Contacts of the helix formed by residues 348 - 354 (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 SER 348 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22J ALA* 4.3 2.9 - - - -
23J GLY* 3.8 21.2 + - - -
344J SER 2.8 18.9 + - - -
345J ILE* 2.6 23.6 + - - -
346J LEU 2.8 2.4 + - - -
347J ALA* 1.4 74.3 - - - +
349J LEU* 1.3 65.9 + - - +
350J SER* 3.7 1.6 + - - -
95S ASP* 4.0 16.1 + - - +
101S PHE* 5.4 0.3 - - - -
102S HIS* 5.2 7.5 + - - -
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Residues in contact with LEU 349 (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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49H GLN* 3.6 30.7 - - + +
143J TYR* 4.0 8.5 - - + +
345J ILE* 3.2 22.8 + - + +
346J LEU* 3.0 23.5 + - + +
347J ALA 4.7 1.0 - - - +
348J SER* 1.3 79.7 - - - +
350J SER* 1.3 62.6 + - - +
351J THR* 3.0 21.1 - - - +
352J PHE* 3.1 17.8 + - - +
353J GLN* 4.1 2.1 + - - +
95S ASP* 4.6 7.0 - - - +
101S PHE 4.4 7.4 - - - +
104S ILE* 6.3 0.2 - - + -
105S ALA* 3.1 38.1 - - + +
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Residues in contact with SER 350 (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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348J SER 3.7 2.6 + - - -
349J LEU* 1.3 71.7 - - - +
351J THR* 1.3 62.7 + - - +
352J PHE 3.4 0.7 + - - -
353J GLN* 3.5 8.6 + - - +
354J GLN* 3.1 22.3 + - - -
95S ASP* 5.3 2.6 + - - -
109S LYS* 4.9 16.5 - - - +
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Residues in contact with THR 351 (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* 2.7 49.0 + - + +
49H GLN* 4.2 9.9 + - - +
346J LEU* 6.0 1.1 - - + -
349J LEU* 3.8 20.5 - - + +
350J SER* 1.3 76.5 + - - +
352J PHE* 1.3 63.5 + - - +
354J GLN* 3.0 28.4 + - - +
355J MET* 4.0 1.8 - - + +
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Residues in contact with PHE 352 (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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104J LEU* 3.5 15.5 - - + -
133J TYR* 3.5 32.5 - + + -
346J LEU* 3.3 42.0 - - + +
347J ALA* 3.7 10.5 - - - -
349J LEU* 3.1 13.7 + - + +
351J THR* 1.3 74.4 - - - +
353J GLN* 1.3 63.9 + - - +
354J GLN 2.9 6.9 + - - -
355J MET* 2.9 56.2 + - + +
356J TRP* 3.2 54.6 + + - -
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Residues in contact with GLN 353 (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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102J PRO* 4.2 13.3 - - - +
131J ALA* 4.9 4.9 - - - +
349J LEU 4.1 2.0 + - - +
350J SER* 3.5 7.7 + - - +
351J THR 3.3 1.2 + - - -
352J PHE* 1.3 77.2 - - - +
354J GLN* 1.3 73.8 + - - +
355J MET 3.3 3.6 + - - -
356J TRP* 2.9 56.9 + - - +
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Residues in contact with GLN 354 (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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350J SER* 3.1 24.2 + - - +
351J THR* 3.0 19.0 - - - +
352J PHE 2.9 0.2 - - - -
353J GLN* 1.3 88.9 - - - +
355J MET* 1.3 69.9 + - - +
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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