Contacts of the helix formed by residues 252 - 263 (chain D) in PDB entry 2ESN
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 252 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174D ASP* 3.3 10.1 + - - +
175D ARG* 2.9 65.7 + - - +
177D VAL* 3.7 31.0 - - + -
250D ALA 3.5 1.2 + - - -
251D PRO* 1.3 68.0 - - - +
253D HIS* 1.3 59.5 + - - +
255D ALA* 4.2 0.4 - - - -
256D ARG* 2.7 84.2 + - + +
266D LEU* 4.5 4.2 - - + +
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Residues in contact with HIS 253 (chain D).
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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108D TYR* 3.7 4.5 - - - +
111D PHE* 3.5 31.3 + + - -
112D ALA* 4.2 23.5 + - + -
116D PRO* 6.3 0.2 - - - +
172D PHE* 3.6 34.7 - + + -
174D ASP* 2.9 21.4 + - - +
252D ARG* 1.3 79.6 - - - +
254D ALA* 1.3 60.6 + - - +
256D ARG* 4.0 5.7 - - - +
257D ALA* 3.4 18.7 + - - +
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Residues in contact with ALA 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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108D TYR* 3.8 25.7 - - + -
111D PHE* 3.7 15.1 - - + -
234D VAL* 4.2 10.1 - - + -
235D LEU* 4.4 7.4 - - + -
238D LEU* 3.7 22.5 - - + +
251D PRO* 3.2 10.7 + - + +
253D HIS* 1.3 77.8 - - - +
255D ALA* 1.3 64.6 + - - +
257D ALA* 3.2 5.4 + - - +
258D LEU* 3.1 19.8 + - - +
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Residues in contact with ALA 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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177D VAL* 4.0 6.7 - - + -
179D VAL* 3.6 31.9 - - + -
238D LEU* 3.8 14.3 - - + +
250D ALA* 5.1 1.3 - - + +
251D PRO 3.1 13.4 + - - +
252D ARG 3.2 5.8 + - - +
254D ALA* 1.3 75.7 - - - +
256D ARG* 1.3 52.3 + - - +
258D LEU* 3.2 2.6 + - - +
259D ALA* 2.8 36.4 + - - +
264D LEU* 4.3 1.6 - - - +
266D LEU* 3.8 17.4 - - + +
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Residues in contact with ARG 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 ARG* 2.7 72.4 + - + +
253D HIS* 4.0 5.8 - - - +
255D ALA* 1.3 68.5 - - - +
257D ALA* 1.3 65.9 + - - +
259D ALA* 3.3 16.8 + - - +
260D GLU 4.7 1.4 + - - -
266D LEU* 3.7 20.6 - - + +
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Residues in contact with ALA 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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239B PHE* 4.2 8.4 - - + -
261B ALA* 3.7 22.1 - - - +
111D PHE* 3.5 31.6 - - + -
253D HIS 3.4 5.1 + - - +
254D ALA 3.2 9.6 + - - +
256D ARG* 1.3 79.8 - - - +
258D LEU* 1.3 70.6 + - + +
259D ALA 3.9 0.2 + - - -
260D GLU* 5.0 1.6 + - - +
261D ALA* 5.0 0.3 + - - +
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Residues in contact with LEU 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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235B LEU* 5.5 0.2 - - + -
239B PHE* 3.5 31.6 - - + -
258B LEU* 4.5 6.1 - - + -
235D LEU* 3.5 49.6 - - + +
238D LEU* 3.7 22.9 - - + -
239D PHE* 3.9 21.1 - - + -
254D ALA 3.1 12.7 + - - +
255D ALA 3.5 2.5 - - - +
257D ALA* 1.3 87.0 - - + +
259D ALA* 1.3 65.7 + - - +
260D GLU 3.3 2.9 - - - -
261D ALA* 3.8 5.8 - - - -
262D ALA* 2.9 30.0 + - + +
264D LEU* 4.0 2.9 - - + -
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Residues in contact with ALA 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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182D ARG* 3.9 17.9 - - - +
255D ALA 2.8 16.1 + - - +
256D ARG* 3.3 15.2 + - - +
257D ALA 3.4 0.2 - - - -
258D LEU* 1.3 76.5 - - - +
260D GLU* 1.3 59.6 + - + +
263D GLY* 2.9 9.2 + - - -
264D LEU* 2.9 33.3 + - - +
266D LEU* 3.9 20.2 - - + -
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Residues in contact with GLU 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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261B ALA* 6.6 0.2 - - - -
182D ARG* 2.7 42.1 + - - +
256D ARG 4.7 1.6 + - - -
257D ALA 5.0 1.0 + - - -
258D LEU 3.3 0.2 - - - -
259D ALA* 1.3 75.7 - - + +
261D ALA* 1.3 67.2 + - - +
262D ALA 3.4 0.5 + - - -
263D GLY* 3.5 8.7 + - - -
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Residues in contact with ALA 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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257B ALA 3.6 24.5 - - - +
258B LEU* 4.2 2.2 - - + -
260B GLU* 6.4 1.1 - - + -
261B ALA* 3.9 25.7 - - + +
239D PHE* 3.8 20.1 - - + -
257D ALA 5.2 0.6 + - - -
258D LEU* 3.2 9.4 + - - +
260D GLU* 1.3 80.6 - - - +
262D ALA* 1.3 58.9 + - - +
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Residues in contact with ALA 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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238D LEU 3.7 15.7 - - - +
239D PHE* 3.9 25.3 - - + +
242D GLY* 3.3 25.0 - - - +
258D LEU* 2.9 18.6 + - + +
261D ALA* 1.3 76.7 - - - +
263D GLY* 1.4 58.0 + - - +
264D LEU* 3.6 17.9 - - + -
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Residues in contact with GLY 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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181D ARG* 3.3 8.8 - - - +
182D ARG* 2.8 38.7 + - - +
242D GLY* 4.6 0.5 - - - +
259D ALA 2.9 11.7 + - - -
260D GLU 3.5 9.0 + - - -
262D ALA* 1.4 79.2 - - - +
264D LEU* 1.3 58.7 + - - -
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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