Contacts of the helix formed by residues 255 - 266 (chain B) in PDB entry 1JQE
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 PRO 255 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253B THR 3.3 4.4 - - - +
254B ALA* 1.3 83.3 - - - +
256B PRO* 1.3 75.9 - - + +
257B ASP* 3.3 5.6 - - + +
258B LEU* 3.1 34.4 + - + +
259B ARG* 3.1 18.6 + - - -
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Residues in contact with PRO 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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254B ALA 3.6 4.6 - - - +
255B PRO* 1.3 82.3 - - + +
257B ASP* 1.3 65.3 + - - +
259B ARG* 3.2 7.4 + - + +
260B ALA* 2.9 21.5 + - - -
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Residues in contact with ASP 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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255B PRO* 3.1 4.6 + - + +
256B PRO* 1.3 75.5 - - - +
258B LEU* 1.3 64.8 + - - +
260B ALA* 2.9 12.3 + - - -
261B GLU* 3.1 21.8 + - + +
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Residues in contact with LEU 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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186B TYR* 3.7 27.1 - - + -
189B ARG* 3.6 42.6 - - + +
250B PHE* 3.7 31.2 - - + -
255B PRO* 3.1 30.0 + - + +
257B ASP* 1.3 78.2 - - - +
259B ARG* 1.3 64.7 + - - +
260B ALA 3.0 1.2 + - - -
261B GLU* 3.1 19.6 + - - +
262B LEU* 3.2 17.8 + - + +
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Residues in contact with ARG 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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229B CYS 3.7 8.7 + - - -
241B TRP* 3.3 54.1 - - - +
250B PHE* 4.3 25.3 - - + +
251B ASN* 4.8 19.2 - - - +
254B ALA 4.7 4.0 - - - +
255B PRO 3.1 10.4 + - - +
256B PRO* 3.5 12.1 - - + +
258B LEU* 1.3 78.4 - - - +
260B ALA* 1.3 63.8 + - - +
262B LEU* 3.8 2.2 + - - +
263B GLY* 3.3 24.5 + - - -
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Residues in contact with ALA 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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256B PRO 2.9 13.7 + - - -
257B ASP* 2.9 6.5 + - - +
259B ARG* 1.3 75.4 - - - +
261B GLU* 1.3 63.8 + - - +
263B GLY* 3.2 11.7 + - - -
264B LYS* 3.4 9.9 + - - +
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Residues in contact with GLU 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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185B LYS* 5.6 4.4 - - - -
186B TYR* 3.4 28.6 + - + +
257B ASP* 3.1 17.2 + - + +
258B LEU* 3.8 10.8 - - - +
260B ALA* 1.3 72.6 - - - +
262B LEU* 1.3 64.2 + - - +
264B LYS* 2.9 18.3 + - - +
265B ASP* 2.9 12.7 + - - +
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Residues in contact with LEU 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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182B LEU* 3.8 17.9 - - + -
186B TYR* 3.4 50.7 + - + -
241B TRP* 3.8 15.0 - - + -
245B THR* 3.8 17.9 - - + -
250B PHE* 3.7 31.0 - - + -
258B LEU* 3.2 17.1 + - + +
259B ARG 4.1 0.7 - - - +
261B GLU* 1.3 78.1 - - - +
263B GLY* 1.3 59.3 + - - +
264B LYS 2.9 0.5 + - - -
265B ASP* 4.3 2.2 - - + +
266B LEU* 2.8 46.1 + - + +
271B PHE* 5.6 0.2 - - + -
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Residues in contact with GLY 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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241B TRP* 3.7 19.8 - - - -
259B ARG* 3.3 16.2 + - - -
260B ALA 3.2 8.1 + - - -
261B GLU 3.2 1.2 - - - -
262B LEU* 1.3 77.9 - - - +
264B LYS* 1.3 56.0 + - - +
266B LEU* 4.6 2.5 - - - +
267B GLN* 2.8 32.2 + - - +
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Residues in contact with LYS 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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260B ALA 3.4 7.3 + - - +
261B GLU* 2.9 11.5 + - - +
263B GLY* 1.3 77.2 - - - +
265B ASP* 1.3 62.5 + - - +
266B LEU 3.3 0.2 - - - -
267B GLN* 2.9 32.3 + - - +
268B GLU* 3.4 12.9 + - + +
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Residues in contact with ASP 265 (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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185B LYS* 2.6 30.2 + - - +
186B TYR* 2.5 34.1 + - + +
261B GLU* 2.9 9.8 + - - +
262B LEU* 4.0 3.8 - - + +
264B LYS* 1.3 73.0 - - - +
266B LEU* 1.3 54.7 + - - +
267B GLN 2.7 6.7 + - - -
268B GLU* 2.6 42.9 + - - +
270B GLU* 4.9 2.1 - - - +
271B PHE* 3.3 32.2 - - + +
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Residues in contact with LEU 266 (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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182B LEU* 4.6 13.9 - - + -
226B ILE* 3.9 11.4 - - + -
229B CYS* 5.6 2.2 - - + -
241B TRP* 3.7 38.1 - - + -
244B LEU* 4.0 25.4 - - + -
262B LEU* 2.8 28.1 + - + +
263B GLY 4.6 4.0 - - - +
265B ASP* 1.3 71.0 - - - +
267B GLN* 1.3 58.8 + - + +
268B GLU 3.5 0.2 - - - -
271B PHE* 4.0 15.3 - - + -
272B SER* 2.7 27.0 + - - -
279B VAL* 3.4 7.8 - - - +
281B PHE* 4.0 27.8 - - + -
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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