Contacts of the strand formed by residues 379 - 386 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196I HIS* 4.8 5.8 - - - +
197I ARG* 3.5 6.1 - - - +
198I HIS* 4.1 35.7 - - + +
247I ASP 4.3 0.7 - - - -
248I LEU* 3.8 1.7 - - - -
249I THR* 3.3 47.2 + - + +
253I ASN* 4.5 6.7 - - - +
255I HIS* 5.2 4.7 - - - +
377I LEU* 3.9 3.6 - - - +
378I LYS* 1.3 112.2 - - + +
380I THR* 1.3 73.1 + - - +
381I THR* 6.0 1.6 - - + -
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Residues in contact with THR 380 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195I GLN* 3.0 22.0 - - - +
196I HIS* 2.9 12.6 - - - -
197I ARG* 2.8 38.2 + - + +
247I ASP 3.3 8.5 - - - -
248I LEU* 3.8 9.7 - - + +
342I LEU* 3.8 33.0 - - + +
365I ILE* 3.7 20.6 - - - +
377I LEU* 4.3 0.5 - - - +
379I MET* 1.3 84.8 + - - +
381I THR* 1.3 69.4 + - - +
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Residues in contact with THR 381 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184I GLU* 5.2 1.0 + - - +
193I VAL* 4.4 7.6 - - - +
195I GLN* 3.1 10.6 + - - -
196I HIS* 3.6 17.9 - - + +
222I LEU* 4.9 7.2 - - + +
245I ARG 3.4 1.0 - - - +
246I ILE* 3.3 6.4 - - - +
247I ASP* 3.0 58.1 + - + +
379I MET* 6.0 1.1 - - + -
380I THR* 1.3 83.9 - - - +
382I MET* 1.3 64.2 + - - +
383I LYS* 3.7 21.0 + - - +
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Residues in contact with MET 382 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193I VAL* 4.7 0.2 - - - -
194I ILE* 2.7 43.1 + - + +
195I GLN* 2.9 23.8 + - + +
227I TRP* 4.1 21.3 - - + -
244I LEU* 4.0 30.1 - - + -
245I ARG 3.3 5.6 - - - -
246I ILE* 4.5 7.2 - - + -
263I PHE* 4.8 6.7 - - + -
288I PHE* 5.1 3.1 - - + -
332I TRP* 4.0 13.9 - - + -
333I TRP* 4.4 23.6 - - + -
342I LEU* 3.6 32.5 - - + -
381I THR* 1.3 75.4 + - - +
383I LYS* 1.3 53.9 + - - +
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Residues in contact with LYS 383 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184I GLU* 3.1 41.4 + - - -
186I GLU* 4.9 1.8 + - - -
191I TRP* 3.2 52.2 - - + +
192I THR 3.9 3.8 - - - -
193I VAL* 4.1 13.5 - - + +
243I ARG 3.8 0.3 - - - +
244I LEU* 3.4 0.2 - - - -
245I ARG* 2.7 58.1 + - + +
247I ASP* 3.1 30.4 + - - +
381I THR* 3.7 13.5 - - - +
382I MET* 1.3 75.1 - - - +
384I LEU* 1.3 66.6 + - - +
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Residues in contact with LEU 384 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191I TRP* 3.5 5.7 - - - -
192I THR* 2.9 46.4 + - + +
194I ILE* 3.7 31.2 - - + -
233I ILE* 4.8 0.2 - - + -
236I LEU* 4.4 12.1 - - + -
237I THR* 3.3 31.4 - - + -
242I TYR* 4.0 24.0 - - + -
243I ARG 3.6 1.3 - - - -
244I LEU* 3.5 29.6 - - + -
263I PHE* 3.8 9.6 - - + -
383I LYS* 1.3 83.1 - - - +
385I LEU* 1.3 59.3 + - - +
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Residues in contact with LEU 385 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155I GLN* 4.5 2.9 - - - +
189I ASN* 3.8 22.7 - - + +
190I GLY 4.5 7.6 - - - +
191I TRP* 3.2 55.0 - - + +
242I TYR* 3.3 5.2 - - - -
243I ARG* 2.6 43.7 + - + +
384I LEU* 1.3 72.8 - - - +
386I PRO* 1.3 105.7 - - + +
389I ARG* 3.3 24.0 - - + +
390I ASP* 5.1 7.2 - - + +
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Residues in contact with PRO 386 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153I ASP* 3.6 22.2 - - - +
155I GLN* 3.6 28.3 - - + -
190I GLY 4.5 3.1 - - - +
192I THR* 5.6 0.2 - - + -
240I GLN* 3.7 18.4 - - - +
241I ALA 3.5 5.8 - - - +
242I TYR* 3.6 9.8 - - + -
243I ARG* 4.9 1.2 - - - +
385I LEU* 1.3 105.5 - - + +
387I MET* 1.3 68.7 + - - +
388I GLY* 2.9 6.4 + - - +
389I ARG* 3.3 16.2 + - + +
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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