Contacts of the helix formed by residues 232 - 246 (chain A) in PDB entry 1LWT
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 ASP 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A VAL* 4.8 1.7 - - - +
229A ASP* 2.7 27.5 + - + +
230A SER 5.0 0.8 - - - -
231A ARG* 1.3 80.4 - - - +
233A THR* 1.3 63.5 + - - +
234A SER* 3.3 11.1 + - - -
235A LEU* 3.4 26.3 + - + +
236A MSE 3.3 18.2 + - - +
400A GLY* 3.0 9.5 - - - -
401A SER* 2.8 46.0 + - - +
402A LYS* 4.4 9.2 + - + +
403A LYS* 5.1 2.8 + - - -
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Residues in contact with THR 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A SER 5.0 3.7 + - - -
231A ARG 3.0 11.1 + - - -
232A ASP* 1.3 70.8 + - - +
234A SER* 1.3 67.4 + - - +
235A LEU 3.1 2.5 - - - -
236A MSE 2.8 28.5 + - + +
237A GLU* 3.0 28.2 - - + +
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Residues in contact with SER 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ASP* 3.3 8.4 + - - -
233A THR* 1.3 78.4 - - - +
235A LEU* 1.3 62.2 + - - +
237A GLU* 3.3 19.4 + - - +
238A ARG* 3.2 19.8 + - - +
399A ALA* 3.1 22.2 - - - +
401A SER* 4.5 10.5 - - - -
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Residues in contact with LEU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A TYR* 3.4 13.2 - - - +
214A LEU* 4.7 8.3 - - + -
228A VAL* 4.3 20.0 - - + -
229A ASP* 5.4 3.1 - - + +
232A ASP* 3.4 31.8 + - + +
234A SER* 1.3 75.2 - - - +
236A MSE 1.3 67.4 + - - +
238A ARG* 3.0 5.5 + - + +
239A VAL* 3.0 33.5 + - + +
324A ASP* 3.4 54.1 - - + +
325A SER* 5.5 1.1 - - - -
399A ALA* 3.7 7.9 + - + -
400A GLY* 3.6 6.5 - - - +
403A LYS* 5.0 1.3 - - - +
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Residues in contact with MSE 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A VAL* 3.9 21.7 - - + +
229A ASP 5.4 0.7 - - - +
230A SER 5.9 0.9 - - - +
232A ASP 3.3 11.7 + - - +
233A THR* 2.8 23.1 + - + +
235A LEU* 1.3 79.3 - - - +
237A GLU* 1.3 59.1 + - + +
239A VAL* 3.1 31.8 - - + +
240A THR* 3.2 15.6 + - - +
250A ALA* 5.7 2.2 - - + -
252A TYR* 4.6 11.7 - - + -
262A LYS* 3.5 38.6 - - + +
264A VAL* 3.7 27.8 - - + -
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Residues in contact with GLU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A THR* 3.0 31.2 + - + +
234A SER* 3.5 16.8 + - - +
235A LEU 3.2 0.2 - - - -
236A MSE 1.3 72.4 - - + +
238A ARG* 1.3 66.9 + - - +
240A THR* 2.8 11.0 + - - -
241A GLU* 2.7 27.3 + - + +
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Residues in contact with ARG 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A LYS* 5.6 0.2 - - - +
210A TYR* 3.8 29.4 - - + +
234A SER 3.2 4.1 + - - +
235A LEU* 3.0 7.5 + - - +
237A GLU* 1.3 76.5 - - - +
239A VAL* 1.3 55.6 + - + +
241A GLU* 3.4 8.9 - - - +
242A TYR* 2.7 97.2 + - + +
317A THR* 5.5 2.4 - - - +
397A LYS* 3.3 23.8 + - - +
398A CYS 3.5 16.8 + - - -
399A ALA* 3.2 49.4 - - + +
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Residues in contact with VAL 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A TYR* 5.8 4.0 - - + -
211A LEU* 5.2 10.6 - - + +
214A LEU* 5.8 7.9 - - + -
226A PHE* 5.1 10.8 - - + -
228A VAL* 4.8 12.3 - - + -
235A LEU* 3.0 27.8 - - + +
236A MSE 3.1 25.6 - - + +
238A ARG* 1.3 77.7 - - + +
240A THR* 1.3 67.6 + - - +
242A TYR* 4.1 2.1 - - - +
243A ALA* 2.8 26.7 + - + +
250A ALA* 5.0 1.6 - - + -
264A VAL* 4.9 16.2 - - + -
266A LEU* 4.9 11.2 - - + -
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Residues in contact with THR 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A MSE 3.2 14.6 + - - +
237A GLU* 2.8 14.5 + - - -
239A VAL* 1.3 75.2 - - - +
241A GLU* 1.3 54.1 - - - +
243A ALA* 3.0 1.6 + - - +
244A GLU* 2.6 50.0 + - + +
250A ALA* 4.1 27.1 - - + +
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Residues in contact with GLU 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A LYS* 5.5 0.5 + - - -
237A GLU* 2.7 17.3 + - - +
238A ARG* 3.4 12.7 - - - +
240A THR* 1.3 73.6 - - - +
242A TYR* 1.3 86.0 + - + +
244A GLU* 3.0 9.0 + - - +
245A LYS* 2.9 49.8 + - + +
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Residues in contact with TYR 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A GLU* 5.6 0.4 - - - -
206A LYS* 2.9 42.4 + - + +
207A VAL* 3.2 42.6 - - + +
210A TYR* 3.6 22.4 - + + -
211A LEU* 3.9 18.6 - - + -
238A ARG* 2.7 73.0 + - + +
239A VAL 4.1 1.1 - - - +
241A GLU* 1.3 92.9 - - + +
243A ALA* 1.3 62.1 + - - +
245A LYS* 3.0 15.1 + - + +
246A LEU* 3.1 15.8 + - - +
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Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A LEU* 4.5 6.1 - - + +
239A VAL 2.8 25.1 + - - +
240A THR* 3.3 5.4 - - - +
242A TYR* 1.3 73.1 - - - +
244A GLU* 1.3 62.9 + - - +
246A LEU* 3.3 13.1 + - - +
247A ASN 3.3 0.3 + - - -
248A LEU* 3.1 29.6 + - + +
249A CYS 4.9 0.4 - - - +
250A ALA* 4.8 4.3 - - + -
266A LEU* 3.7 39.3 - - + -
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Residues in contact with GLU 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A THR* 2.6 32.1 + - + +
241A GLU* 3.0 8.7 + - - +
243A ALA* 1.3 74.8 - - - +
245A LYS* 1.3 54.2 + - + +
247A ASN* 2.6 34.3 + - - +
248A LEU 2.8 25.4 + - - +
249A CYS* 4.2 12.3 - - - -
250A ALA* 4.7 2.1 + - - +
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Residues in contact with LYS 245 (chain A).
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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200A LEU* 4.4 8.5 - - - +
201A THR* 4.0 15.8 + - - +
203A GLU* 2.5 59.5 + - + +
206A LYS* 4.9 2.8 - - - +
207A VAL* 4.3 15.9 - - + -
241A GLU* 2.9 43.3 + - + +
242A TYR* 3.0 9.5 + - + +
244A GLU* 1.3 70.5 - - + +
246A LEU* 1.3 60.4 + - - +
247A ASN* 2.9 7.5 + - - +
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Residues in contact with LEU 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A LEU* 3.3 41.0 - - + +
204A GLY* 4.4 4.0 - - - -
207A VAL* 3.3 29.2 - - + -
208A LEU* 4.2 29.4 - - + +
211A LEU* 3.6 27.4 - - + -
242A TYR 3.1 8.7 + - - +
243A ALA* 3.6 10.8 - - - +
244A GLU 3.2 0.2 - - - -
245A LYS* 1.3 74.8 - - - +
247A ASN* 1.3 69.1 + - - +
248A LEU* 3.8 20.7 - - + +
266A LEU* 6.0 2.0 - - + -
285A PRO* 4.6 7.1 - - + +
286A LEU* 4.7 11.0 - - + +
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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