Contacts of the helix formed by residues 337 - 347 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16G MET* 5.5 0.2 - - - +
18G LYS* 3.9 21.1 - - + -
26G ALA* 5.6 4.3 - - + -
27G PRO* 4.0 32.5 - - + -
30G VAL* 3.4 23.2 - - + +
334G GLU* 2.8 4.5 + - + +
336G LYS* 1.3 119.8 + - + +
338G SER* 1.3 61.2 + - - -
339G VAL 3.4 2.5 - - - -
340G TRP* 3.1 15.1 + - + +
341G ILE* 3.1 34.0 + - + +
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Residues in contact with SER 338 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140G LEU 3.9 2.1 - - - +
141G SER* 3.6 31.2 + - - -
144G ALA* 4.1 6.5 - - - +
300G SER* 5.0 1.9 - - - -
332G PRO* 5.2 5.4 - - - +
334G GLU* 3.7 12.2 + - - +
335G ARG* 4.0 18.6 - - - -
336G LYS 3.7 1.8 + - - -
337G TYR* 1.3 73.2 - - - +
339G VAL* 1.3 65.7 + - - +
340G TRP 3.1 0.5 + - - -
341G ILE* 3.1 4.4 + - - +
342G GLY* 3.0 22.3 + - - -
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Residues in contact with VAL 339 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G ASP* 3.4 33.4 - - - +
106G THR* 4.0 9.4 - - + -
137G GLN* 3.4 44.9 - - + +
140G LEU* 3.3 22.9 - - + +
141G SER* 3.2 22.9 - - - +
154G ASP* 4.4 2.0 - - - +
301G GLY* 5.0 13.0 - - - +
335G ARG 5.4 1.3 + - - +
336G LYS 5.4 0.2 + - - -
337G TYR 3.4 1.0 - - - -
338G SER* 1.3 75.1 - - - +
340G TRP* 1.3 63.8 + - - +
342G GLY 3.5 0.2 + - - -
343G GLY 3.4 3.3 + - - -
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Residues in contact with TRP 340 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G VAL* 3.2 35.9 + - + +
11G ASP* 4.1 11.5 + - + +
18G LYS* 3.3 43.5 - - + -
19G ALA 3.7 0.6 - - - -
20G GLY* 3.4 34.2 - - - +
21G PHE 3.8 11.0 - - - -
24G ASP* 3.2 29.2 - - + -
25G ASP 3.8 1.8 - - - -
26G ALA* 3.4 24.5 - - - -
27G PRO* 3.4 25.6 - - + -
106G THR* 6.2 0.2 - - - -
337G TYR* 3.1 10.6 + - - +
339G VAL* 1.3 80.4 - - - +
341G ILE* 1.3 63.0 + - + +
343G GLY* 3.3 1.0 + - - -
344G SER* 3.0 39.1 + - - -
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Residues in contact with ILE 341 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G ASP 4.4 5.6 - - - +
25G ASP 3.2 28.0 - - - +
26G ALA* 4.8 1.1 - - + -
27G PRO* 5.1 0.7 - - + -
144G ALA* 4.0 7.2 - - + -
337G TYR* 3.1 42.8 + - + +
338G SER* 4.3 3.8 - - - +
340G TRP* 1.3 86.0 - - + +
342G GLY* 1.3 61.3 + - - +
343G GLY 3.3 0.2 - - - -
344G SER* 4.0 2.5 - - - -
345G ILE* 3.2 22.7 + - + +
99N MET* 4.4 7.4 - - + -
101N PHE* 3.8 28.9 - - + -
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Residues in contact with GLY 342 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140G LEU* 3.1 32.8 - - - +
143G TYR* 4.6 5.9 - - - +
144G ALA* 3.4 13.1 - - - +
338G SER 3.0 10.5 + - - -
341G ILE* 1.3 79.2 - - - +
343G GLY* 1.3 56.4 + - - +
345G ILE* 3.7 4.3 + - - +
346G LEU* 3.2 27.0 + - - +
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Residues in contact with GLY 343 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G VAL* 3.8 14.6 - - - -
104G LEU* 4.1 6.4 - - - +
140G LEU* 3.6 22.2 - - - +
339G VAL 3.4 5.9 + - - -
340G TRP 3.3 5.9 + - - -
342G GLY* 1.3 73.5 - - - +
344G SER* 1.3 58.0 + - - +
345G ILE 3.2 0.2 + - - -
346G LEU* 3.3 4.2 + - - -
347G ALA* 2.8 33.8 + - - +
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Residues in contact with SER 344 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G VAL* 3.4 15.7 - - - +
22G ALA* 3.7 5.3 - - - +
23G GLY* 3.1 10.9 + - - -
24G ASP 2.7 42.3 + - - -
340G TRP* 3.0 32.6 + - - -
341G ILE* 3.9 6.2 - - - +
343G GLY* 1.3 74.0 - - - +
345G ILE* 1.3 48.8 + - - +
348G SER* 2.8 24.4 + - - -
101N PHE* 5.5 1.7 - - - -
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Residues in contact with ILE 345 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143G TYR* 4.0 21.3 - - + +
144G ALA* 4.0 22.4 - - - +
341G ILE 3.2 14.4 + - - +
342G GLY* 3.8 4.9 - - - +
343G GLY 3.2 0.6 - - - -
344G SER* 1.3 72.1 - - - +
346G LEU* 1.3 69.0 - - - +
348G SER* 2.6 20.3 + - - -
349G LEU* 3.2 21.2 - - + +
101N PHE* 1.9 96.5 - - + +
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Residues in contact with LEU 346 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E GLN* 5.0 9.2 - - + -
104G LEU* 3.5 22.4 - - + -
133G TYR* 5.1 4.3 - - + -
135G ALA* 5.3 4.9 - - + -
140G LEU* 5.7 4.3 - - + -
143G TYR* 4.7 23.1 - - + -
342G GLY 3.2 16.1 + - - +
343G GLY* 3.6 3.6 - - - +
345G ILE* 1.3 82.7 - - + +
347G ALA* 1.3 56.3 + - - +
348G SER 2.8 8.0 + - - -
349G LEU* 3.0 28.6 + - + +
351G THR* 6.0 1.1 - - + -
352G PHE* 3.3 51.6 - - + +
355G MET* 4.8 6.5 - - - -
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Residues in contact with ALA 347 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G ALA* 5.8 0.3 - - - -
7G ALA* 3.9 23.5 + - + +
9G VAL* 4.8 2.0 - - + -
22G ALA* 3.6 21.4 - - + +
104G LEU* 4.4 13.0 - - + -
343G GLY 2.8 20.7 + - - +
346G LEU* 1.3 70.1 - - - +
348G SER* 1.3 56.8 + - - +
349G LEU 3.6 0.7 - - - +
352G PHE* 3.7 18.3 - - + +
356G TRP* 4.1 14.3 - - + -
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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