Contacts of the helix formed by residues 284 - 292 (chain D) in PDB entry 3MY0
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 284 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283D GLY* 1.3 76.6 - - - +
285D LEU* 1.3 60.7 + - - +
286D TYR* 3.6 6.7 - - - +
287D ASP* 2.6 36.2 + - - -
288D PHE* 2.9 27.0 + - - +
333D SER 3.7 5.6 - - - -
334D ARG* 3.7 25.2 - - - +
336D VAL 3.2 12.8 - - - -
337D LEU* 4.1 8.1 - - - +
338D VAL* 4.4 1.8 - - - -
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Residues in contact with LEU 285 (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 SER* 1.3 69.3 - - - +
286D TYR* 1.3 61.3 + - - +
288D PHE* 4.2 1.6 - - + -
289D LEU* 2.8 51.8 + - + +
302D LEU* 3.9 23.6 - - + -
333D SER* 3.4 20.6 - - - +
336D VAL* 2.7 33.6 + - + +
338D VAL* 3.9 20.7 - - + +
344D CYS* 4.6 7.9 - - - -
404D VAL* 3.8 29.4 - - + +
407D GLU* 6.1 0.4 - - + -
408D ILE* 4.2 15.0 - - + -
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Residues in contact with TYR 286 (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 SER* 3.6 9.0 - - - +
285D LEU* 1.3 78.8 - - - +
287D ASP* 1.3 77.1 + - - +
289D LEU* 3.8 3.9 - - - +
290D GLN* 3.0 49.6 + - - +
333D SER* 3.3 20.5 + - - +
334D ARG* 3.5 58.2 + - + -
421D TYR* 3.2 40.9 - + - -
423D PRO* 5.4 5.3 - - + +
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Residues in contact with ASP 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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282D HIS 3.8 9.4 - - - +
283D GLY* 4.0 4.6 - - - -
284D SER* 2.6 36.7 + - - +
286D TYR* 1.3 90.5 - - - +
288D PHE* 1.3 62.5 + - - +
290D GLN* 3.1 21.8 + - - +
291D ARG* 3.5 7.4 + - - +
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Residues in contact with PHE 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D HIS* 4.1 43.7 + + + +
284D SER 2.9 15.1 + - - +
285D LEU* 3.8 4.5 - - + +
287D ASP* 1.3 75.5 - - - +
289D LEU* 1.3 65.6 + - + +
290D GLN 3.2 0.3 + - - -
291D ARG* 3.3 2.5 + - - -
292D GLN* 2.9 71.4 + - + +
294D LEU* 3.8 22.4 - - + -
298D LEU* 4.2 13.5 - - + -
302D LEU* 3.9 23.1 - - + -
338D VAL* 3.9 20.2 - - + -
342D LEU* 4.5 12.8 - - + -
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Residues in contact with LEU 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D LEU* 2.8 38.5 + - + +
286D TYR* 3.9 1.8 - - - +
288D PHE* 1.3 76.9 - - + +
290D GLN* 1.3 59.4 + - - +
291D ARG 3.4 0.2 - - - -
292D GLN 3.5 2.4 - - - +
294D LEU* 3.6 39.5 - - + -
302D LEU* 4.7 0.4 - - + -
333D SER* 6.2 0.4 - - - -
407D GLU* 2.9 47.6 - - + +
408D ILE* 3.6 8.5 - - + +
411D ARG* 2.5 42.6 + - + +
421D TYR* 3.8 19.1 - - + +
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Residues in contact with GLN 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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286D TYR* 3.0 49.4 + - - +
287D ASP* 3.1 15.4 + - - +
289D LEU* 1.3 77.2 - - - +
291D ARG* 1.3 58.8 + - + +
411D ARG* 3.1 18.4 + - - -
421D TYR* 3.9 29.5 + - - +
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Residues in contact with ARG 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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287D ASP 3.5 6.0 + - - +
288D PHE* 3.3 5.0 + - - +
290D GLN* 1.3 82.1 - - + +
292D GLN* 1.3 68.0 + - + +
293D THR* 4.2 2.1 + - - +
411D ARG* 4.2 4.2 + - - -
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Residues in contact with GLN 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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282D HIS* 5.6 2.4 + - - -
288D PHE* 2.9 57.8 + - + +
289D LEU* 3.5 17.0 - - - +
291D ARG* 1.3 85.5 - - + +
293D THR* 1.3 68.4 + - - +
294D LEU* 4.3 2.6 - - - +
298D LEU* 5.5 3.6 - - - +
342D LEU* 5.7 3.2 - - - +
411D ARG* 3.5 10.8 + - - +
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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