Contacts of the helix formed by residues 203 - 218 (chain A) in PDB entry 1LWS
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 GLU 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A LEU* 4.1 12.6 - - - +
201A THR 2.5 23.9 - - - +
202A ILE* 1.3 88.3 - - + +
204A GLY* 1.3 83.4 + - - +
205A PRO* 3.5 3.4 - - - -
206A LYS* 2.7 47.5 + - + +
207A VAL* 3.2 10.9 + - + +
245A LYS* 3.2 45.8 + - - +
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Residues in contact with GLY 204 (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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193A MSE 3.8 16.2 - - - -
200A LEU* 4.1 17.3 - - - -
201A THR* 4.8 1.1 - - - -
202A ILE 4.0 2.8 - - - +
203A GLU* 1.3 86.2 + - - +
205A PRO* 1.3 62.0 - - - +
206A LYS 2.7 12.3 + - - -
207A VAL* 3.5 6.8 - - - +
208A LEU* 3.1 21.0 + - - +
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Residues in contact with PRO 205 (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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189A PHE* 2.8 38.0 - - + -
190A PHE* 4.6 27.6 - - + -
193A MSE 3.4 28.6 - - + -
199A HIS* 6.0 0.2 - - + -
201A THR* 5.4 9.0 - - + -
202A ILE 5.4 0.4 - - - +
203A GLU* 3.8 3.8 - - - +
204A GLY* 1.3 85.7 - - - +
206A LYS* 1.3 62.2 + - - +
208A LEU* 4.0 0.4 - - - -
209A ALA* 3.1 7.8 + - - +
314A THR* 5.0 6.3 + - - +
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Residues in contact with LYS 206 (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* 2.7 32.4 + - - +
204A GLY 2.7 4.9 + - - -
205A PRO* 1.3 67.8 - - - +
207A VAL* 1.3 65.8 + - + +
208A LEU 2.8 3.6 - - - -
209A ALA* 2.6 29.7 + - - +
210A TYR 2.9 9.7 + - - -
238A ARG* 5.9 0.2 - - - +
242A TYR* 3.6 32.5 + - + +
245A LYS* 4.8 9.1 - - - +
314A THR* 6.4 1.1 - - - +
317A THR* 3.8 19.3 - - + +
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Residues in contact with VAL 207 (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* 6.2 0.4 - - + -
203A GLU* 3.9 10.8 - - + +
204A GLY* 3.5 14.6 - - - +
206A LYS* 1.3 87.0 - - + +
208A LEU* 1.3 67.6 + - + +
210A TYR* 3.8 0.7 - - - -
211A LEU* 3.0 31.2 + - + +
242A TYR* 3.2 48.2 - - + +
245A LYS* 4.0 24.7 - - + +
246A LEU* 4.3 28.9 - - + +
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Residues in contact with LEU 208 (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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189A PHE* 3.5 13.5 - - + -
192A TYR* 5.7 2.2 - - + -
193A MSE 3.3 40.4 - - + -
204A GLY 3.1 14.1 + - - +
205A PRO 3.7 3.8 - - - +
206A LYS 2.7 4.9 + - - -
207A VAL* 1.3 81.2 - - + +
209A ALA* 1.3 50.5 + - - +
211A LEU* 3.0 7.8 + - - +
212A LEU* 2.7 57.0 + - + +
246A LEU* 4.5 19.7 - - + -
285A PRO* 5.4 3.4 - - + -
286A LEU* 4.8 12.6 - - + +
289A ALA* 4.4 16.2 - - + -
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Residues in contact with ALA 209 (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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189A PHE* 4.1 8.7 - - + -
205A PRO 3.1 12.2 + - - +
206A LYS* 2.6 12.6 + - - +
208A LEU* 1.3 76.0 - - - +
210A TYR* 1.3 57.5 + - - +
212A LEU* 3.1 16.4 + - + +
213A GLY* 2.7 27.0 + - - -
314A THR* 4.2 12.8 - - + +
317A THR* 3.6 19.7 - - + -
318A PHE* 3.6 14.2 - - + +
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Residues in contact with TYR 210 (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 2.9 7.0 + - - +
207A VAL 3.7 7.2 - - - +
209A ALA* 1.3 76.0 - - - +
211A LEU* 1.3 74.7 + - + +
213A GLY* 2.9 16.5 + - - -
214A LEU* 3.0 39.7 + - + -
235A LEU* 3.5 7.9 - - + +
238A ARG* 2.9 52.9 + - + -
239A VAL* 5.4 0.7 - - + -
242A TYR* 4.0 20.2 - + + -
317A THR* 3.2 18.4 - - + +
320A ALA* 4.3 6.1 - - + -
321A GLY* 3.7 19.3 - - - -
324A ASP* 2.5 31.6 + - - -
397A LYS* 4.1 3.1 - - + -
399A ALA* 3.4 8.3 - - - +
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Residues in contact with LEU 211 (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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207A VAL 3.0 16.2 + - - +
208A LEU* 3.4 6.5 - - - +
210A TYR* 1.3 90.7 - - + +
212A LEU* 1.3 64.7 + - - +
213A GLY 2.8 5.9 + - - -
214A LEU* 3.1 8.9 + - + +
215A TRP* 3.0 26.6 + - - +
226A PHE* 4.9 9.8 - - + -
239A VAL* 5.4 5.4 - - + +
242A TYR* 3.9 18.8 - - + +
243A ALA* 4.8 12.1 - - - +
246A LEU* 3.9 21.3 - - + -
266A LEU* 4.3 15.5 - - + -
286A LEU* 3.8 33.7 - - + -
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Residues in contact with LEU 212 (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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189A PHE* 3.3 28.3 - - + -
208A LEU* 2.7 24.3 + - + +
209A ALA* 3.1 33.4 - - + +
211A LEU* 1.3 71.9 - - - +
213A GLY* 1.3 63.8 + - - +
215A TRP* 3.4 14.0 - - + -
216A ILE* 3.2 12.3 - - - +
286A LEU* 4.8 4.9 - - + +
289A ALA* 3.7 24.7 - - + -
290A ILE* 4.5 8.3 - - + +
295A PHE* 3.7 35.1 - - + -
318A PHE* 3.2 23.0 - - + -
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Residues in contact with GLY 213 (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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209A ALA 2.7 13.1 + - - -
210A TYR 3.2 4.9 - - - -
211A LEU 2.8 1.4 - - - -
212A LEU* 1.3 74.2 - - - +
214A LEU* 1.3 70.4 + - - +
216A ILE* 2.8 20.1 + - - +
217A GLY 3.6 1.7 + - - -
318A PHE* 3.6 28.7 - - - -
321A GLY* 4.1 0.2 - - - -
322A LEU* 3.7 12.3 + - - -
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Residues in contact with LEU 214 (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* 3.0 40.1 + - + +
211A LEU* 3.6 9.0 - - + +
213A GLY* 1.3 66.9 - - - -
215A TRP* 1.3 54.8 + - - +
217A GLY 2.6 29.5 + - - -
218A ASP 3.0 14.3 + - - +
226A PHE* 3.9 36.6 - - + -
227A SER 5.7 0.2 - - - +
228A VAL* 4.8 3.8 - - + -
235A LEU* 4.3 8.1 - - + -
239A VAL* 4.1 14.4 - - + -
321A GLY* 3.3 21.9 - - - +
324A ASP* 4.1 6.7 - - + -
325A SER* 2.6 39.9 + - - +
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Residues in contact with TRP 215 (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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211A LEU 3.0 13.4 + - - +
212A LEU* 3.4 14.1 - - - -
214A LEU* 1.3 78.2 - - - +
216A ILE* 1.3 101.9 + - + +
218A ASP 4.1 1.3 - - - -
219A GLY* 2.9 44.9 + - - -
220A LEU 2.7 31.4 - - - -
221A SER* 4.0 13.7 - - - -
223A ARG 3.5 17.0 - - - -
224A ALA* 4.8 1.6 - - - -
225A THR 4.4 2.2 - - - -
226A PHE* 4.6 10.7 - + + -
286A LEU* 4.7 3.8 - - + -
287A TRP* 4.2 7.6 - + - -
290A ILE* 3.3 56.3 - - + +
295A PHE* 4.4 5.2 + + + +
296A LEU* 4.5 8.7 - - + -
301A LYS* 3.5 25.3 + - + +
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Residues in contact with ILE 216 (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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212A LEU 3.2 16.2 - - - +
213A GLY 2.8 11.5 + - - +
215A TRP* 1.3 98.8 - - + +
217A GLY* 1.3 57.7 + - - +
295A PHE* 4.4 22.0 - - + +
301A LYS* 2.4 38.6 + - + -
302A ASN 4.7 4.3 - - - +
303A ILE* 3.8 27.8 - - + -
318A PHE* 3.5 20.4 - - + -
322A LEU* 4.1 16.6 - - + -
346A VAL* 4.5 13.9 - - + -
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Residues in contact with GLY 217 (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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213A GLY 3.6 2.0 + - - -
214A LEU 2.6 12.7 + - - -
216A ILE* 1.3 82.1 - - - +
218A ASP* 1.3 57.0 + - - -
219A GLY 3.8 0.2 + - - -
301A LYS* 3.4 8.5 + - - -
322A LEU* 4.7 7.1 - - - +
325A SER* 3.9 7.9 - - - -
326A ASP* 2.7 22.4 - - - -
501A CA 2.8 14.9 - - - -
15B C 5.2 1.4 + - - -
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Residues in contact with ASP 218 (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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214A LEU* 3.0 11.6 + - + +
215A TRP 3.5 2.2 - - - -
217A GLY* 1.3 72.2 - - - -
219A GLY* 1.3 49.2 + - - +
226A PHE* 2.4 33.2 - - - +
227A SER* 3.6 34.2 - - - +
228A VAL* 5.8 0.9 - - - -
325A SER* 2.8 24.7 - - - +
326A ASP* 2.8 3.0 - - - +
501A CA 2.6 23.6 - - - -
502A CA 2.6 26.7 - - - -
27C C 4.9 2.3 - - - +
28C C 4.0 13.4 + - - -
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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