Contacts of the helix formed by residues 283 - 293 (chain B) in PDB entry 2CNW
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 TYR 283 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90B ALA* 3.8 22.4 - - + -
280B GLU* 5.5 4.5 - - + -
281B PRO* 3.3 51.0 - - + +
282B PHE* 1.3 77.1 - - - +
284B PRO* 1.4 60.5 - - - +
285B GLU* 3.2 4.7 - - + +
286B ARG* 2.8 84.0 + - + +
287B LEU* 3.3 5.7 + - - +
58D ALA 5.7 0.2 + - - -
59D SER* 5.2 13.5 + - - -
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Residues in contact with PRO 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B LYS* 3.6 24.4 - - - +
86B LEU* 3.4 34.2 - - + +
87B GLY* 4.0 1.1 - - - -
88B GLY 3.7 13.7 - - - +
89B GLU 3.7 16.4 - - - +
90B ALA* 3.7 16.2 - - - +
282B PHE* 3.6 26.6 - - + +
283B TYR* 1.4 82.4 - - + +
285B GLU* 1.3 56.2 + - - +
287B LEU 3.5 0.3 + - - -
288B ALA* 3.0 25.5 + - - +
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Residues in contact with GLU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B TYR* 3.1 48.0 + - + +
83B LYS* 3.8 37.7 + - + +
88B GLY 4.6 1.9 + - - +
283B TYR* 3.1 3.7 + - + -
284B PRO* 1.3 77.7 - - - +
286B ARG* 1.3 62.2 + - + +
288B ALA* 3.3 4.0 + - - +
289B GLY* 3.2 11.8 + - - -
87D LYS* 3.0 33.3 + - - +
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Residues in contact with ARG 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B GLU* 4.3 16.6 + - - -
283B TYR* 2.8 60.8 + - + +
285B GLU* 1.3 74.2 - - + +
287B LEU* 1.3 56.0 + - - +
289B GLY* 3.5 2.4 + - - -
290B ARG* 3.0 27.4 + - - +
59D SER 5.2 7.3 + - - -
61D ARG* 6.0 4.6 - - - +
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B LEU* 3.8 17.3 - - + -
244B LEU* 3.9 5.6 - - + -
247B LEU* 4.0 17.9 - - + -
252B ARG 3.9 6.1 - - - +
253B GLY* 3.6 8.3 - - - +
256B ALA* 3.5 32.3 - - + -
282B PHE* 3.7 34.3 - - + -
283B TYR 3.3 3.6 + - - +
284B PRO 4.2 0.9 - - - +
286B ARG* 1.3 77.5 - - - +
288B ALA* 1.3 60.5 + - - +
290B ARG* 3.5 30.1 - - - -
291B ILE* 2.9 39.6 + - + +
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B TYR* 4.2 18.4 - - + +
82B LEU* 3.4 34.7 - - + +
83B LYS* 4.0 15.0 - - + +
86B LEU* 3.5 2.2 - - + +
284B PRO 3.0 15.8 + - - +
285B GLU* 3.5 10.5 - - - +
286B ARG 3.3 0.2 - - - -
287B LEU* 1.3 77.4 - - - +
289B GLY* 1.3 56.7 + - - +
291B ILE 3.3 0.2 + - - -
292B LEU* 3.0 27.4 + - - +
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Residues in contact with GLY 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B GLN* 5.2 10.0 - - - +
79B TYR* 3.8 17.0 - - - -
285B GLU 3.2 9.9 + - - -
286B ARG* 3.5 3.6 + - - -
288B ALA* 1.3 78.3 - - - +
290B ARG* 1.3 55.7 + - - +
292B LEU* 3.4 5.2 + - - +
293B GLY* 2.8 26.0 + - - -
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Residues in contact with ARG 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B ALA* 5.4 0.8 - - - +
246B LYS 4.8 0.8 + - - -
247B LEU* 3.1 42.1 + - - +
249B GLY 3.0 28.5 + - - -
250B ASP* 3.9 2.0 - - - +
251B ALA* 2.7 29.6 + - - +
252B ARG* 2.7 64.7 + - - +
286B ARG 3.0 19.0 + - - +
287B LEU* 3.5 19.5 - - - +
289B GLY* 1.3 71.9 - - - +
291B ILE* 1.3 64.5 + - - +
293B GLY* 3.2 3.3 + - - -
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Residues in contact with ILE 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B SER* 5.5 0.5 + - - -
37B ALA* 5.0 4.3 - - - +
38B LEU* 4.0 24.7 - - + -
41B ALA* 3.8 25.9 - - + +
43B VAL* 4.7 3.4 - - + -
82B LEU* 4.1 17.0 - - + -
86B LEU* 4.5 14.8 - - + -
252B ARG* 3.5 24.5 - - - +
253B GLY 3.8 17.7 - - - +
254B GLY* 3.9 12.3 - - - +
257B LEU* 4.9 5.2 - - + -
287B LEU* 2.9 34.6 + - + +
288B ALA 3.8 3.4 - - - +
290B ARG* 1.3 74.6 - - - +
292B LEU* 1.3 61.7 + - - +
293B GLY 3.2 4.6 + - - -
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B GLN 5.6 0.2 - - - -
5B LEU* 3.7 19.9 - - + +
6B SER* 3.1 25.4 + - - -
9B LEU* 3.6 26.9 - - + +
34B ILE* 5.2 3.1 - - + -
37B ALA* 5.7 1.8 - - + -
38B LEU* 4.6 14.6 - - + -
75B LEU* 5.3 6.3 - - + +
78B VAL* 3.8 30.7 - - + -
79B TYR* 3.9 28.7 - - + +
82B LEU* 3.7 18.8 - - + -
288B ALA 3.0 21.1 + - - +
289B GLY* 3.6 4.5 - - - +
291B ILE* 1.3 76.3 - - - +
293B GLY* 1.3 58.7 + - - +
88D LEU* 6.2 0.4 - - + -
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Residues in contact with GLY 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B GLN 3.4 22.6 - - - +
6B SER* 3.5 25.6 - - - -
252B ARG* 3.4 31.4 + - - -
289B GLY 2.8 15.3 + - - -
290B ARG* 3.2 5.6 + - - -
291B ILE 3.2 2.8 - - - -
292B LEU* 1.3 81.6 - - - +
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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