Contacts of the helix formed by residues 337 - 347 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16E MET* 5.5 0.2 - - - +
18E LYS* 3.9 21.8 - - + -
26E ALA* 5.6 4.5 - - + -
27E PRO* 4.0 31.2 - - + -
30E VAL* 3.4 22.9 - - + +
334E GLU* 2.8 4.5 + - + +
336E LYS* 1.3 119.6 + - + +
338E SER* 1.3 61.1 + - - -
339E VAL 3.4 2.7 - - - -
340E TRP* 3.1 15.5 + - + +
341E ILE* 3.1 33.0 + - + +
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Residues in contact with SER 338 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E LEU 3.9 2.4 - - - +
141E SER* 3.6 31.1 + - - -
144E ALA* 4.1 6.6 - - - +
300E SER* 5.0 0.8 - - - -
332E PRO* 5.2 5.5 - - - +
334E GLU* 3.7 12.5 + - - +
335E ARG* 4.0 19.0 - - - -
336E LYS 3.7 1.6 - - - -
337E TYR* 1.3 73.2 - - - +
339E VAL* 1.3 64.6 + - - +
340E TRP 3.1 0.3 + - - -
341E ILE* 3.1 4.6 + - - +
342E GLY* 3.0 22.2 + - - -
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Residues in contact with VAL 339 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E ASP* 3.4 33.7 - - - +
106E THR* 4.0 9.4 - - + -
137E GLN* 3.4 44.6 - - + +
140E LEU* 3.3 23.6 - - + +
141E SER* 3.2 22.2 - - - +
154E ASP* 4.4 2.2 - - - +
301E GLY* 5.0 13.2 - - - +
335E ARG 5.4 1.3 + - - +
336E LYS 5.4 0.4 + - - -
337E TYR 3.3 1.0 + - - -
338E SER* 1.3 74.7 - - - +
340E TRP* 1.3 63.1 + - - +
342E GLY 3.5 0.2 + - - -
343E GLY 3.4 3.5 + - - -
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Residues in contact with TRP 340 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E VAL* 3.2 36.2 + - + +
11E ASP* 4.1 11.2 + - + +
18E LYS* 3.3 44.0 - - + -
19E ALA 3.7 0.6 - - - -
20E GLY* 3.4 33.3 - - - +
21E PHE 3.8 11.4 - - - -
24E ASP* 3.2 29.4 - - + -
25E ASP 3.8 1.6 - - - -
26E ALA* 3.4 24.0 - - - -
27E PRO* 3.4 26.5 - - + -
337E TYR* 3.1 10.1 + - - +
339E VAL* 1.3 80.4 - - - +
341E ILE* 1.3 63.2 + - + +
343E GLY* 3.3 1.4 + - - -
344E SER* 3.0 37.3 + - - -
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Residues in contact with ILE 341 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E ASP 4.4 6.1 - - - +
25E ASP 3.2 27.6 - - - +
26E ALA* 4.8 1.1 - - + -
27E PRO* 5.1 0.9 - - + -
144E ALA* 4.0 7.6 - - + -
337E TYR* 3.1 43.0 + - + +
338E SER* 4.3 3.4 - - - +
340E TRP* 1.3 87.0 - - + +
342E GLY* 1.3 61.7 + - - +
344E SER* 3.9 2.4 - - - -
345E ILE* 3.2 21.9 + - + +
99L MET* 4.4 6.5 - - + -
101L PHE* 3.8 30.1 - - + -
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Residues in contact with GLY 342 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E LEU* 3.1 32.9 - - - +
143E TYR* 4.6 6.1 - - - +
144E ALA* 3.4 13.8 - - - +
338E SER 3.0 10.6 + - - -
341E ILE* 1.3 80.1 - - - +
343E GLY* 1.3 55.0 + - - +
345E ILE* 3.7 3.9 + - - +
346E LEU* 3.2 27.0 + - - +
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Residues in contact with GLY 343 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E VAL* 3.8 13.7 - - - -
104E LEU* 4.1 6.4 - - - +
140E LEU* 3.6 21.6 - - - +
339E VAL 3.4 6.1 + - - -
340E TRP 3.3 5.9 + - - -
342E GLY* 1.3 73.5 - - - +
344E SER* 1.3 59.0 + - - +
346E LEU* 3.3 4.3 + - - +
347E ALA* 2.8 33.3 + - - +
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Residues in contact with SER 344 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E VAL* 3.4 15.2 - - - +
21E PHE 3.8 0.2 + - - -
22E ALA* 3.7 5.4 - - - +
23E GLY* 3.1 12.1 + - - -
24E ASP 2.7 41.6 + - - -
340E TRP* 3.0 33.4 + - - -
341E ILE* 3.9 6.5 - - - +
343E GLY* 1.3 73.4 - - - +
345E ILE* 1.3 50.1 + - - +
347E ALA 4.3 0.2 - - - -
348E SER* 2.8 23.9 + - - -
101L PHE* 5.5 1.4 - - - -
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Residues in contact with ILE 345 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E TYR* 4.0 23.3 - - + +
144E ALA* 4.0 21.8 - - + -
341E ILE 3.2 13.8 + - - +
342E GLY* 3.8 4.5 - - - +
343E GLY 3.2 0.6 - - - -
344E SER* 1.3 72.6 - - - +
346E LEU* 1.3 70.3 + - - +
348E SER* 2.6 20.1 + - - -
349E LEU* 3.2 20.4 - - + +
101L PHE* 1.9 97.1 - - + +
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Residues in contact with LEU 346 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C GLN* 5.0 8.7 - - + -
104E LEU* 3.5 22.0 - - + -
133E TYR* 5.1 4.9 - - + -
135E ALA* 5.3 4.5 - - + -
140E LEU* 5.7 4.0 - - + -
143E TYR* 4.7 22.0 - - + -
342E GLY 3.2 17.9 + - - +
343E GLY* 3.6 5.2 - - - +
345E ILE* 1.3 82.7 - - + +
347E ALA* 1.3 56.2 + - - +
348E SER 2.8 7.4 + - - -
349E LEU* 3.0 29.1 + - + +
351E THR* 6.0 1.1 - - + -
352E PHE* 3.3 52.2 - - + +
355E MET* 4.8 6.3 - - - -
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Residues in contact with ALA 347 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E ALA* 5.8 0.3 - - - -
7E ALA* 3.9 22.9 + - + +
9E VAL* 4.8 2.5 - - + -
22E ALA* 3.6 21.7 - - + +
104E LEU* 4.4 13.0 - - + -
343E GLY 2.8 20.2 + - - +
346E LEU* 1.3 70.1 - - - +
348E SER* 1.3 55.7 + - - +
349E LEU 4.7 0.9 - - - +
352E PHE* 3.7 17.9 - - + -
356E 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