Contacts of the strand formed by residues 379 - 386 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C HIS* 4.9 6.1 - - - +
197C ARG* 3.5 7.0 - - - +
198C HIS* 4.1 34.5 - - + +
247C ASP 4.4 0.9 - - - +
248C LEU* 3.9 1.2 - - - -
249C THR* 3.3 44.8 + - + +
253C ASN* 4.5 6.7 - - - +
255C HIS* 5.2 4.9 - - - +
377C LEU* 3.9 4.9 - - - +
378C LYS* 1.3 111.5 - - + +
380C THR* 1.3 71.9 + - - +
381C THR* 6.0 1.1 - - + -
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Residues in contact with THR 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C GLN* 3.0 21.3 - - - +
196C HIS* 2.8 13.0 - - - -
197C ARG* 2.8 38.0 + - + +
247C ASP 3.3 8.7 + - - -
248C LEU* 3.9 9.8 - - + +
342C LEU* 3.8 34.3 - - + +
365C ILE* 3.7 20.5 - - - +
377C LEU* 4.3 0.5 - - - +
379C MET* 1.3 84.9 + - - +
381C THR* 1.3 67.7 + - - +
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Residues in contact with THR 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C GLU* 5.2 1.1 + - - +
193C VAL* 4.4 8.5 - - - +
195C GLN* 3.1 11.3 + - - -
196C HIS* 3.5 18.4 - - + +
222C LEU* 4.9 7.7 - - + +
245C ARG 3.5 1.0 - - - +
246C ILE* 3.3 6.4 - - - +
247C ASP* 3.0 56.2 + - + +
379C MET* 6.0 1.1 - - + -
380C THR* 1.3 85.2 - - - +
382C MET* 1.3 64.8 + - - +
383C LYS* 3.7 19.5 + - - +
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Residues in contact with MET 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C ILE* 2.7 42.4 + - + +
195C GLN* 2.9 24.9 + - + +
227C TRP* 4.1 24.7 - - + -
244C LEU* 4.0 28.5 - - + -
245C ARG 3.3 5.6 - - - -
246C ILE* 4.5 8.1 - - + -
263C PHE* 4.7 7.4 - - + -
288C PHE* 5.1 3.4 - - + -
332C TRP* 4.1 10.3 - - + -
333C TRP* 4.4 23.1 - - + -
342C LEU* 3.6 32.5 - - + -
381C THR* 1.3 75.8 + - - +
383C LYS* 1.3 54.1 + - - +
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Residues in contact with LYS 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C GLU* 3.1 42.2 + - - -
186C GLU* 4.9 1.8 + - - -
191C TRP* 3.2 50.8 - - + +
192C THR 3.9 4.0 - - - -
193C VAL* 4.1 13.5 - - + +
243C ARG 3.8 0.5 - - - +
244C LEU* 3.5 0.2 - - - +
245C ARG* 2.7 59.6 + - + +
247C ASP* 3.1 30.1 + - - +
381C THR* 3.7 12.1 - - - +
382C MET* 1.3 74.7 - - - +
384C LEU* 1.3 66.6 + - - +
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Residues in contact with LEU 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C TRP* 3.5 6.0 - - - -
192C THR* 2.9 45.7 + - + +
194C ILE* 3.7 30.5 - - + -
233C ILE* 4.9 0.7 - - + -
236C LEU* 4.4 11.9 - - + -
237C THR* 3.3 30.7 - - + -
242C TYR* 4.0 23.6 - - + -
243C ARG 3.6 1.8 - - - -
244C LEU* 3.6 30.1 - - + -
263C PHE* 3.8 10.3 - - + -
383C LYS* 1.3 83.2 - - - +
385C LEU* 1.3 60.3 + - - +
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Residues in contact with LEU 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C GLN* 4.6 2.5 - - - +
189C ASN* 3.8 22.0 - - + +
190C GLY 4.5 6.7 - - - +
191C TRP* 3.2 57.0 - - + +
242C TYR* 3.3 4.9 - - - -
243C ARG* 2.6 45.2 + - + +
384C LEU* 1.3 73.2 - - - +
386C PRO* 1.3 105.6 - - + +
389C ARG* 3.3 25.4 - - + +
390C ASP* 6.2 2.5 - - + -
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Residues in contact with PRO 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C ASP* 3.6 23.3 - - - +
155C GLN* 3.6 27.4 - - + -
190C GLY 4.5 3.4 - - - +
240C GLN* 3.7 18.2 - - - +
241C ALA 3.5 6.7 - - - +
242C TYR* 3.6 10.5 - - + -
243C ARG* 4.9 1.4 - - - +
385C LEU* 1.3 106.6 - - + +
387C MET* 1.3 68.1 + - - +
388C GLY* 2.9 5.8 + - - +
389C ARG* 3.3 16.1 + - + +
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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