Contacts of the helix formed by residues 286 - 294 (chain A) in PDB entry 3MDY
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A LDN 4.5 2.4 - - - -
285A GLY* 1.3 75.3 - - - -
287A LEU* 1.3 60.0 + - - +
288A TYR* 3.1 19.9 + - - +
289A ASP* 3.0 23.7 + - - -
290A TYR* 2.9 27.5 + - - +
335A SER 3.4 8.3 - - - -
336A LYS* 3.7 20.6 - - - +
338A ILE 3.0 14.6 - - - -
339A LEU* 3.8 7.7 - - - +
340A VAL* 4.3 2.5 - - - -
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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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286A SER* 1.3 72.6 - - - +
288A TYR* 1.3 57.1 + - - +
290A TYR* 4.3 1.6 - - + -
291A LEU* 2.9 52.4 + - + +
304A LEU* 4.0 26.0 - - + -
308A SER* 4.5 6.5 - - - +
335A SER* 3.4 13.5 - - - +
338A ILE* 2.7 35.0 + - + +
340A VAL* 3.8 23.0 - - + +
346A CYS* 4.1 7.4 - - - -
406A ILE* 3.7 29.8 - - + -
410A VAL* 3.9 13.5 - - + -
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Residues in contact with TYR 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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286A SER* 3.1 8.0 + - - +
287A LEU* 1.3 78.0 - - - +
289A ASP* 1.3 79.8 + - - +
291A LEU* 4.2 1.2 - - - +
292A LYS* 2.8 61.5 + - + +
335A SER* 3.3 16.0 + - - +
336A LYS* 3.7 48.4 + - + +
423A TYR* 3.4 43.0 - + - -
425A LEU* 4.4 16.2 - - + -
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Residues in contact with ASP 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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1A LDN 3.5 43.7 - - - -
284A ASN 3.9 11.4 - - - +
285A GLY* 4.6 0.2 - - - -
286A SER* 3.0 32.0 + - - +
288A TYR* 1.3 92.7 - - - +
290A TYR* 1.3 64.1 + - - +
292A LYS* 3.2 7.9 + - - +
293A SER* 3.0 23.4 + - - -
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Residues in contact with TYR 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ASN* 4.2 35.0 + - + +
286A SER 2.9 16.1 + - - +
287A LEU* 3.8 2.2 - - + +
289A ASP* 1.3 79.0 - - - +
291A LEU* 1.3 65.4 + - + +
293A SER* 2.7 26.7 + - - -
294A THR* 3.1 33.5 + - + +
296A LEU* 4.2 7.6 - - + +
300A SER* 5.6 3.6 + - - -
304A LEU* 4.2 26.2 - - + -
340A VAL* 3.8 35.0 - - + -
344A GLY* 5.3 6.7 - - - -
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Residues in contact with LEU 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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287A LEU* 2.9 36.7 + - + +
288A TYR 4.3 0.4 - - - +
290A TYR* 1.3 70.8 - - + +
292A LYS* 1.3 64.0 + - - +
294A THR 3.2 3.9 - - - +
296A LEU* 3.8 33.0 - - + -
304A LEU* 4.3 13.0 - - + -
335A SER* 5.4 0.7 - - - -
409A GLU* 3.9 21.1 - - + +
410A VAL* 3.8 26.9 - - + +
413A ARG* 2.6 44.2 + - + -
423A TYR* 3.7 25.3 - - + +
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Residues in contact with LYS 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 TYR* 2.8 60.4 + - + +
289A ASP* 3.2 8.1 + - - +
291A LEU* 1.3 77.6 - - - +
293A SER* 1.3 59.9 + - - +
294A THR 3.5 0.4 + - - -
413A ARG* 4.0 7.0 + - - +
423A TYR* 3.4 32.5 - - + -
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Residues in contact with SER 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 ASP 3.0 13.1 + - - -
290A TYR* 2.7 28.5 + - - -
292A LYS* 1.3 79.8 - - - +
294A THR* 1.3 64.9 + - - +
413A ARG* 4.7 1.1 - - - -
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Residues in contact with THR 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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290A TYR* 3.1 47.4 + - + +
291A LEU* 3.2 18.0 - - - +
292A LYS 3.5 1.6 + - - -
293A SER* 1.3 85.6 + - - +
295A THR* 1.3 78.8 + - - +
296A LEU* 4.3 5.9 - - + +
413A ARG* 3.2 13.3 + - - +
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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