Contacts of the helix formed by residues 255 - 266 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A THR 4.2 3.1 - - - +
254A ALA* 1.3 86.9 - - + +
256A PRO* 1.3 73.4 - - + +
257A ASP* 3.1 18.2 - - - +
258A LEU* 2.9 35.8 + - + +
259A ARG* 3.0 10.4 + - - +
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Residues in contact with PRO 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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254A ALA 3.3 6.7 - - - +
255A PRO* 1.3 82.9 - - + +
257A ASP* 1.3 58.2 + - - +
259A ARG* 3.7 7.5 + - + +
260A ALA* 3.1 26.3 + - - +
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Residues in contact with ASP 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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255A PRO* 3.2 20.0 - - - +
256A PRO* 1.3 74.0 - - - +
258A LEU* 1.3 65.6 + - - +
260A ALA* 3.3 7.1 + - - +
261A GLU* 2.8 33.1 + - - +
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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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186A TYR* 3.6 33.2 - - + -
189A ARG* 4.2 35.0 - - + +
190A PHE* 5.0 4.9 - - + -
250A PHE* 4.3 22.7 - - + -
255A PRO* 2.9 34.8 + - + +
257A ASP* 1.3 82.7 + - - +
259A ARG* 1.3 56.8 + - - +
261A GLU* 3.2 5.8 + - + +
262A LEU* 2.8 32.9 + - + +
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Residues in contact with ARG 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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229A CYS 3.0 26.1 + - - -
230A PHE* 4.9 6.7 - - - +
232A ASP* 4.0 20.5 + - - +
241A TRP* 3.2 28.7 - - - +
250A PHE* 4.1 22.6 - - + -
251A ASN* 2.7 34.5 + - - +
254A ALA* 4.8 4.9 - - + +
255A PRO 3.0 10.9 + - - +
256A PRO* 3.8 11.9 - - + +
258A LEU* 1.3 79.6 - - - +
260A ALA* 1.3 59.9 + - - +
262A LEU* 3.8 1.9 - - - +
263A GLY* 2.9 35.3 + - - -
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Residues in contact with ALA 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 PRO 3.1 20.3 + - - +
257A ASP* 3.5 8.5 - - - +
258A LEU 3.2 0.2 - - - -
259A ARG* 1.3 82.2 - - - +
261A GLU* 1.3 61.4 + - - +
263A GLY* 3.5 1.6 + - - -
264A LYS* 3.3 21.0 + - - +
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Residues in contact with GLU 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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185A LYS* 3.8 13.5 - - - +
186A TYR* 3.1 27.3 + - + +
189A ARG* 2.9 32.4 + - - -
257A ASP* 2.8 19.2 + - - +
258A LEU* 3.2 8.2 + - - +
260A ALA* 1.3 74.5 - - - +
262A LEU* 1.3 66.1 + - - +
264A LYS* 3.0 9.0 + - - +
265A ASP* 3.0 23.0 + - - +
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Residues in contact with LEU 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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182A LEU* 3.7 18.4 - - + -
186A TYR* 3.5 42.8 - - + -
190A PHE* 3.9 20.0 - - + -
241A TRP* 3.8 13.2 - - + -
245A THR* 4.0 5.6 - - + -
250A PHE* 3.4 34.8 - - + -
258A LEU* 2.8 23.1 + - + +
259A ARG 3.8 1.8 - - - +
261A GLU* 1.3 71.9 - - - +
263A GLY* 1.3 59.1 + - - +
264A LYS 3.0 0.3 + - - -
265A ASP* 3.2 1.0 + - + +
266A LEU* 2.8 44.9 + - + +
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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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230A PHE* 3.2 17.6 - - - -
241A TRP* 3.7 15.8 - - - -
259A ARG* 2.9 28.8 + - - -
260A ALA 3.9 2.0 - - - -
262A LEU* 1.3 76.8 - - - +
264A LYS* 1.3 60.7 + - - +
267A GLN* 2.9 22.6 + - - +
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Residues in contact with LYS 264 (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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260A ALA 3.3 11.5 + - - +
261A GLU* 3.0 11.3 + - + +
262A LEU 3.0 0.4 - - - -
263A GLY* 1.3 77.2 - - - +
265A ASP* 1.3 65.8 + - - +
267A GLN* 3.1 23.4 + - - +
268A GLU* 3.6 4.3 + - - +
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Residues in contact with ASP 265 (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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185A LYS* 2.7 26.6 + - - -
186A TYR* 2.3 36.1 + - + +
261A GLU* 3.0 12.7 + - - +
262A LEU 4.0 1.6 - - - +
264A LYS* 1.3 72.0 - - - +
266A LEU* 1.3 56.1 + - + +
267A GLN 2.8 5.8 - - - -
268A GLU* 2.7 29.9 + - - +
271A PHE* 3.2 42.6 - - + -
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Residues in contact with LEU 266 (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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182A LEU* 4.4 14.6 - - + -
226A ILE* 3.9 7.6 - - + +
229A CYS* 5.9 0.4 - - + -
230A PHE* 4.1 14.4 - - + -
241A TRP* 3.4 39.7 - - + -
244A LEU* 4.1 22.4 - - + -
262A LEU* 2.8 26.7 + - + +
265A ASP* 1.3 71.5 - - + +
267A GLN* 1.3 57.8 + - - +
268A GLU 3.4 0.4 - - - -
271A PHE* 3.8 16.6 - - + -
272A SER* 3.0 27.6 + - - -
279A VAL* 3.9 6.6 - - - +
281A PHE* 3.8 30.7 - - + -
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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