Contacts of the helix formed by residues 337 - 347 (chain J) in PDB entry 3LUE
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 337 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16J MET* 5.5 0.3 - - - +
18J LYS* 3.9 21.1 - - + -
26J ALA* 5.6 4.0 - - + -
27J PRO* 4.0 32.3 - - + -
30J VAL* 3.4 22.7 - - + +
334J GLU* 2.8 4.5 + - + +
336J LYS* 1.3 120.5 + - + +
338J SER* 1.3 61.1 + - - -
339J VAL 3.4 2.2 - - - -
340J TRP* 3.1 15.0 + - + +
341J ILE* 3.1 33.4 + - + +
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Residues in contact with SER 338 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J LEU 3.9 2.3 - - - +
141J SER* 3.6 32.8 + - - -
144J ALA* 4.1 7.4 - - - +
300J SER* 5.0 1.1 - - - -
332J PRO* 5.2 5.4 - - - +
334J GLU* 3.7 11.6 + - - +
335J ARG* 4.0 18.9 - - - +
336J LYS 3.7 1.8 - - - -
337J TYR* 1.3 72.7 - - - +
339J VAL* 1.3 64.3 + - - +
340J TRP 3.1 0.2 + - - -
341J ILE* 3.1 4.8 + - - +
342J GLY* 3.0 22.3 + - - -
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Residues in contact with VAL 339 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J ASP* 3.4 33.2 - - - +
106J THR* 4.0 9.6 - - + -
137J GLN* 3.4 43.5 - - + +
140J LEU* 3.3 22.9 - - + +
141J SER* 3.2 23.8 - - - +
154J ASP* 4.4 2.2 - - - +
301J GLY* 5.0 13.0 - - - +
335J ARG 5.4 1.3 + - - +
336J LYS 5.4 0.4 + - - -
337J TYR 3.4 1.0 - - - -
338J SER* 1.3 73.9 - - - +
340J TRP* 1.3 64.3 + - - +
342J GLY 3.5 0.2 + - - -
343J GLY 3.4 3.5 + - - -
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Residues in contact with TRP 340 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J VAL* 3.2 36.2 + - + +
11J ASP* 4.1 12.5 + - + +
18J LYS* 3.3 42.8 - - + -
19J ALA 3.7 0.8 - - - -
20J GLY* 3.4 32.9 - - - +
21J PHE 3.8 11.4 - - - -
24J ASP* 3.2 28.9 - - + -
25J ASP 3.8 1.8 - - - -
26J ALA* 3.4 24.5 - - - -
27J PRO* 3.4 26.7 - - + -
337J TYR* 3.1 10.0 + - - +
339J VAL* 1.3 79.3 - - - +
341J ILE* 1.3 63.3 + - + +
343J GLY* 3.3 1.6 + - - -
344J SER* 3.0 37.0 + - - -
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Residues in contact with ILE 341 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J ASP 4.4 5.6 - - - +
25J ASP 3.2 28.7 - - - +
26J ALA* 4.8 1.1 - - + -
27J PRO* 5.1 0.7 - - + -
144J ALA* 4.0 8.1 - - + -
337J TYR* 3.1 43.3 + - + +
338J SER* 4.3 3.1 - - - +
340J TRP* 1.3 86.3 - - + +
342J GLY* 1.3 61.8 + - - +
344J SER* 4.0 2.2 - - - -
345J ILE* 3.2 22.1 + - + +
99S MET* 4.4 7.9 - - + -
101S PHE* 3.8 29.2 - - + -
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Residues in contact with GLY 342 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J LEU* 3.1 34.0 - - - +
143J TYR* 4.6 6.1 - - - +
144J ALA* 3.4 13.1 - - - +
338J SER 3.0 10.8 + - - -
341J ILE* 1.3 79.4 - - - +
343J GLY* 1.3 54.3 + - - +
345J ILE* 3.7 4.5 + - - +
346J LEU* 3.2 26.9 + - - +
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Residues in contact with GLY 343 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J VAL* 3.8 15.0 - - - -
104J LEU* 4.1 6.4 - - - +
140J LEU* 3.6 21.2 - - - +
339J VAL 3.4 5.9 + - - -
340J TRP 3.3 5.8 + - - -
342J GLY* 1.3 75.0 - - - +
344J SER* 1.3 57.8 + - - +
345J ILE 3.2 0.4 + - - -
346J LEU* 3.3 4.0 + - - -
347J ALA* 2.8 34.0 + - - +
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Residues in contact with SER 344 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J VAL* 3.4 15.6 - - - +
22J ALA* 3.7 5.2 - - - +
23J GLY* 3.1 11.3 + - - -
24J ASP 2.7 41.5 + - - -
340J TRP* 3.0 33.5 + - - -
341J ILE* 3.9 6.2 - - - +
343J GLY* 1.3 72.9 - - - +
345J ILE* 1.3 48.9 + - - +
348J SER* 2.8 24.6 + - - -
101S PHE* 5.6 1.8 - - - -
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Residues in contact with ILE 345 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143J TYR* 4.0 22.2 - - + +
144J ALA* 4.0 22.2 - - - -
341J ILE 3.2 15.8 + - - +
342J GLY* 3.8 4.7 - - - +
343J GLY 3.2 1.2 - - - -
344J SER* 1.3 71.2 - - - +
346J LEU* 1.3 70.5 + - - +
348J SER* 2.6 19.5 + - - -
349J LEU* 3.2 21.0 - - + +
101S PHE* 1.9 97.1 - - + -
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Residues in contact with LEU 346 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H GLN* 5.0 9.2 - - + -
104J LEU* 3.5 22.2 - - + -
133J TYR* 5.1 4.3 - - + -
135J ALA* 5.3 4.5 - - + -
140J LEU* 5.7 3.8 - - + -
143J TYR* 4.7 21.5 - - + -
342J GLY 3.2 17.4 + - - +
343J GLY* 3.6 4.7 - - - +
345J ILE* 1.3 82.2 - - + +
347J ALA* 1.3 55.7 + - - +
348J SER 2.8 7.8 + - - -
349J LEU* 3.0 28.4 + - + +
351J THR* 6.0 1.1 - - + -
352J PHE* 3.3 52.8 - - + +
355J MET* 4.8 6.3 - - - -
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Residues in contact with ALA 347 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J ALA* 5.8 0.3 - - - -
7J ALA* 3.9 23.2 + - + +
9J VAL* 4.8 2.0 - - + -
22J ALA* 3.6 22.0 - - + +
104J LEU* 4.4 13.0 - - + -
343J GLY 2.8 20.6 + - - +
346J LEU* 1.3 69.5 - - - +
348J SER* 1.4 55.7 + - - +
349J LEU 3.6 0.6 - - - +
352J PHE* 3.7 17.7 - - + +
356J TRP* 4.1 13.9 - - + -
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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