Contacts of the helix formed by residues 289 - 299 (chain D) in PDB entry 5MR5
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 ASN 289 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274D ASN 4.6 2.9 - - - +
285D CYS* 4.2 9.1 - - - +
286D PRO 3.1 15.5 + - - +
287D ALA* 3.1 10.4 - - + +
288D ASP* 1.3 73.1 - - - +
290D TYR* 1.3 62.8 + - - +
291D GLN* 3.3 10.0 + - - +
292D ALA* 3.0 37.3 + - + +
293D CYS* 3.7 13.9 + - - +
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Residues in contact with TYR 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283D THR* 3.3 44.1 - - + +
285D CYS* 3.7 11.7 - - - -
288D ASP 3.3 6.8 + - - -
289D ASN* 1.3 74.3 - - - +
291D GLN* 1.3 65.3 + - + +
293D CYS* 3.0 7.9 + - - +
294D LEU* 3.0 27.1 + - + +
350D ASN* 3.5 23.5 + - + +
351D ALA* 3.2 41.6 - - + +
354D ALA* 3.4 25.0 - - + +
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Residues in contact with GLN 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D SER* 5.2 3.1 - - - -
217D TYR* 3.9 32.1 - - - -
289D ASN* 3.3 7.2 + - - +
290D TYR* 1.3 80.0 - - + +
292D ALA* 1.3 56.9 + - - +
294D LEU* 3.3 17.3 + - - +
295D GLY* 2.9 26.9 + - - -
355D PHE* 4.3 13.3 - - - -
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Residues in contact with ALA 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D ASN* 3.6 21.4 + - + +
289D ASN* 3.0 32.9 + - + +
291D GLN* 1.3 76.6 - - - +
293D CYS* 1.3 57.9 + - - +
295D GLY* 4.0 1.2 - - - -
296D SER* 2.9 33.6 + - - -
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Residues in contact with CYS 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D ASN* 3.5 18.0 - - - +
275D CYS* 2.0 61.9 - - - -
289D ASN 3.7 7.1 + - - +
290D TYR 3.0 9.3 + - - +
292D ALA* 1.3 76.3 - - - +
294D LEU* 1.3 65.6 + - - +
296D SER 3.2 0.9 + - - -
297D TYR* 2.9 20.3 + - - +
347D CYS* 4.0 14.6 - - - -
348D LEU* 3.9 21.3 - - - -
351D ALA* 4.3 6.5 - - + -
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Residues in contact with LEU 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D TYR* 4.4 7.6 - - + -
221D PHE* 3.5 28.9 - - + -
290D TYR* 3.0 16.9 + - + +
291D GLN* 3.7 17.5 - - - +
293D CYS* 1.3 76.3 - - - +
295D GLY* 1.3 57.6 + - - +
297D TYR* 3.2 5.7 + - - +
298D ALA* 2.9 28.6 + - - +
348D LEU* 4.8 3.6 - - + -
351D ALA* 3.5 47.6 - - + +
352D ILE* 3.8 18.8 - - + +
355D PHE* 3.8 29.6 - - + -
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Residues in contact with GLY 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D TYR* 3.0 28.2 + - - -
291D GLN 2.9 14.8 + - - -
292D ALA* 4.0 1.8 - - - -
294D LEU* 1.3 76.6 - - - +
296D SER* 1.3 57.1 + - - +
298D ALA* 3.4 1.8 + - - +
299D GLY* 2.9 26.3 + - - -
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Residues in contact with SER 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267D ARG* 4.5 3.6 - - - +
270D ASP* 3.6 11.4 + - - +
271D PHE* 3.5 32.2 - - - +
274D ASN* 2.9 23.9 + - - -
292D ALA 2.9 20.7 + - - -
293D CYS* 3.2 4.9 + - - -
295D GLY* 1.3 73.2 - - - +
297D TYR* 1.3 66.9 + - - +
299D GLY* 3.5 8.2 + - - -
300D MET* 3.7 17.8 + - - +
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Residues in contact with TYR 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220D LEU* 4.4 13.2 - - + -
221D PHE* 3.7 28.7 - + + -
271D PHE* 4.2 11.6 - + + -
293D CYS 2.9 13.7 + - - +
294D LEU* 3.2 9.2 + - - +
296D SER* 1.3 76.3 - - - +
298D ALA* 1.3 67.1 + - - +
300D MET* 3.1 26.7 + - + +
301D ILE* 4.2 8.7 + - + +
307D PRO* 3.5 51.2 + - + +
308D ASN* 3.6 5.7 + - - -
309D TYR* 4.2 5.6 + + - -
319D VAL* 3.5 39.5 - - + +
342D PHE* 5.2 1.3 - + - -
348D LEU* 4.1 27.8 - - + -
352D ILE* 5.3 1.6 - - + -
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Residues in contact with ALA 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D PHE* 4.3 21.3 - - + +
217D TYR* 4.0 21.5 - - + -
220D LEU* 3.9 20.2 - - + -
221D PHE* 4.8 0.7 - - + -
294D LEU 2.9 15.0 + - - +
295D GLY 3.8 4.5 - - - +
297D TYR* 1.3 77.3 - - - +
299D GLY* 1.3 57.5 + - - +
300D MET 3.1 4.9 + - - -
301D ILE* 3.2 31.3 + - - +
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Residues in contact with GLY 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D PHE* 6.0 1.6 - - - -
267D ARG* 2.8 46.4 + - - +
295D GLY 2.9 17.0 + - - -
296D SER* 3.9 4.3 - - - -
297D TYR 3.2 1.0 - - - -
298D ALA* 1.3 76.5 - - - +
300D MET* 1.3 58.3 + - - +
301D ILE 3.5 1.1 - - - -
303D PHE* 3.2 11.5 - - - -
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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