Contacts of the helix formed by residues 282 - 302 (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 GLY 282 (chain A).
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Specific contacts
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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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Residues in contact with GLY 283 (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* 2.8 41.5 + - - -
281A TRP* 4.4 1.0 - - - +
282A GLY* 1.3 76.0 + - - +
284A GLU* 1.3 66.1 + - - -
285A GLU* 3.3 6.7 - - - -
287A LEU* 3.2 14.2 + - - +
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Residues in contact with GLU 284 (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* 3.5 36.4 - - + -
283A GLY* 1.3 72.3 - - - -
285A GLU* 1.3 61.8 + - - +
287A LEU* 3.1 10.0 + - + +
288A ASP* 3.0 39.7 + - - +
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Residues in contact with GLU 285 (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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282A GLY 3.6 13.4 - - - +
283A GLY* 3.5 4.1 - - - -
284A GLU* 1.3 83.8 + - - +
286A GLY* 1.3 64.3 + - - +
288A ASP* 3.2 10.8 + - - +
289A GLU* 2.9 29.8 + - + +
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Residues in contact with GLY 286 (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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281A TRP* 3.0 29.1 - - - +
282A GLY 3.1 17.0 + - - -
285A GLU* 1.3 77.4 - - - +
287A LEU* 1.3 62.1 + - - +
289A GLU* 3.2 19.2 + - - +
290A GLU* 3.0 21.5 + - - +
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Residues in contact with LEU 287 (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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235A ASP 3.9 14.4 - - - +
236A TYR* 3.8 31.4 - - + +
237A PHE* 3.3 35.9 - - + -
277A ALA* 5.2 0.7 - - + -
278A PHE* 4.3 17.5 - - + -
281A TRP* 3.8 24.2 - - + +
283A GLY 3.2 11.5 + - - +
284A GLU* 3.1 14.6 + - + +
286A GLY* 1.3 73.8 - - - +
288A ASP* 1.3 54.8 + - - +
290A GLU* 3.0 4.7 + - - +
291A TRP* 2.8 34.2 + - + +
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Residues in contact with ASP 288 (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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284A GLU* 3.0 27.5 + - - +
285A GLU* 3.4 13.0 - - - +
287A LEU* 1.3 73.2 - - - +
289A GLU* 1.3 66.5 + - - +
291A TRP* 3.0 18.5 + - + +
292A GLN* 2.8 33.5 + - + +
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Residues in contact with GLU 289 (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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281A TRP 4.9 1.7 - - - +
285A GLU* 2.9 20.0 + - - +
286A GLY* 3.2 20.6 + - - +
288A ASP* 1.3 73.5 - - - +
290A GLU* 1.3 64.0 + - - +
292A GLN* 3.1 17.9 + - - +
293A ARG* 3.1 21.4 + - - +
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Residues in contact with GLU 290 (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* 3.9 9.4 - - + -
281A TRP* 3.4 47.2 - - + -
286A GLY 3.0 7.7 + - - +
287A LEU 3.0 9.1 + - - +
289A GLU* 1.3 76.3 - - - +
291A TRP* 1.3 68.0 + - - +
293A ARG* 2.8 39.8 + - - +
294A ARG* 2.9 51.2 + - - +
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Residues in contact with TRP 291 (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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234A GLU 6.0 0.4 - - - -
237A PHE* 3.6 25.4 - + + -
287A LEU* 2.8 16.9 + - + +
288A ASP* 3.1 24.0 - - + +
290A GLU* 1.3 74.1 - - - +
292A GLN* 1.3 80.8 + - + +
293A ARG 3.1 0.2 + - - -
294A ARG* 3.2 8.1 + - - +
295A GLU* 3.3 47.6 + - + +
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Residues in contact with GLN 292 (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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288A ASP* 2.8 28.8 + - + +
289A GLU* 3.2 17.6 + - - +
291A TRP* 1.3 84.6 - - + +
293A ARG* 1.3 64.6 + - - +
295A GLU* 3.3 5.3 + - - +
296A GLU* 3.1 40.4 + - - +
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Residues in contact with ARG 293 (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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289A GLU 3.1 9.4 + - - +
290A GLU* 2.8 40.4 + - - +
291A TRP 3.2 0.4 - - - -
292A GLN* 1.3 78.7 - - - +
294A ARG* 1.3 89.4 + - - +
296A GLU* 3.5 12.7 + - - +
297A GLY* 3.1 17.0 + - - -
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Residues in contact with ARG 294 (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* 3.6 43.9 + - + +
239A THR* 6.3 1.2 - - - +
281A TRP* 3.6 24.4 - - - -
290A GLU* 2.9 40.2 + - - +
291A TRP* 3.2 4.7 + - - +
293A ARG* 1.3 102.5 - - - +
295A GLU* 1.3 57.0 + - + +
297A GLY* 3.1 4.1 + - - -
298A LYS* 3.1 27.0 + - - +
301A ARG* 4.5 5.0 + - - -
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Residues in contact with GLU 295 (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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291A TRP* 3.3 55.4 + - + +
292A GLN* 3.7 7.6 - - - +
294A ARG* 1.3 75.1 - - + +
296A GLU* 1.3 56.5 + - - +
298A LYS* 2.7 36.2 + - - +
299A ALA* 2.8 34.9 + - - +
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Residues in contact with GLU 296 (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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292A GLN* 3.1 42.1 + - - +
293A ARG* 3.7 12.2 + - - +
294A ARG 3.4 0.2 - - - -
295A GLU* 1.3 72.0 - - - +
297A GLY* 1.3 56.5 + - - +
299A ALA* 3.5 6.8 - - + +
300A HIS* 2.7 37.4 + - - +
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Residues in contact with GLY 297 (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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293A ARG 3.1 10.4 + - - -
294A ARG* 3.1 10.0 + - - -
296A GLU* 1.3 76.1 - - - +
298A LYS* 1.3 51.3 + - - +
300A HIS* 3.0 8.9 + - - +
301A ARG* 2.6 55.8 + - - +
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Residues in contact with LYS 298 (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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294A ARG 3.1 12.1 + - - +
295A GLU* 2.7 35.5 + - - +
297A GLY* 1.3 70.8 - - - +
299A ALA* 1.3 64.3 + - - +
301A ARG* 3.6 25.5 - - - +
302A ARG* 3.2 61.5 + - - +
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Residues in contact with ALA 299 (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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295A GLU 2.8 21.7 + - - +
296A GLU* 3.5 8.7 - - + +
298A LYS* 1.3 69.6 - - - +
300A HIS* 1.3 66.7 + - - +
302A ARG* 3.0 28.0 + - - +
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Residues in contact with HIS 300 (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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296A GLU 2.7 21.6 + - - +
297A GLY* 3.4 8.5 - - - +
299A ALA* 1.3 71.3 - - - +
301A ARG* 1.3 73.6 + - + +
302A ARG 3.2 10.4 + - - -
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Residues in contact with ARG 301 (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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294A ARG 4.5 4.2 + - - -
297A GLY* 2.6 39.3 + - - +
298A LYS* 3.6 35.8 - - + +
299A ALA 3.3 0.4 - - - -
300A HIS* 1.3 81.2 - - + +
302A ARG* 1.3 60.0 + - - +
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Residues in contact with ARG 302 (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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298A LYS* 3.2 51.3 + - - +
299A ALA* 3.0 24.2 + - - +
300A HIS 3.2 11.7 - - - -
301A ARG* 1.3 75.4 - - - +
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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