Contacts of the helix formed by residues 231 - 238 (chain K) 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 231 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230K MET* 1.3 83.9 + - + +
232K CYS* 1.3 76.8 + - - +
233K GLU* 3.0 26.0 - - + +
234K ASP* 3.5 10.7 - - + +
235K ILE* 3.5 13.5 + - - +
248K ILE* 3.6 15.1 - - - +
250K PRO* 5.7 0.4 - - - -
269K GLY 3.2 7.6 + - - -
271K THR* 3.1 14.8 + - - -
322K LEU* 4.2 14.5 - - + +
328K GLN* 2.9 30.7 + - - -
474K LEU* 2.8 31.6 + - + -
475K ARG* 3.1 11.9 - - - -
476K PRO* 3.4 10.1 - - + +
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Residues in contact with CYS 232 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231K HIS* 1.3 75.5 - - - +
233K GLU* 1.3 55.6 + - - +
234K ASP 3.1 1.8 - - - -
235K ILE* 2.8 7.9 + - - +
236K TYR* 2.7 34.8 + - - +
248K ILE* 4.8 0.7 - - - -
259K VAL* 3.9 6.5 - - - -
261K CYS* 2.0 56.8 - - - -
263K MET* 3.7 13.9 - - + +
269K GLY* 3.7 8.5 - - - +
270K TRP 3.9 0.2 - - - -
271K THR* 3.2 37.4 + - - +
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Residues in contact with GLU 233 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231K HIS* 3.0 23.0 - - + -
232K CYS* 1.3 77.0 - - - +
234K ASP* 1.3 62.9 + - - +
236K TYR* 3.1 13.7 + - - +
237K ARG* 2.9 56.5 + - - +
268K GLY 4.6 1.1 - - - +
269K GLY* 3.2 16.6 + - - +
475K ARG* 3.3 28.6 + - - +
476K PRO* 3.8 19.1 - - + +
477K LYS 4.4 12.0 - - - +
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Residues in contact with ASP 234 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229K GLY* 3.2 9.7 - - - -
230K MET* 3.1 37.0 + - + +
231K HIS* 3.5 18.4 + - + +
233K GLU* 1.3 81.5 - - - +
235K ILE* 1.3 62.7 + - - +
237K ARG* 3.2 20.9 + - - +
238K ASN* 3.1 34.3 + - - +
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Residues in contact with ILE 235 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227K VAL* 4.3 5.2 - - + -
228K SER* 3.6 23.3 - - - -
229K GLY 3.6 2.7 - - - +
231K HIS 3.6 7.2 - - - +
232K CYS* 2.8 11.3 + - - +
234K ASP* 1.3 75.8 - - - +
236K TYR* 1.3 57.4 + - - +
238K ASN* 2.7 26.8 + - - +
239K GLY 3.2 0.3 + - - -
240K GLY* 3.0 27.0 + - - +
246K TYR* 3.3 63.3 - - + -
247K TYR 3.8 6.7 - - - +
248K ILE* 3.7 18.2 - - + -
261K CYS* 4.0 6.7 - - - -
263K MET* 4.8 2.7 - - - -
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Residues in contact with TYR 236 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232K CYS 2.7 14.0 + - - +
233K GLU* 3.1 19.5 + - - +
235K ILE* 1.3 72.2 - - - +
237K ARG* 1.3 60.7 + - + +
238K ASN 2.8 6.8 + - - -
239K GLY 2.8 13.3 + - - -
240K GLY 3.3 15.7 + - - -
241K ARG* 2.9 70.4 + - + -
263K MET* 3.8 34.8 + - + -
267K GLY 4.1 15.6 + - - -
268K GLY 5.5 0.2 - - - -
269K GLY* 4.2 12.3 - - - -
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Residues in contact with ARG 237 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233K GLU* 2.9 43.3 + - - +
234K ASP* 3.2 25.3 + - - +
236K TYR* 1.3 78.9 - - + +
238K ASN* 1.3 67.5 + - - +
239K GLY 3.4 0.4 - - - -
241K ARG* 5.0 4.4 + - - +
477K LYS 6.2 1.4 - - - -
209L VAL* 3.7 13.7 - - - +
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Residues in contact with ASN 238 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227K VAL* 3.3 26.0 - - + +
228K SER 3.1 19.4 - - - +
234K ASP* 3.1 21.2 + - - +
235K ILE 2.7 12.6 + - - +
237K ARG* 1.3 90.9 + - - +
239K GLY* 1.3 55.5 + - - +
240K GLY 3.4 0.7 - - - -
209L VAL* 4.1 6.7 - - - +
210L SER* 4.3 6.4 + - - -
212L ARG* 5.4 4.6 - - - +
213L GLU* 3.7 43.4 + - + +
214L GLY 4.6 1.6 - - - +
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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