Contacts of the helix formed by residues 348 - 354 (chain D) 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 SER 348 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D ALA* 4.3 2.9 - - - -
23D GLY* 3.8 22.3 + - - -
344D SER 2.8 18.8 + - - -
345D ILE* 2.6 23.6 + - - -
346D LEU 2.8 2.6 + - - -
347D ALA* 1.3 74.1 - - - +
349D LEU* 1.3 66.7 + - - +
350D SER 3.7 1.6 + - - -
95M ASP* 3.9 16.8 + - - +
101M PHE* 5.4 0.5 - - - -
102M HIS* 5.2 7.1 + - - -
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Residues in contact with LEU 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B GLN* 3.6 32.1 - - + +
143D TYR* 4.0 8.7 - - + +
345D ILE* 3.2 22.4 + - + +
346D LEU* 3.0 22.4 + - + +
347D ALA 4.7 0.9 - - - -
348D SER* 1.3 80.1 - - - +
350D SER* 1.3 61.6 + - - +
351D THR* 3.0 20.4 - - - +
352D PHE* 3.1 17.8 + - - +
353D GLN* 4.1 2.1 + - - +
95M ASP* 4.6 7.0 - - - +
101M PHE 4.4 6.3 - - - +
104M ILE* 6.3 0.2 - - + -
105M ALA* 3.1 37.9 - - + -
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Residues in contact with SER 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348D SER 3.7 2.8 + - - -
349D LEU* 1.3 70.9 - - - +
351D THR* 1.3 63.2 + - - +
352D PHE 3.4 0.5 + - - -
353D GLN* 3.5 8.2 + - - +
354D GLN* 3.1 22.7 + - - -
95M ASP* 5.3 2.2 + - - -
109M LYS* 4.9 17.3 + - - +
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Residues in contact with THR 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B GLN* 2.7 49.7 + - + +
49B GLN* 4.2 9.8 + - - +
346D LEU* 6.0 1.1 - - + -
349D LEU* 3.8 20.4 - - + +
350D SER* 1.3 75.3 + - - +
352D PHE* 1.3 62.7 + - + +
354D GLN* 3.0 28.5 + - - +
355D MET* 4.0 1.9 - - + +
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Residues in contact with PHE 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D LEU* 3.5 15.3 - - + -
133D TYR* 3.5 32.5 - + + -
346D LEU* 3.3 42.8 - - + +
347D ALA* 3.7 10.5 - - - +
349D LEU* 3.1 14.1 + - + +
351D THR* 1.3 73.9 - - - +
353D GLN* 1.3 63.5 + - - +
354D GLN 2.9 7.1 + - - -
355D MET* 2.9 57.1 + - + +
356D TRP* 3.2 53.7 + + - -
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Residues in contact with GLN 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D PRO* 4.2 13.1 - - - +
131D ALA* 4.9 5.9 - - - +
349D LEU 4.1 2.4 + - - +
350D SER* 3.5 7.4 + - - +
351D THR 3.3 1.4 + - - -
352D PHE* 1.3 75.7 - - - +
354D GLN* 1.3 72.6 + - - +
355D MET 3.3 3.5 + - - -
356D TRP* 2.9 57.9 + - - +
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Residues in contact with GLN 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350D SER* 3.1 23.4 + - - -
351D THR* 3.0 19.4 - - - +
353D GLN* 1.3 89.0 - - - +
355D MET* 1.3 69.6 + - - +
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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