Contacts of the helix formed by residues 335 - 346 (chain D) in PDB entry 5LK5
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 ASP 335 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D PRO* 3.6 38.3 - - + +
92D VAL* 4.0 3.6 - - - -
333D THR* 3.5 11.5 + - - +
334D ASN* 1.3 81.4 - - - +
336D GLU* 1.3 58.7 + - - +
337D ALA* 3.0 23.5 + - - +
338D TYR* 3.1 15.9 + - + +
339D ALA* 3.0 22.9 + - - +
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Residues in contact with GLU 336 (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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90D THR* 4.1 13.1 + - + +
92D VAL* 4.0 8.2 - - + +
175D ILE* 3.7 34.0 - - + +
177D ARG* 2.7 47.1 + - - +
183D GLU* 4.4 1.7 - - - +
185D LYS* 5.4 6.1 + - - +
334D ASN 4.2 0.6 + - - -
335D ASP* 1.3 69.1 + - - +
337D ALA* 1.3 66.0 + - - +
339D ALA* 3.3 5.3 + - - +
340D GLU* 3.0 22.3 + - - +
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Residues in contact with ALA 337 (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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335D ASP* 3.0 10.2 + - - +
336D GLU* 1.3 76.3 - - - +
338D TYR* 1.3 66.9 + - - +
340D GLU* 3.2 9.4 + - - +
341D GLU* 3.0 33.9 + - - +
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Residues in contact with TYR 338 (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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19D PRO* 4.2 18.4 - - + -
21D VAL* 4.0 23.7 - - + +
24D LYS* 2.6 27.7 + - - -
331D LEU* 4.1 21.3 - - + -
333D THR* 4.0 16.6 - - - -
335D ASP* 3.1 26.4 + - + +
337D ALA* 1.3 80.4 - - - +
339D ALA* 1.3 63.5 - - - +
341D GLU* 3.1 27.8 + - + +
342D PHE* 2.9 32.9 + - + +
345D GLU* 5.2 5.6 + - - -
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Residues in contact with ALA 339 (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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92D VAL* 3.6 31.9 - - + -
94D GLN* 3.0 23.0 + - - +
173D THR* 4.8 2.9 - - + -
175D ILE* 6.1 0.4 - - + -
331D LEU* 3.8 15.9 - - + -
333D THR* 4.2 4.3 - - + -
335D ASP 3.0 11.7 + - - +
336D GLU* 3.5 9.4 - - - +
337D ALA 3.3 0.2 - - - -
338D TYR* 1.3 77.4 - - - +
340D GLU* 1.3 57.0 + - - +
342D PHE* 3.8 0.2 - - - +
343D GLY* 2.9 24.1 + - - -
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Residues in contact with GLU 340 (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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185D LYS* 3.7 19.8 + - - +
188D ASN* 3.0 44.3 + - - +
336D GLU 3.0 13.6 + - - +
337D ALA* 3.5 11.8 - - - +
338D TYR 3.1 0.2 - - - -
339D ALA* 1.3 74.3 - - - +
341D GLU* 1.3 64.9 + - - +
343D GLY 3.3 0.2 + - - -
344D ASN* 3.0 31.0 + - - +
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Residues in contact with GLU 341 (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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337D ALA* 3.0 29.0 + - - +
338D TYR* 3.4 29.1 + - + +
340D GLU* 1.3 76.2 - - + +
342D PHE* 1.3 58.5 + - - +
344D ASN* 3.1 8.4 + - - +
345D GLU* 3.0 41.1 + - - +
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Residues in contact with PHE 342 (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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24D LYS* 3.5 37.2 - - + -
26D GLN* 3.6 34.1 - - + -
94D GLN* 4.1 7.2 - - - -
329D ASN 3.9 15.5 - - - -
330D PHE 4.1 3.4 - - - -
331D LEU* 3.7 39.0 - - + -
338D TYR* 2.9 24.7 + - + +
339D ALA 3.8 3.4 - - - +
341D GLU* 1.3 74.3 - - - +
343D GLY* 1.3 55.2 + - - +
345D GLU* 3.2 15.9 + - + -
346D THR* 2.7 59.0 + - + +
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Residues in contact with GLY 343 (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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94D GLN* 3.5 15.7 - - - +
171D LEU* 3.8 17.5 - - - -
188D ASN* 3.9 4.9 - - - -
339D ALA 2.9 11.8 + - - -
340D GLU 3.7 4.3 - - - -
342D PHE* 1.3 77.5 - - - +
344D ASN* 1.3 56.8 + - - +
346D THR* 3.6 5.2 - - - -
347D TRP* 3.0 31.0 + - - +
348D GLY 3.0 5.4 + - - -
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Residues in contact with ASN 344 (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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188D ASN* 2.9 22.1 + - - +
340D GLU* 3.0 27.4 + - - +
341D GLU* 3.1 9.2 + - - +
343D GLY* 1.3 76.0 - - - +
345D GLU* 1.3 58.6 + - + +
346D THR 3.3 0.2 - - - -
347D TRP* 4.1 13.3 - - - -
348D GLY* 3.4 25.3 - - - -
349D VAL* 3.5 5.2 + - - +
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Residues in contact with GLU 345 (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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338D TYR* 5.2 6.1 + - - -
341D GLU* 3.0 26.7 + - - +
342D PHE* 3.2 21.2 + - + +
344D ASN* 1.3 76.0 - - + +
346D THR* 1.3 65.2 + - + +
349D VAL* 3.4 23.4 - - + +
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Residues in contact with THR 346 (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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26D GLN* 3.7 17.0 - - - +
96D THR* 4.9 0.2 - - - +
171D LEU* 4.7 4.0 - - - +
329D ASN* 3.4 41.6 - - - +
342D PHE* 2.7 40.5 + - + +
343D GLY* 3.3 7.1 + - - -
345D GLU* 1.3 82.5 - - + +
347D TRP* 1.3 73.3 + - - +
348D GLY 3.1 0.4 - - - -
349D VAL* 3.0 5.4 + - - +
350D THR* 3.0 26.2 + - - -
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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