Contacts of the helix formed by residues 252 - 263 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A ASP* 3.3 10.9 + - - +
175A ARG* 2.9 71.7 + - - +
177A VAL* 3.7 29.3 - - + +
250A ALA 3.3 1.2 + - - -
251A PRO* 1.3 72.5 - - - +
253A HIS* 1.3 56.7 + - - +
255A ALA* 4.3 0.2 - - - -
256A ARG* 2.9 80.7 + - + +
266A LEU* 4.8 2.4 - - + +
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Residues in contact with HIS 253 (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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108A TYR* 3.6 11.4 - - - +
111A PHE* 3.8 26.1 + + - -
112A ALA* 4.3 18.2 + - + -
172A PHE* 3.5 29.7 - + + -
174A ASP* 2.9 19.4 + - - +
251A PRO 3.1 0.2 - - - -
252A ARG* 1.3 79.4 - - - +
254A ALA* 1.3 60.6 + - - +
256A ARG* 4.2 23.7 + - - +
257A ALA* 3.5 20.0 + - + +
303A ASP* 3.6 35.4 + - - -
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Residues in contact with ALA 254 (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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108A TYR* 3.8 26.9 - - + -
111A PHE* 3.7 12.8 - - + -
234A VAL* 4.4 7.9 - - + -
235A LEU* 3.9 13.0 - - + -
238A LEU* 3.7 22.7 - - + +
251A PRO* 3.3 9.2 + - + +
253A HIS* 1.3 77.0 - - - +
255A ALA* 1.4 64.4 + - - +
257A ALA* 3.1 12.6 + - - +
258A LEU* 3.3 10.9 + - - +
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Residues in contact with ALA 255 (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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177A VAL* 3.9 5.8 - - + -
179A VAL* 3.6 27.1 - - + -
238A LEU* 3.9 14.3 - - + +
250A ALA* 5.0 1.1 - - + -
251A PRO 3.1 16.0 + - - +
252A ARG 3.8 2.2 - - - +
254A ALA* 1.4 73.6 - - - +
256A ARG* 1.3 58.2 + - - +
258A LEU* 3.2 3.1 + - - -
259A ALA* 2.8 29.8 + - - +
264A LEU* 4.2 1.9 - - - +
266A LEU* 3.5 24.4 - - + +
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Residues in contact with ARG 256 (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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252A ARG* 2.9 65.6 + - + +
253A HIS* 4.2 26.2 + - - +
255A ALA* 1.3 71.7 - - - +
257A ALA* 1.3 65.9 + - - +
258A LEU 3.2 0.5 + - - -
259A ALA* 3.4 14.9 + - - +
260A GLU 5.0 0.7 + - - -
266A LEU* 3.8 17.9 - - + -
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Residues in contact with ALA 257 (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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111A PHE* 3.7 30.5 - - + -
253A HIS 3.5 5.7 + - - +
254A ALA 3.1 5.8 + - - +
256A ARG* 1.3 79.6 - - - +
258A LEU* 1.3 65.5 + - + +
260A GLU* 5.2 0.9 + - - +
261A ALA* 5.1 0.3 + - - +
239C PHE* 4.1 11.8 - - + -
261C ALA* 3.6 24.1 - - - +
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Residues in contact with LEU 258 (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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111A PHE* 5.0 0.4 - - + -
235A LEU* 3.5 42.6 - - + +
238A LEU* 3.8 25.4 - - + -
239A PHE* 3.8 22.9 - - + -
254A ALA 3.3 12.3 + - - +
255A ALA 3.2 4.8 + - - +
256A ARG 3.1 0.2 - - - -
257A ALA* 1.3 87.8 - - + +
259A ALA* 1.3 56.9 + - - +
260A GLU 3.3 2.7 - - - -
261A ALA* 3.2 8.2 + - + -
262A ALA* 2.7 37.9 + - + +
264A LEU* 4.1 1.8 - - + -
235C LEU* 6.2 0.4 - - + -
239C PHE* 3.5 31.9 - - + -
258C LEU* 5.7 2.0 - - + -
261C ALA* 5.6 0.4 - - + -
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Residues in contact with ALA 259 (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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255A ALA 2.8 16.0 + - - +
256A ARG* 3.4 13.5 + - - +
258A LEU* 1.3 75.4 - - - +
260A GLU* 1.3 57.5 + - - +
263A GLY* 3.0 7.4 + - - -
264A LEU* 2.8 42.8 + - - +
266A LEU* 4.2 17.0 - - + -
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Residues in contact with GLU 260 (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 ARG 5.0 0.6 + - - -
257A ALA 5.2 0.8 + - - -
258A LEU 3.3 0.6 - - - -
259A ALA* 1.3 78.2 - - - +
261A ALA* 1.3 64.8 + - - +
263A GLY* 3.4 10.4 + - - -
260C GLU* 6.5 1.6 - - + -
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Residues in contact with ALA 261 (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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239A PHE* 3.6 22.1 - - + -
257A ALA 5.3 0.4 + - - -
258A LEU* 3.2 10.9 + - + +
260A GLU* 1.3 77.3 - - - +
262A ALA* 1.3 59.9 + - - +
257C ALA 3.7 23.1 - - - +
258C LEU* 5.2 1.1 - - + -
261C ALA* 4.1 25.4 - - + +
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Residues in contact with ALA 262 (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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238A LEU 3.6 26.0 - - - +
239A PHE* 3.8 25.0 - - + +
242A GLY* 3.4 22.7 - - - +
258A LEU* 2.7 24.5 + - + +
261A ALA* 1.3 73.8 - - - +
263A GLY* 1.3 60.2 + - - +
264A LEU* 3.7 10.3 - - + -
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Residues in contact with GLY 263 (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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181A ARG* 3.6 6.6 - - - +
182A ARG* 2.7 37.2 + - - +
242A GLY* 4.4 1.7 - - - +
259A ALA 3.0 9.0 + - - -
260A GLU 3.4 8.5 + - - -
261A ALA 3.9 0.2 + - - -
262A ALA* 1.3 79.8 - - - +
264A LEU* 1.3 54.8 + - - +
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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