Contacts of the helix formed by residues 254 - 264 (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 GLY 254 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B ALA 2.9 22.8 + - - -
42B ASP* 3.5 8.0 - - - +
43B VAL* 3.6 20.5 - - - -
252B ARG 3.5 1.6 - - - -
253B GLY* 1.3 71.5 - - - +
255B ALA* 1.3 59.2 + - - +
256B ALA 3.0 6.1 - - - -
257B LEU* 3.1 16.4 + - - +
258B SER* 3.4 11.8 + - - -
291B ILE* 3.9 10.3 - - - +
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Residues in contact with ALA 255 (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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42B ASP* 3.5 6.2 + - - +
218B LEU* 3.6 10.5 - - + +
219B ASP 4.7 3.6 - - - +
220B ALA 4.8 4.5 + - - +
222B THR* 3.3 36.2 + - - +
223B GLY 4.4 0.7 - - - +
226B ALA* 3.5 19.4 - - + +
244B LEU* 5.6 1.1 - - + -
253B GLY 3.1 0.8 - - - -
254B GLY* 1.3 77.0 - - - +
256B ALA* 1.3 56.4 + - - +
257B LEU 3.3 0.2 - - - -
258B SER* 3.5 10.1 + - - -
259B ALA* 3.0 29.6 + - - +
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Residues in contact with ALA 256 (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* 4.3 2.7 - - + -
218B LEU* 4.4 8.4 - - - +
242B LEU* 5.7 1.3 - - + -
244B LEU* 4.0 18.5 - - + +
253B GLY 3.0 15.5 + - - +
254B GLY 3.0 0.2 - - - -
255B ALA* 1.3 76.9 - - - +
257B LEU* 1.3 60.7 + - - +
259B ALA* 3.6 2.2 + - - +
260B ARG* 3.0 29.5 + - - +
267B ILE* 3.8 20.9 - - + +
287B LEU* 3.5 21.3 - - + -
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Residues in contact with LEU 257 (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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38B LEU* 5.3 1.8 - - + -
43B VAL* 3.8 28.7 - - + -
47B VAL* 4.0 15.5 - - + -
51B PHE* 4.6 15.7 - - + -
82B LEU* 3.9 22.9 - - + -
85B ALA* 3.4 41.5 - - + +
86B LEU* 4.1 15.2 - - + +
253B GLY 4.2 0.6 + - - -
254B GLY 3.1 11.6 + - - +
256B ALA* 1.3 75.2 - - - +
258B SER* 1.3 55.7 + - - +
260B ARG* 3.2 1.6 + - - -
261B HIS* 2.7 42.9 + - + +
291B ILE* 4.9 4.3 - - + -
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Residues in contact with SER 258 (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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42B ASP 4.1 0.7 + - - -
44B ASN* 3.0 40.9 + - - +
47B VAL* 4.2 13.2 - - - +
226B ALA* 4.1 3.9 - - - +
227B LEU* 3.8 22.6 - - - +
254B GLY 3.4 9.1 + - - -
255B ALA* 3.7 10.1 - - - -
256B ALA 3.4 0.2 - - - -
257B LEU* 1.3 76.7 - - - +
259B ALA* 1.3 63.6 + - - +
261B HIS* 3.3 2.1 + - - +
262B VAL* 3.2 26.3 + - - +
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Residues in contact with ALA 259 (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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216B LEU* 5.0 0.4 - - + -
218B LEU* 3.8 10.5 - - + -
226B ALA 5.0 2.9 - - - +
230B ALA* 3.8 23.6 - - + -
242B LEU* 3.5 28.9 - - + +
255B ALA 3.0 18.2 + - - +
256B ALA 4.0 2.0 - - - +
258B SER* 1.3 77.8 - - - +
260B ARG* 1.3 54.7 + - - +
262B VAL* 3.5 3.6 - - - +
263B THR* 2.7 35.7 + - - +
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Residues in contact with ARG 260 (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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84B GLU* 4.4 6.7 + - - -
85B ALA 3.0 26.7 + - - +
86B LEU* 3.7 17.5 - - - +
87B GLY* 3.5 23.8 + - - +
91B ARG* 5.4 3.6 - - - +
242B LEU* 4.9 2.0 - - + +
256B ALA 3.0 19.0 + - - +
257B LEU* 4.0 2.7 - - - +
259B ALA* 1.3 74.9 - - - +
261B HIS* 1.3 60.0 + - - +
263B THR* 3.8 4.5 - - - -
264B GLY* 2.8 44.7 + - - -
265B LYS 3.1 40.4 + - - +
266B PRO* 3.6 7.1 - - - +
267B ILE* 4.4 13.2 - - + +
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Residues in contact with HIS 261 (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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47B VAL* 3.5 39.1 - - + +
50B ASP* 3.9 26.7 + - + -
85B ALA 5.3 1.7 + - - -
227B LEU* 4.5 4.5 - - + +
257B LEU* 2.7 28.3 + - + +
258B SER 3.6 4.3 - - - +
260B ARG* 1.3 75.8 - - - +
262B VAL* 1.3 62.4 + - - +
263B THR 3.8 0.2 + - - -
264B GLY* 4.4 2.3 + - - -
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Residues in contact with VAL 262 (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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227B LEU* 3.7 37.0 - - + +
230B ALA* 3.8 13.0 - - + -
231B ARG* 3.8 40.4 - - + +
234B ASP* 4.4 3.3 - - - +
258B SER 3.2 13.1 + - - +
259B ALA 3.5 11.9 - - - +
261B HIS* 1.3 77.9 - - - +
263B THR* 1.3 65.5 + - + +
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Residues in contact with THR 263 (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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216B LEU* 5.7 1.3 - - + -
230B ALA* 3.6 27.1 - - + +
231B ARG* 5.2 0.2 - - - -
234B ASP* 3.5 27.1 - - + +
239B VAL* 4.9 8.5 - - + -
242B LEU* 4.1 5.7 - - + +
259B ALA 2.7 24.4 + - - +
260B ARG* 3.8 1.6 - - - -
262B VAL* 1.3 82.1 - - + +
264B GLY* 1.3 64.7 + - - +
265B LYS* 3.4 39.4 + - + +
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Residues in contact with GLY 264 (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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91B ARG* 5.8 0.3 + - - -
260B ARG* 2.8 36.0 + - - -
261B HIS 4.4 2.3 + - - -
262B VAL 3.8 0.6 - - - -
263B THR* 1.3 77.0 - - - +
265B LYS* 1.3 60.0 + - - +
266B PRO* 4.2 2.1 - - - +
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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