Contacts of the helix formed by residues 253 - 263 (chain D) in PDB entry 2DB3
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 ARG 253 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252D LEU* 1.3 71.4 - - - +
254D ASP* 1.3 66.3 + - - +
255D ILE* 3.1 7.5 - - + +
256D ILE* 2.6 40.2 + - + +
257D ILE* 3.3 7.6 + - - -
305D SER* 2.8 38.5 + - - +
308D LEU* 3.6 33.9 + - + +
309D GLU* 4.0 19.2 - - + +
346D TYR* 6.0 3.0 - - - -
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Residues in contact with ASP 254 (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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252D LEU 3.4 5.5 + - - +
253D ARG* 1.3 80.2 + - - +
255D ILE* 1.3 61.8 + - - +
257D ILE* 3.2 11.8 + - - +
258D ASP* 3.0 29.2 + - - +
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Residues in contact with ILE 255 (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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253D ARG* 2.8 7.7 + - + +
254D ASP* 1.3 77.1 - - - +
256D ILE* 1.3 82.3 + - + +
258D ASP* 3.2 21.8 + - + +
259D ASN* 2.9 22.8 + - - +
308D LEU* 3.9 18.6 - - + -
343D PHE 3.9 9.4 - - - +
344D GLU* 2.9 33.0 - - + +
345D SER* 3.4 21.3 - - - -
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Residues in contact with ILE 256 (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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252D LEU* 4.8 9.2 - - + -
253D ARG* 2.6 24.0 + - + +
255D ILE* 1.3 86.7 - - + +
257D ILE* 1.3 56.9 + - - +
259D ASN* 3.1 5.2 + - - +
260D VAL* 2.9 31.8 + - + +
301D LEU* 3.6 40.2 - - + +
304D LEU* 4.0 18.2 - - + -
305D SER* 4.0 22.0 - - - +
308D LEU* 4.0 9.4 - - + -
341D PHE* 3.3 24.0 - - + +
342D ALA* 4.8 4.3 - - - -
345D SER* 5.6 0.4 - - - -
347D LEU* 5.4 0.4 - - + -
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Residues in contact with ILE 257 (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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247D PHE* 4.8 9.4 - - + -
248D THR* 2.9 61.0 - - + +
252D LEU* 3.7 42.4 - - + +
253D ARG 4.0 4.9 - - - +
254D ASP* 3.2 11.1 + - - +
256D ILE* 1.3 71.7 - - - +
258D ASP* 1.3 62.5 + - - +
260D VAL* 3.6 8.4 - - + +
261D ASN* 3.0 38.7 + - - +
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Residues in contact with ASP 258 (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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254D ASP* 3.0 20.3 + - - +
255D ILE* 3.3 19.5 - - + +
257D ILE* 1.3 80.8 - - - +
259D ASN* 1.3 59.7 + - - +
261D ASN* 3.2 8.0 + - - +
262D LYS* 3.0 39.4 + - - +
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Residues in contact with ASN 259 (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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215D PHE* 3.7 4.9 - - + -
255D ILE* 2.9 22.3 + - - +
256D ILE* 3.1 6.7 + - - +
258D ASP* 1.3 75.9 - - - +
260D VAL* 1.3 60.8 + - - +
262D LYS* 3.2 11.0 + - - +
263D SER* 2.8 34.6 + - - -
340D LYS 3.4 20.6 - - - +
341D PHE* 3.0 28.0 + - - +
342D ALA 4.1 0.4 - - - -
343D PHE* 3.2 47.9 + - - +
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Residues in contact with VAL 260 (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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247D PHE* 4.2 25.8 - - + -
252D LEU* 5.2 1.8 - - + -
256D ILE* 2.9 24.5 + - + +
257D ILE* 3.6 12.8 - - + +
259D ASN* 1.3 73.9 - - - +
261D ASN* 1.3 66.7 - - - +
263D SER* 3.1 16.0 + - - -
264D GLY 3.3 7.8 + - - -
265D TYR* 3.3 37.0 + - + +
301D LEU* 3.7 34.3 - - + -
341D PHE* 4.4 6.5 - - + -
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Residues in contact with ASN 261 (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 ILE* 3.0 29.9 + - - +
258D ASP* 3.4 11.7 - - - +
259D ASN 3.1 0.2 - - - -
260D VAL* 1.3 80.8 - - - +
262D LYS* 1.3 58.4 + - + +
264D GLY* 3.0 19.2 + - - -
265D TYR 4.6 8.0 + - - +
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Residues in contact with LYS 262 (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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215D PHE* 3.3 44.5 - - + +
258D ASP* 3.0 23.6 + - - +
259D ASN* 3.2 7.1 + - - +
261D ASN* 1.3 72.0 - - + +
263D SER* 1.3 61.0 + - - +
264D GLY* 2.9 7.2 + - - -
343D PHE* 3.6 26.5 - - - -
344D GLU* 4.3 6.5 + - - -
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Residues in contact with SER 263 (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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215D PHE* 4.0 5.3 - - - -
259D ASN 2.8 22.5 + - - -
260D VAL* 3.1 9.8 + - - -
262D LYS* 1.3 76.0 - - - +
264D GLY* 1.3 59.5 + - - +
265D TYR* 3.4 29.5 + - - -
340D LYS* 3.2 38.0 + - - +
341D PHE* 3.7 4.8 - - - -
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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