Contacts of the helix formed by residues 260 - 278 (chain A) in PDB entry 1H1W
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 CYS 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ILE* 3.3 19.2 - - - +
237A ALA* 3.6 22.9 - - + +
252A GLU* 4.1 9.4 - - - -
259A ALA* 1.3 76.2 - - - +
261A LYS* 1.3 68.0 + - - +
262A SER* 3.1 26.5 - - - -
263A SER* 2.8 30.5 + - - -
321A ALA* 4.1 10.8 - - - -
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Residues in contact with LYS 261 (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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197A HIS* 3.1 77.6 + - + +
198A GLY* 5.3 0.4 - - - -
200A GLY* 4.2 10.5 - - - -
201A ILE 5.0 0.7 - - - +
202A ILE* 3.5 10.5 - - + +
230A LEU* 3.9 26.7 - - + -
237A ALA* 4.9 1.0 - - - +
260A CYS* 1.3 74.1 - - - +
262A SER* 1.3 58.2 + - - +
264A ASP* 2.9 20.1 + - - +
265A LEU* 3.6 2.6 + - + -
327A CYS* 6.3 2.5 - - + -
328A GLU* 3.2 37.1 + - + +
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Residues in contact with SER 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A CYS* 3.1 16.0 - - - +
261A LYS* 1.3 76.2 - - - +
263A SER* 1.3 65.6 + - - +
264A ASP 3.1 0.2 - - - -
265A LEU* 3.0 21.3 + - - +
266A TRP 3.1 6.1 + - - -
321A ALA* 2.6 29.4 + - - -
324A ARG* 2.9 39.0 + - - +
327A CYS* 3.9 12.3 - - - +
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Residues in contact with SER 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ILE* 4.9 4.0 - - - -
204A ARG* 5.9 4.3 - - - -
248A TYR 5.1 1.0 - - - +
250A SER* 3.4 17.0 + - - -
252A GLU* 2.8 24.1 + - - -
253A LEU* 4.5 5.8 - - - -
259A ALA* 3.5 11.0 - - - -
260A CYS 2.8 30.2 + - - -
262A SER* 1.3 77.6 - - - +
264A ASP* 1.3 63.1 + - - +
266A TRP* 3.3 6.1 + - - +
267A ALA* 3.3 18.0 + - - +
324A ARG* 3.8 1.3 - - - +
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Residues in contact with ASP 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LEU* 4.2 14.8 - - + +
196A LEU* 4.7 0.3 - - - +
197A HIS* 2.9 27.8 + - + +
202A ILE* 3.5 9.4 - - - +
203A HIS* 2.8 31.7 + - - +
204A ARG* 3.0 27.9 + - - -
205A ASP 4.7 0.3 + - - -
206A LEU* 4.1 10.1 + - + +
261A LYS 2.9 9.5 + - - +
263A SER* 1.3 77.1 - - - +
265A LEU* 1.3 59.4 + - - +
267A ALA* 3.1 10.5 + - - +
268A LEU* 2.8 26.2 + - - +
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Residues in contact with LEU 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LEU* 4.6 5.4 - - + -
197A HIS* 4.5 4.9 - - + +
261A LYS* 3.6 4.7 + - + +
262A SER* 3.0 22.9 + - - +
264A ASP* 1.3 73.8 - - - +
266A TRP* 1.3 65.9 + - - +
268A LEU* 3.2 17.5 + - + +
269A GLY 3.0 17.2 + - - -
316A LEU* 3.9 17.9 - - + +
324A ARG* 4.3 7.4 - - + +
325A LEU 3.6 13.5 - - - +
326A GLY 3.4 6.5 - - - +
327A CYS* 3.3 39.9 - - + +
333A TYR* 3.9 20.6 - - + +
336A LEU* 4.2 17.0 - - + -
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Residues in contact with TRP 266 (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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247A GLN 5.1 0.2 + - - -
248A TYR 3.6 17.0 - - - -
249A VAL 3.2 11.9 + - - -
250A SER* 3.8 11.0 - - - -
251A PRO* 3.5 31.4 - - + -
262A SER 3.1 5.5 + - - -
263A SER 3.4 9.6 - - - +
264A ASP 3.2 0.4 - - - -
265A LEU* 1.3 77.4 - - - +
267A ALA* 1.3 63.6 + - - +
269A GLY 3.0 10.0 + - - -
270A CYS* 3.1 24.1 + - - -
282A PHE* 3.4 26.7 - + - -
294A ILE* 3.9 17.0 - - + -
297A LEU* 3.8 21.5 - - + -
316A LEU 4.2 9.0 - - - -
317A LEU* 3.4 24.7 - - + +
318A VAL 3.7 29.4 - - - -
319A LEU* 4.2 2.2 - - + -
324A ARG* 3.7 25.7 - - - +
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Residues in contact with ALA 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A LEU* 3.8 35.4 - - + +
248A TYR* 4.2 14.5 - - + +
263A SER 3.3 8.5 + - - +
264A ASP* 3.1 12.4 + - - +
266A TRP* 1.3 86.1 - - - +
268A LEU* 1.3 62.6 + - - +
270A CYS* 3.0 7.8 + - - +
271A ILE* 2.9 28.2 + - - +
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Residues in contact with LEU 268 (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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186A THR* 4.4 2.7 - - + -
189A ILE* 3.8 33.9 - - + -
190A VAL* 3.8 27.4 - - + -
193A LEU* 4.3 10.3 - - + -
206A LEU* 4.6 1.5 - - - +
264A ASP 2.8 12.7 + - - +
265A LEU* 3.2 29.4 - - + +
266A TRP 3.2 0.2 - - - -
267A ALA* 1.3 76.0 - - - +
269A GLY* 1.3 57.5 + - - +
271A ILE* 3.1 10.9 + - + +
272A ILE* 2.9 49.2 + - + +
316A LEU* 4.1 14.4 - - + -
336A LEU* 4.4 7.9 - - + -
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Residues in contact with GLY 269 (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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265A LEU 3.0 11.3 + - - -
266A TRP 3.0 4.8 + - - -
268A LEU* 1.3 78.4 - - - +
270A CYS* 1.3 60.5 + - - +
272A ILE* 3.5 3.6 + - - +
273A TYR* 3.1 22.7 + - - +
313A VAL* 3.9 9.1 - - - +
316A LEU* 3.8 23.8 - - - +
317A LEU* 3.8 15.5 - - - -
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Residues in contact with CYS 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A GLN 3.8 16.8 - - - +
248A TYR* 3.7 22.0 - - + -
266A TRP* 3.1 40.3 + - - -
267A ALA* 3.0 8.1 + - - +
269A GLY* 1.3 75.5 - - - +
271A ILE* 1.3 59.0 + - - +
273A TYR* 3.3 3.5 + - - +
274A GLN* 2.9 28.8 + - - +
281A PRO* 3.6 23.1 - - + +
282A PHE* 4.2 11.4 - - - -
317A LEU* 4.0 7.6 - - - -
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Residues in contact with ILE 271 (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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167A LEU* 4.8 3.4 - - + -
171A ILE* 6.0 0.2 - - + -
189A ILE* 4.1 24.2 - - + -
206A LEU* 3.7 36.1 - - + -
207A LYS* 4.0 13.5 - - - -
208A PRO* 4.1 24.7 - - + -
211A ILE* 4.0 11.7 - - + -
248A TYR* 4.3 7.0 - - + -
267A ALA 2.9 18.0 + - - +
268A LEU* 3.1 8.9 + - + +
270A CYS* 1.3 74.7 - - - +
272A ILE* 1.3 65.9 + - + +
274A GLN* 3.1 8.5 + - - +
275A LEU* 2.9 33.9 + - + +
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Residues in contact with ILE 272 (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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182A THR* 4.6 5.2 - - + -
186A THR* 3.5 39.9 - - + +
268A LEU* 2.9 25.0 + - + +
269A GLY 3.9 4.3 - - - +
271A ILE* 1.3 76.5 - - + +
273A TYR* 1.3 64.3 + - - +
275A LEU* 3.2 10.4 + - + +
276A VAL* 3.1 33.2 + - + +
309A ALA* 4.7 10.3 - - + +
312A LEU* 3.7 14.8 - - + -
313A VAL* 3.7 16.6 - - + -
316A LEU* 3.7 29.6 - - + -
341A PHE* 5.1 3.6 - - + -
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Residues in contact with TYR 273 (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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269A GLY 3.1 12.0 + - - +
270A CYS 3.4 7.6 - - - +
272A ILE* 1.3 80.3 - - - +
274A GLN* 1.3 52.6 + - - +
276A VAL* 3.3 1.4 + - - +
277A ALA* 2.8 47.9 + - + +
279A LEU 3.1 22.4 - - - -
280A PRO 4.0 1.8 - - - -
281A PRO* 3.4 34.4 + - + +
283A ARG* 4.6 8.1 + - - -
299A TYR* 3.8 16.8 - + - -
300A ASP 2.6 29.2 + - - -
301A PHE* 3.9 24.2 - + - -
302A PRO* 3.7 9.7 - - + +
305A PHE* 3.8 21.9 - + + -
313A VAL* 4.2 4.2 - - + +
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Residues in contact with GLN 274 (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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168A LEU* 3.8 26.5 - - - +
171A ILE* 4.1 17.1 - - + +
172A ARG* 5.9 0.6 - - - +
208A PRO* 3.3 16.9 - - + +
248A TYR* 2.5 36.1 + - - -
270A CYS 2.9 15.2 + - - +
271A ILE 3.1 5.8 + - - +
273A TYR* 1.3 78.1 - - - +
275A LEU* 1.3 55.4 + - - +
278A GLY* 2.7 34.9 + - - +
279A LEU* 3.5 18.2 - - - +
280A PRO* 3.7 26.0 - - + +
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Residues in contact with LEU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LEU* 4.4 11.2 - - + -
171A ILE* 3.7 27.4 - - + -
176A SER* 3.6 3.8 - - - -
177A PHE* 2.8 57.4 + - + +
182A THR* 4.3 24.5 - - + +
185A TYR* 4.6 12.3 - - + -
186A THR* 3.9 23.6 - - - +
189A ILE* 5.0 3.8 - - + -
271A ILE* 2.9 29.5 + - + +
272A ILE* 3.2 8.5 + - + +
274A GLN* 1.3 77.1 - - - +
276A VAL* 1.3 61.6 + - - +
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Residues in contact with VAL 276 (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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176A SER* 3.5 14.4 + - - -
177A PHE 4.5 6.0 - - - +
182A THR* 3.6 28.0 - - + +
272A ILE* 3.1 14.8 + - + +
275A LEU* 1.3 78.4 - - - +
277A ALA* 1.3 60.1 + - - +
302A PRO* 6.2 0.2 - - + -
305A PHE* 3.7 50.0 - - + -
306A PHE* 3.7 32.1 - - + -
309A ALA* 4.4 4.7 - - + -
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Residues in contact with ALA 277 (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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176A SER* 4.3 4.1 - - - -
273A TYR* 2.8 47.3 + - + +
276A VAL* 1.3 74.8 - - - +
278A GLY* 1.3 58.6 + - - +
279A LEU* 3.2 10.2 + - + +
302A PRO* 4.3 19.7 - - + -
305A PHE* 4.4 3.1 - - + -
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Residues in contact with GLY 278 (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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171A ILE* 3.9 13.5 - - - +
172A ARG* 5.9 0.3 + - - -
175A GLY 3.2 25.8 - - - +
176A SER* 4.1 2.0 - - - -
274A GLN* 2.7 27.6 + - - +
276A VAL 3.5 1.6 - - - -
277A ALA* 1.3 72.9 - - - +
279A LEU* 1.3 72.0 + - - +
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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
------------------------------------------------------------
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