Contacts of the helix formed by residues 279 - 289 (chain A) in PDB entry 1LTQ
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 279 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A ASP* 5.8 0.4 - - - +
254A ASP* 2.8 39.9 + - - +
277A ASP* 3.3 4.8 + - - +
278A ASP* 1.3 85.3 + - - +
280A THR* 1.3 67.7 + - - +
281A GLN* 3.8 32.3 + - + +
282A VAL* 2.9 27.1 + - + +
283A VAL* 2.9 12.6 + - - +
299A GLY* 3.6 13.0 - - - +
301A PHE* 2.9 53.1 + - + -
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Residues in contact with THR 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A TRP* 6.1 1.3 - - - +
278A ASP 3.3 2.8 + - - -
279A ARG* 1.3 69.7 - - - +
281A GLN* 1.3 58.6 + - - +
283A VAL* 3.4 5.8 + - - +
284A GLU* 2.9 40.4 + - + +
295A GLN* 3.3 19.8 + - - +
299A GLY 2.8 22.6 + - - -
300A ASP* 2.9 27.9 + - - +
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Residues in contact with GLN 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A TRP* 5.1 9.0 - - + +
117A THR* 4.5 14.9 + - - +
253A LYS* 3.9 12.5 - - - +
254A ASP* 3.7 9.4 - - - +
255A ASP* 2.8 61.0 + - - +
279A ARG* 3.1 35.1 + - + +
280A THR* 1.3 79.4 - - - +
282A VAL* 1.3 69.9 + - + +
284A GLU* 3.8 7.1 + - - +
285A MSE 3.2 23.2 + - - +
288A ARG* 4.5 1.7 + - - -
301A PHE 5.3 0.3 - - - +
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Residues in contact with VAL 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ASP* 4.0 25.8 - - + +
255A ASP* 5.2 1.3 - - - +
258A LYS* 3.7 24.5 - - + +
277A ASP* 3.1 30.3 - - - +
279A ARG* 2.9 20.3 + - + +
281A GLN* 1.3 86.3 - - + +
283A VAL* 1.3 60.5 + - - +
284A GLU 3.1 1.3 - - - -
285A MSE 3.0 11.0 + - + +
286A TRP* 2.9 42.4 + - + +
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ASP* 4.0 24.9 - - + +
279A ARG 2.9 23.6 + - - +
280A THR 3.7 4.9 - - - +
282A VAL* 1.3 76.4 - - - +
284A GLU* 1.3 61.3 + - - +
286A TRP* 3.5 2.4 + - - +
287A ARG* 3.3 60.4 + - - +
293A CYS* 3.8 25.8 - - - -
295A GLN* 3.9 25.1 - - + +
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Residues in contact with GLU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A TRP* 3.3 37.0 + - + +
133A ILE* 4.9 3.3 - - - +
137A ARG* 2.6 48.1 + - - +
280A THR* 2.9 28.0 + - - +
281A GLN 3.8 6.5 - - - +
283A VAL* 1.3 77.2 - - - +
285A MSE 1.3 63.2 + - - +
287A ARG* 3.7 16.2 + - - +
288A ARG* 3.0 36.7 + - + +
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Residues in contact with MSE 285 (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 ASP 5.4 0.2 - - - +
255A ASP* 3.8 20.6 - - - +
258A LYS* 3.6 30.7 - - + -
259A GLU* 3.9 30.5 - - - +
281A GLN 3.2 16.3 + - - +
282A VAL* 3.0 17.2 + - + +
284A GLU* 1.3 73.8 - - - +
286A TRP* 1.3 106.4 + - + +
288A ARG* 3.3 25.1 + - - +
289A ILE* 3.0 31.1 + - + +
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Residues in contact with TRP 286 (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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163A ILE* 3.8 36.5 - - + +
210A VAL* 5.2 7.4 - - + -
258A LYS* 4.4 16.6 - - + -
262A PHE* 3.7 37.0 - + + -
266A ILE* 6.5 0.4 - - + -
275A ALA* 4.0 14.4 - - + +
276A ILE 5.4 0.6 + - - -
277A ASP* 3.4 21.3 + - + +
282A VAL* 2.9 28.0 + - + +
283A VAL 3.7 1.6 - - - +
284A GLU 3.4 0.2 - - - -
285A MSE 1.3 106.9 - - + +
287A ARG* 1.3 61.3 + - - +
289A ILE* 3.2 14.7 + - + +
291A VAL* 2.9 39.6 + - + +
293A CYS* 3.5 36.6 - - + -
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Residues in contact with ARG 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ARG* 6.5 0.4 - - - -
283A VAL* 3.3 38.7 + - - +
284A GLU* 4.2 16.1 + - - +
286A TRP* 1.3 78.6 - - - +
288A ARG* 1.3 63.0 + - - +
290A GLY* 3.2 13.5 + - - -
291A VAL 3.2 9.9 - - - +
292A GLU* 4.8 2.2 - - - +
293A CYS* 2.8 40.3 + - + +
294A TRP* 4.5 0.6 - - - +
295A GLN* 4.1 17.2 - - - +
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Residues in contact with ARG 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A TRP* 3.2 43.4 - - - +
140A TYR* 3.4 22.9 + - + -
141A LYS* 5.9 3.9 - - + +
144A ARG* 3.2 50.6 + - - +
151A VAL* 4.4 6.8 - - - +
255A ASP* 3.5 18.8 + - - -
259A GLU* 5.1 2.9 + - - -
281A GLN 4.5 0.2 + - - -
284A GLU* 3.0 28.1 + - + +
285A MSE 3.4 30.7 - - - +
286A TRP 3.2 0.2 - - - -
287A ARG* 1.3 80.9 - - - +
289A ILE* 1.3 62.1 + - - +
290A GLY 3.4 0.7 + - - -
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Residues in contact with ILE 289 (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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144A ARG* 4.1 19.7 - - - +
150A PRO 4.3 7.2 - - - +
151A VAL* 4.0 4.5 - - - -
152A TYR* 2.6 35.2 + - - +
259A GLU* 3.6 35.4 - - + +
262A PHE* 3.7 35.9 - - + -
263A TRP* 4.3 4.7 - - + -
285A MSE 3.0 30.7 + - - +
286A TRP* 3.2 22.4 + - + +
288A ARG* 1.3 80.0 - - - +
290A GLY* 1.3 51.0 + - - +
291A VAL* 4.2 5.6 - - + -
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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