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Residues in contact with GLU 274 (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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222A GLU 4.2 9.8 - - - +
236A TYR* 3.2 34.7 + - + +
270A ARG* 2.7 31.8 + - - +
271A CYS* 4.2 4.8 - - - +
273A VAL* 1.4 72.4 - - - +
275A ALA* 1.3 65.7 + - - +
277A ALA 3.3 0.5 + - - -
278A PHE* 2.9 62.4 + - + -
284A GLU* 5.8 0.2 - - - +
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Residues in contact with ALA 275 (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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271A CYS 3.1 20.3 + - - +
272A GLU* 3.3 5.4 + - - +
274A GLU* 1.3 75.2 - - - +
276A PHE* 1.3 64.9 + - - +
278A PHE* 3.4 7.8 + - - +
279A LYS* 3.0 29.6 + - + +
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Residues in contact with PHE 276 (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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238A LEU* 3.7 17.9 - - + -
242A GLU* 3.7 43.1 - - + -
248A LEU* 3.6 39.9 - - + -
249A PHE* 3.5 29.8 - + + -
272A GLU 3.1 5.4 + - - +
273A VAL 3.7 1.8 - - - +
274A GLU 3.2 0.2 - - - -
275A ALA* 1.3 79.4 - - - +
277A ALA* 1.3 57.2 + - - +
279A LYS* 3.0 17.3 + - + +
280A LYS* 2.8 32.5 + - + +
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Residues in contact with ALA 277 (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 TYR* 3.7 43.7 - - + +
238A LEU* 4.1 7.0 - - + -
273A VAL 2.9 17.5 + - - +
274A GLU 3.8 1.8 - - - +
276A PHE* 1.3 73.4 - - - +
278A PHE* 1.3 64.9 + - + +
280A LYS* 4.0 7.4 - - - -
281A TRP* 2.8 37.7 + - + +
283A GLY 4.8 0.2 - - - +
287A LEU* 5.2 2.0 - - + +
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Residues in contact with PHE 278 (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 TYR* 4.9 0.7 - + - -
274A GLU* 2.9 56.4 + - + +
275A ALA* 3.8 7.2 - - - +
277A ALA* 1.3 78.2 - - + +
279A LYS* 1.3 61.5 + - + +
282A GLY* 3.0 7.3 + - - -
283A GLY* 2.8 42.3 + - - +
284A GLU* 3.5 44.9 - - + -
287A LEU* 4.3 16.8 - - + -
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Residues in contact with LYS 279 (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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275A ALA* 3.0 17.1 + - + +
276A PHE* 3.0 17.9 + - + +
278A PHE* 1.3 79.5 - - - +
280A LYS* 1.3 61.2 + - - +
282A GLY* 4.1 2.9 + - - -
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Residues in contact with LYS 280 (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 PHE 3.1 20.0 + - - -
238A LEU* 3.9 11.9 - - + -
239A THR* 3.8 12.3 - - - +
242A GLU* 3.0 38.4 + - - +
276A PHE* 2.8 22.5 + - + +
277A ALA* 3.2 8.5 + - - +
279A LYS* 1.3 78.5 - - - +
281A TRP* 1.3 96.1 - - + +
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Residues in contact with TRP 281 (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 TYR 3.0 25.7 + - - -
237A PHE* 3.6 29.8 - - + +
277A ALA* 2.8 25.5 + - - +
280A LYS* 1.3 109.7 - - + +
282A GLY* 1.3 59.0 + - - +
283A GLY 4.6 1.1 - - - +
286A GLY* 3.0 18.7 - - - +
287A LEU* 3.8 32.5 - - + +
289A GLU* 4.9 1.9 - - - +
290A GLU* 3.4 40.8 - - + -
294A ARG* 3.6 12.3 - - - -
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Residues in contact with GLY 282 (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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278A PHE 3.0 10.5 + - - -
279A LYS 4.1 3.3 + - - -
280A LYS 3.6 2.0 + - - -
281A TRP* 1.3 75.2 - - - +
283A GLY* 1.3 59.2 + - - -
285A GLU* 3.6 11.0 - - - +
286A GLY* 3.1 19.6 + - - -
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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