Contacts of the strand formed by residues 379 - 386 (chain L) in PDB entry 1LWU
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 MET 379 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196L HIS* 4.8 6.3 - - - +
197L ARG* 3.5 6.1 - - - +
198L HIS* 4.0 36.3 - - + +
247L ASP 4.3 0.7 - - - -
248L LEU* 3.8 1.4 - - - -
249L THR* 3.3 47.9 + - + +
253L ASN* 4.5 6.1 - - - +
255L HIS* 5.2 4.7 - - - +
377L LEU* 4.0 3.6 - - - +
378L LYS* 1.3 112.4 - - + +
380L THR* 1.3 70.7 + - - +
381L THR* 6.0 1.6 - - + -
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Residues in contact with THR 380 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195L GLN* 3.0 21.1 - - - +
196L HIS* 2.8 12.3 - - - -
197L ARG* 2.8 40.3 + - + +
247L ASP 3.3 8.7 + - - -
248L LEU* 3.8 9.6 - - + +
342L LEU* 3.8 34.0 - - + +
365L ILE* 3.7 20.3 - - - +
377L LEU* 4.3 0.7 - - - +
379L MET* 1.3 84.1 + - - +
381L THR* 1.3 69.0 + - - +
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Residues in contact with THR 381 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184L GLU* 5.2 1.2 + - - +
193L VAL* 4.4 8.5 - - - +
195L GLN 3.1 10.4 + - - -
196L HIS* 3.6 17.9 - - + +
222L LEU* 4.9 6.8 - - + +
245L ARG 3.4 0.9 - - - +
246L ILE* 3.3 6.6 - - - +
247L ASP* 3.0 57.3 + - + +
379L MET* 6.0 0.9 - - + -
380L THR* 1.3 84.8 - - - +
382L MET* 1.3 64.7 + - - +
383L LYS* 3.7 19.5 + - - +
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Residues in contact with MET 382 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194L ILE* 2.7 44.3 + - + +
195L GLN* 2.9 23.8 + - - +
227L TRP* 4.1 24.2 - - + -
244L LEU* 4.0 28.9 - - + -
245L ARG 3.3 5.6 - - - -
246L ILE* 4.4 7.6 - - + -
263L PHE* 4.7 7.2 - - + -
288L PHE* 5.1 3.1 - - + -
332L TRP* 4.1 10.1 - - + -
333L TRP* 4.4 24.7 - - + -
342L LEU* 3.6 32.1 - - + -
381L THR* 1.3 74.9 - - - +
383L LYS* 1.3 54.6 + - - +
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Residues in contact with LYS 383 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184L GLU* 3.1 40.6 + - - -
186L GLU* 4.9 1.8 + - - -
191L TRP* 3.2 53.7 - - + +
192L THR 3.9 4.0 - - - -
193L VAL* 4.1 13.2 - - + +
243L ARG 3.8 0.5 - - - +
244L LEU* 3.4 0.2 - - - -
245L ARG* 2.7 58.8 + - + +
247L ASP* 3.0 30.0 + - - +
381L THR* 3.7 11.0 - - - +
382L MET* 1.3 74.3 - - - +
384L LEU* 1.3 65.9 + - - +
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Residues in contact with LEU 384 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191L TRP* 3.5 5.9 - - - -
192L THR* 2.9 45.2 + - + +
194L ILE* 3.7 30.1 - - + -
233L ILE* 4.9 0.2 - - + -
236L LEU* 4.4 12.3 - - + -
237L THR* 3.3 31.6 - - + -
242L TYR* 4.0 24.2 - - + -
243L ARG 3.6 1.1 - - - -
244L LEU* 3.5 30.1 - - + -
263L PHE* 3.8 10.8 - - + -
383L LYS* 1.3 83.6 - - - +
385L LEU* 1.3 60.3 + - - +
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Residues in contact with LEU 385 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155L GLN* 4.5 3.4 - - - +
189L ASN* 3.8 22.4 - - + +
190L GLY 4.5 6.7 - - - +
191L TRP* 3.2 54.5 - - + +
242L TYR* 3.3 5.7 - - - -
243L ARG* 2.6 46.2 + - + +
384L LEU* 1.3 73.0 - - - +
386L PRO* 1.3 104.8 - - + +
389L ARG* 3.3 23.8 - - + +
390L ASP* 6.2 2.5 - - + -
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Residues in contact with PRO 386 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153L ASP* 3.6 22.4 - - - +
155L GLN* 3.6 28.0 - - + -
190L GLY 4.5 3.1 - - - +
192L THR* 5.6 0.2 - - + -
240L GLN* 3.7 18.2 - - - +
241L ALA 3.5 5.4 - - - +
242L TYR* 3.6 10.1 - - + -
243L ARG* 4.9 1.2 - - - +
385L LEU* 1.3 106.8 - - + +
387L MET* 1.3 69.0 + - - +
388L GLY 2.9 6.7 + - - +
389L ARG* 3.3 15.4 + - + +
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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