Contacts of the helix formed by residues 286 - 294 (chain A) in PDB entry 5DVX
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 286 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A GLU 3.5 2.2 + - - -
285A GLU* 1.3 69.8 - - - +
287A SER* 1.3 63.8 + - - +
288A ALA* 3.1 13.9 + - - +
289A TYR* 3.1 40.4 + - + -
290A GLU* 3.0 8.7 + - - +
315A ALA 4.6 4.5 + - - +
349A VAL* 4.8 4.2 - - - +
350A SER 3.1 32.2 + - - +
351A LEU* 4.2 3.0 - - + +
355A GLN* 2.8 37.2 + - - +
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Residues in contact with SER 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLU* 3.4 9.7 + - - -
286A ASN* 1.3 73.1 + - - +
288A ALA* 1.3 66.0 + - - +
290A GLU* 3.4 14.3 + - - +
291A GLN* 3.4 17.9 + - - +
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Residues in contact with ALA 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 ASN* 3.1 6.3 + - - +
287A SER* 1.3 80.5 + - - +
289A TYR* 1.3 62.6 + - - +
291A GLN* 3.1 28.2 + - - +
292A LEU 4.1 0.9 + - - -
311A LEU* 3.9 5.3 - - + +
312A ASP 5.2 1.3 - - - +
315A ALA* 3.5 44.4 - - + +
316A LEU* 3.9 14.9 - - + +
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Residues in contact with TYR 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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227A LEU* 4.2 20.2 - - + -
250A ILE* 3.4 16.1 - - + +
279A LEU* 3.6 34.5 - - + +
286A ASN* 3.1 37.0 + - + +
288A ALA* 1.3 74.4 - - - +
290A GLU* 1.3 60.7 + - - +
292A LEU* 2.9 13.2 + - + +
293A LEU* 2.9 46.0 + - + +
315A ALA 4.7 0.2 - - - -
316A LEU* 2.7 56.1 + - + -
349A VAL* 4.2 7.0 - - + -
351A LEU* 3.8 23.6 - - + -
355A GLN* 4.4 0.4 - - - +
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Residues in contact with GLU 290 (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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285A GLU* 3.8 23.8 - - - +
286A ASN 3.0 17.0 + - - +
287A SER* 3.6 10.8 - - - +
288A ALA 3.2 0.4 - - - -
289A TYR* 1.3 77.9 - - - +
291A GLN* 1.3 58.7 + - - +
293A LEU* 4.3 6.7 - - - +
294A SER* 2.8 52.9 + - - -
354A LYS* 6.0 2.6 - - - -
355A GLN* 3.0 28.4 + - - +
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Residues in contact with GLN 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 SER* 3.4 12.2 + - - +
288A ALA* 3.1 21.3 - - - +
289A TYR 3.1 0.2 - - - -
290A GLU* 1.3 79.6 - - - +
292A LEU* 1.3 62.1 + - + +
294A SER* 3.5 3.7 + - - -
295A ARG* 3.4 23.0 + - - +
308A VAL* 5.1 2.6 - - - +
309A PRO* 4.9 6.1 - - - +
310A GLY 4.4 4.0 - - - +
311A LEU* 3.1 36.9 - - + +
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Residues in contact with LEU 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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195A LEU* 4.3 19.5 - - + +
204A LEU* 4.5 20.6 - - + -
225A LEU* 4.5 10.1 - - + -
227A LEU* 5.6 9.9 - - + -
288A ALA 4.8 1.8 - - - +
289A TYR* 2.9 14.5 + - + +
291A GLN* 1.3 81.7 - - + +
293A LEU* 1.3 68.1 + - + +
294A SER 3.2 2.2 - - - -
295A ARG* 3.0 18.5 + - - +
296A LEU* 3.6 14.6 + - + +
308A VAL* 4.3 22.9 - - + -
311A LEU* 4.5 20.0 - - + -
316A LEU* 4.1 29.2 - - + -
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Residues in contact with LEU 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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227A LEU* 5.3 5.8 - - + -
289A TYR* 2.9 26.1 + - + +
290A GLU* 4.3 8.7 - - - +
292A LEU* 1.3 78.9 - - + +
294A SER* 1.3 62.2 + - - +
295A ARG 3.0 1.8 + - - -
296A LEU* 3.2 39.4 + - + +
297A GLU 4.8 0.7 + - - -
351A LEU* 4.0 14.8 - - + -
355A GLN* 3.5 48.2 - - + +
358A THR* 3.7 19.4 - - + +
359A LEU* 3.9 29.4 - - + +
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Residues in contact with SER 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 GLU* 2.8 40.0 + - - +
291A GLN* 3.5 10.6 + - - -
293A LEU* 1.3 76.8 - - - +
295A ARG* 1.3 67.4 + - - +
296A LEU 3.5 0.7 - - - -
297A GLU* 4.9 5.9 + - - +
298A GLU* 4.6 2.8 - - - +
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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