Contacts of the helix formed by residues 241 - 258 (chain B) in PDB entry 1WSQ
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 THR 241 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B HIS* 3.2 51.8 + - + +
171B PRO* 4.1 23.9 - - + +
172B ILE 3.9 10.5 - - - +
173B ILE* 3.8 18.3 - - + +
202B PHE* 4.1 7.8 - - + -
240B THR* 1.3 77.6 + - - +
242B LYS* 1.3 63.4 + - - +
243B ALA 3.1 0.2 - - - -
244B ASP* 3.1 11.5 + - - +
245B ILE* 3.6 3.1 + - - +
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Residues in contact with LYS 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B GLU* 4.6 0.4 - - - +
240B THR* 3.0 17.2 + - - +
241B THR* 1.3 80.0 + - - +
243B ALA* 1.3 53.8 + - - +
245B ILE* 3.0 26.5 + - + +
246B TRP 3.2 0.5 + - - -
298B PRO* 3.0 34.9 + - + +
299B ASP* 4.0 10.5 + - - +
301B ARG* 2.7 57.7 + - + +
302B PRO 3.5 24.7 - - - +
303B ASP* 4.0 13.7 - - + +
306B GLN* 5.6 0.2 - - - -
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Residues in contact with ALA 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ILE* 4.9 2.5 - - + -
225B TYR 4.9 1.6 - - - +
227B ALA* 4.1 11.3 + - + +
229B GLU* 3.6 19.1 + - - +
230B MET* 3.7 32.1 - - + +
239B ILE* 4.3 6.7 - - + -
240B THR 3.1 15.0 + - - +
242B LYS* 1.3 78.0 - - - +
244B ASP* 1.3 62.9 + - - +
246B TRP* 3.5 4.9 + - - +
247B ALA* 3.2 19.4 + - - +
301B ARG* 3.7 3.1 - - - +
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Residues in contact with ASP 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B VAL* 4.7 1.1 - - + +
165B LEU* 5.1 0.2 - - - +
166B HIS* 2.9 28.1 + - + +
173B ILE* 3.4 10.8 - - - +
174B HIS* 2.8 26.5 + - - +
175B ARG* 2.9 28.1 + - - -
177B LEU* 3.6 23.0 - - + +
240B THR 4.3 0.4 + - - -
241B THR 3.1 10.9 + - - +
243B ALA* 1.3 77.0 - - - +
245B ILE* 1.3 62.0 + - - +
247B ALA* 3.1 7.0 + - - +
248B LEU* 2.8 31.6 + - - +
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Residues in contact with ILE 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B HIS* 4.2 15.3 - - + -
241B THR 3.9 8.5 - - - +
242B LYS* 3.0 17.5 + - + +
244B ASP* 1.3 77.2 - - - +
246B TRP* 1.3 64.2 + - - +
248B LEU* 3.1 10.7 + - + +
249B GLY 3.0 16.8 + - - -
293B MET* 3.7 25.7 - - + +
301B ARG* 3.8 15.0 - - + -
302B PRO* 3.4 24.5 - - + +
303B ASP* 3.8 4.9 - - - +
304B ILE* 3.7 40.8 - - + +
307B VAL* 3.8 7.6 - - + -
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Residues in contact with TRP 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B SER 5.2 0.4 + - - -
225B TYR 3.5 19.0 - - - -
226B ARG 3.5 10.5 + - - -
227B ALA* 3.6 13.7 - - + -
228B PRO* 3.6 18.2 - - + -
242B LYS 3.2 3.6 + - - -
243B ALA 3.6 8.3 - - - +
244B ASP 3.3 0.2 - - - -
245B ILE* 1.3 79.6 - - - +
247B ALA* 1.3 60.6 + - - +
249B GLY* 3.0 11.8 + - - -
250B CYS* 3.0 25.3 + - - -
262B PHE* 3.3 32.8 - + - -
269B ILE* 3.6 28.1 - - + +
272B GLY* 4.1 9.9 - - - -
293B MET 4.0 8.7 - - - -
294B LEU* 3.5 39.3 - - + +
295B GLU 3.6 24.7 - - - -
296B PRO* 3.6 7.0 - - + -
301B ARG* 3.8 17.8 - - - +
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Residues in contact with ALA 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ARG 6.3 1.6 - - - -
177B LEU* 3.9 31.6 - - + +
225B TYR* 3.6 28.5 - - + +
243B ALA 3.2 8.9 + - - +
244B ASP* 3.1 13.2 + - - +
246B TRP* 1.3 78.5 - - - +
248B LEU* 1.3 58.1 + - - +
250B CYS* 3.2 4.8 + - - +
251B LEU* 2.8 28.9 + - - +
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Residues in contact with LEU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B PHE* 3.4 23.5 - - + -
158B THR* 3.8 30.1 - - + -
159B CYS* 4.6 10.3 - - - +
162B VAL* 4.2 12.1 - - + -
177B LEU* 3.9 18.8 - - + -
244B ASP 2.8 17.1 + - - +
245B ILE* 3.3 16.6 - - + +
247B ALA* 1.3 75.6 - - - +
249B GLY* 1.3 57.4 - - - +
251B LEU* 3.5 7.5 - - + +
252B LEU* 2.9 24.4 + - - +
293B MET* 3.8 12.1 - - - -
304B ILE* 3.7 30.1 - - + -
307B VAL* 5.0 1.1 - - + -
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Residues in contact with GLY 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ILE 3.0 7.1 + - - -
246B TRP 3.0 8.9 + - - -
248B LEU* 1.3 75.9 - - - +
250B CYS* 1.3 61.8 + - - +
252B LEU* 3.4 3.3 + - - +
253B TYR* 3.1 22.7 + - - +
290B ILE* 4.1 7.8 - - - +
293B MET* 3.6 29.5 - - - -
294B LEU* 4.0 13.2 - - - -
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Residues in contact with CYS 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B SER 3.7 17.9 - - - +
225B TYR* 3.7 19.5 - - + -
246B TRP* 3.0 40.6 + - - -
247B ALA 3.4 7.4 - - - +
249B GLY* 1.3 73.9 - - - +
251B LEU* 1.3 59.4 + - - +
253B TYR* 3.4 3.5 + - - +
254B LYS* 3.0 27.7 + - - +
260B LEU* 3.9 7.3 - - + +
261B PRO* 4.0 29.1 - - + +
262B PHE* 4.0 7.0 - - - -
294B LEU* 3.9 1.5 - - - +
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Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ILE* 5.3 1.1 - - + -
155B PHE* 4.5 10.1 - - + -
158B THR* 4.7 13.9 - - + +
177B LEU* 4.2 11.0 - - + -
178B LYS* 3.7 36.3 - - - +
179B VAL* 4.0 14.8 - - + +
182B ILE* 4.5 19.3 - - + -
225B TYR* 3.8 9.1 - - + -
247B ALA 2.8 16.3 + - - +
248B LEU* 3.5 9.9 - - + +
249B GLY 3.3 0.2 - - - -
250B CYS* 1.3 77.0 - - - +
252B LEU* 1.3 57.8 + - - +
254B LYS* 3.1 6.7 + - - +
255B LEU* 2.8 57.1 + - + +
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Residues in contact with LEU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B VAL* 3.5 29.4 - - + -
152B LEU* 5.3 1.3 - - + -
155B PHE* 3.8 28.0 - - + -
248B LEU 2.9 17.6 + - - +
249B GLY 3.8 4.3 - - - +
250B CYS 3.4 0.2 - - - -
251B LEU* 1.3 72.8 - - - +
253B TYR* 1.3 67.5 + - - +
255B LEU* 3.2 4.2 + - + +
256B CYS* 3.0 21.1 + - - -
286B MET* 3.7 21.1 - - + -
289B LEU* 3.8 19.5 - - + -
290B ILE* 3.7 23.3 - - + -
293B MET* 3.8 20.2 - - + -
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Residues in contact with TYR 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B GLY 3.1 14.7 + - - +
250B CYS 3.5 8.3 - - - +
252B LEU* 1.3 75.9 - - - +
254B LYS* 1.3 58.5 + - - +
256B CYS 3.1 2.1 + - - -
257B TYR* 2.9 55.8 + + + -
259B THR* 3.2 40.0 - - + +
260B LEU 4.0 2.0 - - - -
261B PRO* 3.6 39.5 + - + +
274B PHE* 3.9 11.2 - + - -
275B THR* 2.8 28.8 + - - -
276B ILE* 4.2 2.9 - - + -
277B PRO* 3.8 11.1 - - - +
290B ILE* 4.0 29.1 - - + +
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Residues in contact with LYS 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B VAL* 5.7 1.2 - - - +
138B MET* 3.3 19.7 - - + +
179B VAL* 3.7 27.3 - - + +
180B GLU* 4.0 12.3 + - - -
225B TYR* 3.8 11.2 + - - +
250B CYS 3.0 16.3 + - - +
251B LEU* 3.1 4.9 + - - +
253B TYR* 1.3 74.5 - - - +
255B LEU* 1.3 62.6 + - - +
258B PHE* 2.8 39.1 + - - +
259B THR* 3.3 24.0 - - - +
260B LEU* 3.8 34.0 - - + +
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Residues in contact with LEU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B VAL* 4.1 16.8 - - + -
138B MET* 3.5 21.3 - - + -
146B PHE* 3.5 19.8 - - + -
151B VAL* 4.0 31.3 - - + +
154B ILE* 3.8 24.9 - - + -
155B PHE* 4.4 8.3 - - + +
179B VAL* 4.0 11.0 - - + -
251B LEU* 2.8 38.6 + - + +
252B LEU* 3.2 10.3 + - - +
254B LYS* 1.3 76.2 - - - +
256B CYS* 1.3 60.5 + - - +
258B PHE* 3.4 17.5 - - - -
282B TYR* 4.5 1.2 + - - -
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Residues in contact with CYS 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B GLY* 5.7 2.1 - - - -
146B PHE 5.6 0.3 + - - -
151B VAL* 4.1 12.1 - - - -
252B LEU* 3.0 17.1 + - - -
253B TYR 3.5 7.4 - - - +
255B LEU* 1.3 79.5 - - - +
257B TYR* 1.3 79.5 + - + +
258B PHE* 3.7 3.6 - - - -
282B TYR* 3.4 41.1 + - + -
286B MET* 3.8 36.8 - - - -
290B ILE* 4.3 6.1 - - - -
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Residues in contact with TYR 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B TYR* 2.9 63.6 + + + +
256B CYS* 1.3 90.4 - - + +
258B PHE* 1.3 72.9 + - - +
259B THR* 3.1 11.4 + - + +
276B ILE* 3.5 7.4 - - + +
277B PRO* 3.6 37.0 - - + -
279B ASN* 5.8 0.7 - - - -
280B SER* 2.6 36.7 + - - -
281B ARG 5.1 0.2 - - - -
282B TYR* 3.9 15.0 - + - +
287B HIS* 3.4 18.4 + - - -
290B ILE* 4.1 5.8 - - + +
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Residues in contact with PHE 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B MET* 3.2 55.6 - - + -
141B ARG* 3.5 17.5 - - + -
142B LEU* 4.1 20.6 - - + -
145B GLY* 3.9 24.9 - - - -
146B PHE* 3.9 14.6 - + - -
254B LYS* 2.8 34.6 + - - +
255B LEU 3.4 18.6 - - - -
256B CYS 4.6 2.0 - - - -
257B TYR* 1.3 80.7 - - - +
259B THR* 1.3 60.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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