Contacts of the helix formed by residues 286 - 291 (chain D) in PDB entry 5MKE
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 SER 286 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257D PHE* 4.5 15.8 + - - +
260D THR* 6.0 3.0 - - - +
261D PRO 5.0 8.6 + - - -
262D VAL* 5.0 4.9 - - - -
263D SER* 4.5 0.4 - - - -
270D PHE* 5.0 2.3 + - - +
281D LYS 4.5 0.9 - - - -
282D PHE* 3.1 48.4 + - - -
284D GLU 3.5 2.4 - - - -
285D GLY* 1.3 80.3 - - - +
287D LEU* 1.3 56.8 + - - +
288D LEU 3.4 0.4 - - - -
289D ASP* 3.7 1.8 + - - +
290D GLY* 2.6 32.1 + - - -
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Residues in contact with LEU 287 (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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257D PHE* 3.3 44.2 - - + -
282D PHE* 3.6 27.0 + - + -
286D SER* 1.3 79.1 - - - +
288D LEU* 1.3 60.0 + - - +
290D GLY* 3.8 1.1 - - - +
291D LEU* 2.6 40.9 + - + +
424D ILE* 4.9 12.1 - - + -
426D PHE* 4.2 24.0 - - + -
439D VAL* 5.3 1.3 - - + -
441D LEU* 3.7 30.7 - - + -
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Residues in contact with LEU 288 (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 2.9 19.0 + - - +
284D GLU* 3.2 31.0 - - + +
287D LEU* 1.3 81.4 - - - +
289D ASP* 1.3 69.4 + - - +
291D LEU* 2.9 20.9 - - - +
395D LEU* 5.8 3.4 - - + -
399D ARG* 3.5 22.4 + - - +
402D THR* 3.3 45.1 - - + +
403D ALA* 4.3 21.5 - - + -
406D VAL* 5.9 3.4 - - + -
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Residues in contact with ASP 289 (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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284D GLU* 3.8 17.4 + - - +
285D GLY* 4.6 8.5 - - - -
286D SER 3.8 4.7 + - - +
288D LEU* 1.3 88.5 - - - +
290D GLY* 1.3 65.7 + - - +
291D LEU 4.5 0.9 - - - -
292D TYR* 3.6 20.5 - - + -
293D TRP* 3.8 27.3 - - + -
399D ARG* 4.4 2.9 - - - +
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Residues in contact with GLY 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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256D LEU 5.3 1.6 - - - -
257D PHE* 3.3 29.5 - - - -
286D SER 2.6 25.9 + - - -
287D LEU 2.9 4.2 + - - -
289D ASP* 1.3 78.3 - - - +
291D LEU* 1.3 57.1 + - - -
292D TYR* 3.4 10.0 + - - +
310D PHE* 4.0 10.9 - - - -
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Residues in contact with LEU 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D PHE* 3.8 11.8 - - + -
287D LEU* 2.6 25.9 + - + +
288D LEU* 2.9 13.4 - - - +
290D GLY* 1.3 67.8 - - - +
292D TYR* 1.3 56.7 + - - +
309D ILE* 4.7 16.4 - - + -
315D LEU* 4.0 32.1 - - + -
319D PRO* 4.2 18.6 - - + -
395D LEU* 5.8 2.2 - - + -
399D ARG* 2.7 32.7 + - - +
426D PHE* 3.8 36.8 - - + -
428D VAL* 5.1 6.7 - - + -
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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