Contacts of the helix formed by residues 283 - 292 (chain A) in PDB entry 2DH3
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 ASP 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A SER* 3.3 10.9 + - - +
282A SER* 1.3 77.2 + - - +
284A LEU* 1.3 68.5 + - - +
285A GLN* 3.3 24.1 + - - +
286A GLN* 3.3 28.8 + - + +
287A ILE* 3.2 25.7 + - - +
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Residues in contact with LEU 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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282A SER 3.5 3.9 + - - -
283A ASP* 1.3 76.3 + - - +
285A GLN* 1.3 75.2 + - - +
287A ILE* 3.1 9.3 + - + +
288A LEU* 2.9 51.4 + - + +
303A TYR* 4.1 28.2 - - + +
320A GLN* 4.9 21.5 - - + +
321A TYR* 4.1 31.6 - - + -
324A ALA* 5.1 4.5 - - + -
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Residues in contact with GLN 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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283A ASP* 3.3 22.6 + - - +
284A LEU* 1.3 95.6 - - - +
286A GLN* 1.3 63.9 + - - +
288A LEU* 4.2 11.6 - - + +
289A SER* 3.3 24.4 + - - -
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Residues in contact with GLN 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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250A GLU* 3.8 24.7 - - - +
279A THR* 4.4 1.8 + - - -
281A SER* 2.9 34.3 + - - +
283A ASP* 3.3 25.7 + - - +
284A LEU 3.3 0.4 - - - -
285A GLN* 1.3 76.1 - - - +
287A ILE* 1.3 59.3 + - - +
289A SER* 2.8 20.8 + - - +
290A LEU* 3.5 21.9 - - + +
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Residues in contact with ILE 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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279A THR* 4.7 8.1 - - + -
281A SER* 4.2 5.6 - - - +
282A SER 4.1 13.2 - - - +
283A ASP 3.2 20.1 + - - +
284A LEU* 3.1 9.7 + - + +
286A GLN* 1.3 76.3 - - - +
288A LEU* 1.3 66.3 + - + +
290A LEU* 3.3 12.6 + - + +
291A LEU* 3.2 24.6 + - + +
299A LEU* 3.6 22.6 - - + +
301A SER* 3.9 27.8 - - - +
303A TYR* 4.2 15.3 - - + -
321A TYR* 4.1 26.2 - - + +
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Residues in contact with LEU 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 LEU* 2.9 39.0 + - + +
285A GLN* 4.2 10.8 - - + +
286A GLN 3.5 0.2 - - - -
287A ILE* 1.3 76.8 - - + +
289A SER* 1.3 52.2 - - - +
291A LEU* 3.0 11.7 + - + +
292A GLU* 2.7 37.7 + - - +
295A LYS* 4.5 9.7 + - - +
321A TYR* 5.4 1.1 - - + -
324A ALA* 3.9 30.1 - - + +
325A THR* 3.7 30.1 - - + -
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Residues in contact with SER 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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256A SER* 4.3 9.5 - - - -
285A GLN 3.3 12.9 + - - -
286A GLN* 2.8 26.0 + - - +
288A LEU* 1.3 74.4 - - - +
290A LEU* 1.3 65.4 + - - +
292A GLU* 3.5 19.4 + - - +
293A SER 4.1 1.9 + - - -
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Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A ILE* 3.6 36.3 - - + +
250A GLU* 6.1 2.0 - - + -
255A ALA* 4.0 25.6 - - + -
256A SER* 4.4 9.8 - - - +
259A LEU* 4.6 12.3 - - + +
279A THR* 4.8 10.1 - - + +
281A SER* 6.4 0.4 - - - -
286A GLN* 3.5 26.0 + - + +
287A ILE* 3.3 8.9 + - + +
288A LEU 3.3 0.4 - - - -
289A SER* 1.3 81.9 + - - +
291A LEU* 1.3 61.4 + - - +
293A SER* 3.3 23.0 - - - -
294A ASN 4.6 0.3 + - - -
297A LEU* 5.4 6.5 - - + +
299A LEU* 4.2 20.6 - - + -
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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 ILE* 3.2 21.8 + - + +
288A LEU* 3.0 13.8 + - + +
290A LEU* 1.3 75.5 - - - +
292A GLU* 1.3 60.6 + - - +
293A SER 3.0 7.6 + - - -
294A ASN 3.7 18.1 + - - +
295A LYS* 3.7 36.3 + - + +
297A LEU* 3.6 31.2 - - + +
299A LEU* 4.3 19.1 - - + -
321A TYR* 3.5 26.7 - - + +
325A THR* 4.1 18.8 - - + -
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Residues in contact with GLU 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 LEU* 2.7 16.9 + - - +
289A SER* 3.6 16.8 - - - +
290A LEU 3.3 1.0 - - - -
291A LEU* 1.3 72.0 - - - +
293A SER* 1.3 63.4 + - - +
295A LYS* 4.9 9.7 + - - +
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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