Contacts of the strand formed by residues 255 - 265 (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 HIS 255 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247I ASP* 6.3 2.2 - - + -
248I LEU 3.5 5.8 - - - +
249I THR* 3.2 23.3 + - - +
253I ASN* 3.3 45.3 + - - -
254I THR* 1.3 75.5 - - - +
256I ARG* 1.3 64.6 + - - +
257I TYR* 5.7 1.0 - - - -
283I ASP* 4.4 3.1 - - - +
379I MET* 5.2 5.7 - - - +
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Residues in contact with ARG 256 (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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247I ASP* 3.8 2.1 - - - +
248I LEU* 3.2 30.5 + - - +
254I THR* 3.9 12.8 + - + +
255I HIS* 1.3 77.7 - - - +
257I TYR* 1.3 62.4 + - - +
283I ASP* 2.8 47.7 + - - +
284I ALA* 3.9 10.1 - - + -
370I TRP* 3.1 57.1 - - + +
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Residues in contact with TYR 257 (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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245I ARG* 3.7 18.2 + - - -
246I ILE 3.1 13.0 - - - +
247I ASP* 3.6 15.3 - - - +
255I HIS 5.7 0.9 - - - -
256I ARG* 1.3 79.1 - - - +
258I ALA* 1.3 57.5 + - - +
259I ASP* 2.8 40.4 - - - -
281I ASP* 2.5 26.8 + - + -
282I GLY* 3.1 37.2 - - - -
283I ASP* 2.9 31.1 + - - -
284I ALA* 3.1 18.7 + - - -
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Residues in contact with ALA 258 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244I LEU 3.8 0.3 - - - +
245I ARG* 3.4 1.2 - - - -
246I ILE* 2.9 36.9 + - + +
248I LEU* 5.3 0.2 - - + -
257I TYR* 1.3 75.9 - - - +
259I ASP* 1.3 68.5 + - - +
260I TYR* 4.0 10.5 - - + -
279I TYR* 4.1 10.5 - - + -
281I ASP 3.9 5.2 - - - -
282I GLY* 4.3 0.4 - - - -
284I ALA* 4.2 1.1 - - + -
285I GLY 4.2 0.7 - - - +
367I TRP* 4.0 36.6 - - + +
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Residues in contact with ASP 259 (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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243I ARG* 3.1 21.9 + - + +
244I LEU 3.3 8.3 - - - +
245I ARG* 3.0 32.7 + - - +
257I TYR* 2.8 30.2 - - - -
258I ALA* 1.3 90.6 - - - +
260I TYR* 1.3 71.7 + - - +
279I TYR* 3.4 4.9 - - - -
280I LEU* 3.0 34.4 + - + -
281I ASP* 3.1 17.1 + - + +
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Residues in contact with TYR 260 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242I TYR 3.9 0.3 - - - +
243I ARG* 3.4 2.4 - - - -
244I LEU* 2.8 55.2 + - + +
246I ILE* 4.4 2.2 - - + -
258I ALA* 4.0 21.3 - - + -
259I ASP* 1.3 93.6 - - - +
261I GLY* 1.3 61.0 + - - +
263I PHE* 4.0 1.1 - - + +
276I TYR* 3.3 41.1 - + + -
278I MET 3.4 9.2 - - - -
279I TYR* 3.6 7.6 - + - -
280I LEU* 3.8 1.6 - - - -
286I ASN* 3.1 44.9 + - - -
287I ALA 3.5 1.2 + - - -
288I PHE* 3.2 52.8 + + + +
367I TRP* 3.9 4.2 - + - -
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Residues in contact with GLY 261 (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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260I TYR* 1.3 70.3 - - - +
262I HIS* 1.3 60.9 + - - -
263I PHE 2.8 12.6 + - - -
276I TYR* 3.1 4.7 - - - +
277I SER* 2.8 26.4 + - - -
278I MET 3.2 2.8 + - - -
280I LEU* 2.9 28.1 - - - +
387I MET* 3.4 17.7 - - - -
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Residues in contact with HIS 262 (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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241I ALA* 3.7 19.4 - - + +
242I TYR 3.0 16.0 + - - +
261I GLY* 1.3 70.9 - - - +
263I PHE* 1.3 67.0 + - - +
264I LYS* 3.5 5.9 + - - +
275I PHE* 3.6 24.6 - - + -
276I TYR* 4.0 0.7 - - - -
277I SER* 2.9 37.7 - - - +
280I LEU* 5.9 0.2 - - + -
387I MET* 3.2 29.6 - - + +
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Residues in contact with PHE 263 (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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194I ILE* 5.6 2.9 - - + -
233I ILE* 4.2 14.1 - - + -
237I THR* 3.6 31.2 - - + +
240I GLN 5.4 0.2 - - - +
242I TYR* 2.8 20.0 + - - +
244I LEU* 3.3 48.9 - - + +
260I TYR 4.0 3.1 - - - +
261I GLY 2.8 5.0 + - - +
262I HIS* 1.3 78.7 - - - +
264I LYS* 1.3 71.1 + - - +
265I LEU* 3.9 17.7 - - + -
274I LEU* 3.2 28.7 - - + -
275I PHE 3.2 9.4 - - - -
276I TYR* 4.1 7.4 - + + -
288I PHE* 5.4 0.9 - + - -
333I TRP* 4.6 9.4 - + - -
382I MET* 4.8 9.6 - - + -
384I LEU* 3.8 18.6 - - + -
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Residues in contact with LYS 264 (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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237I THR* 3.4 28.3 - - - +
238I GLY* 4.9 11.1 - - - +
262I HIS 3.7 2.7 - - - +
263I PHE* 1.3 81.2 - - - +
265I LEU* 1.3 87.6 + - - +
266I THR* 4.8 10.0 - - + +
273I ARG 3.7 0.2 - - - +
274I LEU* 4.2 0.9 - - - +
275I PHE* 2.9 59.8 + - + -
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Residues in contact with LEU 265 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230I ASN* 4.4 15.7 - - - +
233I ILE* 3.6 33.4 - - + -
234I HIS* 2.6 40.1 + - + -
237I THR* 3.4 4.9 + - - -
238I GLY* 5.6 0.5 + - - -
263I PHE* 3.9 9.6 - - + -
264I LYS* 1.3 95.1 - - - +
266I THR* 1.3 59.6 + - - +
272I TYR* 4.3 17.3 - - + +
273I ARG 3.1 14.1 - - - +
274I LEU* 3.9 4.0 - - - -
275I PHE* 5.7 0.2 - - - -
333I TRP* 3.3 41.1 - - + +
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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