Contacts of the helix formed by residues 260 - 277 (chain A) in PDB entry 4UAL
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 PRO 260 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A HIS* 3.4 39.7 - - + +
197A VAL* 3.6 11.2 - - + -
225A MET* 3.4 29.8 - - + -
229A GLY* 3.3 16.2 - - - +
259A GLY* 1.3 79.3 - - - +
261A GLU* 1.3 68.4 + - - +
262A CYS 2.9 4.6 + - - -
263A ASP* 3.0 12.4 + - - +
264A TRP* 3.8 4.3 + - + +
329A GLY 5.8 4.3 - - - +
330A GLN 5.9 3.1 - - - +
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Residues in contact with GLU 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLU* 3.2 16.3 - - - +
258A TYR* 3.3 5.8 - - - +
259A GLY* 2.8 35.5 + - - -
260A PRO* 1.3 84.0 - - - +
262A CYS* 1.3 60.7 + - - +
263A ASP 3.1 0.2 - - - -
264A TRP* 3.1 23.8 + - + +
265A TRP 3.2 3.6 + - - -
324A ARG* 2.8 49.2 + - + +
327A ARG* 2.8 27.0 + - + +
330A GLN* 5.8 8.5 - - + -
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Residues in contact with CYS 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A VAL* 3.4 33.4 - - - -
199A ARG* 4.3 6.5 - - - -
244A SER* 3.4 23.4 - - - +
246A GLU* 3.4 9.2 - - - +
247A ILE* 3.6 26.5 - - + -
258A TYR* 4.1 8.3 - - + -
259A GLY 3.4 8.0 + - - +
260A PRO 2.9 1.2 + - - -
261A GLU* 1.3 82.3 - - - +
263A ASP* 1.3 68.2 + - - +
265A TRP* 3.5 2.8 + - - +
266A SER* 3.1 25.2 + - - -
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Residues in contact with ASP 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ILE* 4.0 15.2 - - + +
191A ILE* 5.7 0.2 - - - +
192A HIS* 2.7 31.4 + - + +
197A VAL* 3.6 6.4 - - - +
198A HIS* 3.0 29.6 + - - +
199A ARG* 2.8 29.1 + - - -
201A ILE* 4.0 11.8 - - + +
260A PRO 3.0 9.8 + - - +
262A CYS* 1.3 79.5 - - - +
264A TRP* 1.3 59.7 - - - +
266A SER* 3.4 9.2 + - - -
267A LEU* 3.0 25.3 + - - +
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Residues in contact with TRP 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A VAL* 3.6 26.0 - - - -
188A ILE* 3.6 30.5 - - + -
189A ASP* 3.9 5.8 - - - -
192A HIS* 3.5 22.5 + + - -
260A PRO* 3.9 13.8 - - + +
261A GLU* 3.1 14.1 + - - +
263A ASP* 1.3 75.8 - - - +
265A TRP* 1.3 64.2 - - - +
267A LEU* 3.2 26.6 + - + +
268A GLY 3.0 17.2 + - - -
320A LEU* 3.6 18.5 - - + +
327A ARG* 4.2 4.9 - - - -
328A LEU 3.7 24.9 - - - +
329A GLY* 3.3 24.7 + - - -
333A ILE* 3.7 26.0 - - + -
336A PHE* 3.4 24.2 - + - -
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Residues in contact with TRP 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ASP 5.3 0.2 + - - -
242A TYR 3.5 15.5 + - - -
243A ILE 3.5 11.1 + - - -
244A SER* 3.6 13.5 - - - -
245A PRO* 3.4 40.6 - - + -
261A GLU 3.2 5.7 + - - -
262A CYS 3.7 6.1 - - - +
263A ASP 3.4 0.2 - - - -
264A TRP* 1.3 76.9 - - - +
266A SER* 1.3 60.2 + - - +
268A GLY* 2.8 18.4 + - - -
269A VAL* 3.1 24.0 + - + +
281A PHE* 3.4 27.9 - + - -
293A ILE* 4.0 9.0 - - + -
296A HIS* 3.7 19.1 - + + -
320A LEU 3.6 18.6 - - - -
321A ILE* 3.6 17.9 - - + +
322A CYS 3.6 25.4 - - - -
327A ARG* 3.5 30.7 - - - +
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Residues in contact with SER 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ARG 5.8 2.3 - - - -
201A ILE* 3.4 33.5 + - - -
242A TYR* 2.9 27.8 + - - +
244A SER 5.4 0.2 + - - -
262A CYS 3.1 12.2 + - - -
263A ASP* 3.6 10.2 - - - -
265A TRP* 1.3 80.2 - - - +
267A LEU* 1.3 63.1 + - - +
269A VAL* 3.1 7.2 + - - +
270A CYS* 3.0 26.1 + - - -
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Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ILE* 4.1 20.4 - - + -
184A MET* 3.7 44.0 - - + -
185A VAL* 3.8 17.9 - - + -
188A ILE* 4.1 8.7 - - + -
201A ILE* 4.4 4.7 - - - +
263A ASP 3.0 14.2 + - - +
264A TRP* 3.4 37.5 - - + +
265A TRP 3.2 0.2 - - - -
266A SER* 1.3 75.5 - - - +
268A GLY* 1.3 63.2 + - - +
270A CYS* 3.1 6.6 + - - +
271A MET* 2.9 20.3 + - - +
320A LEU* 4.0 17.0 - - + -
336A PHE* 4.2 2.7 - - + -
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Residues in contact with GLY 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A TRP 3.0 7.3 + - - -
265A TRP 2.8 9.7 + - - -
267A LEU* 1.3 78.3 - - - +
269A VAL* 1.3 60.0 + - - +
271A MET* 3.2 5.1 + - - +
272A TYR* 2.9 24.4 + - - +
317A ILE* 4.5 4.7 - - - +
320A LEU* 3.6 28.7 - - - +
321A ILE* 3.7 12.8 - - - +
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Residues in contact with VAL 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ASP 3.5 20.9 - - - +
242A TYR* 3.5 28.3 - - + -
265A TRP* 3.1 36.1 + - + +
266A SER 3.1 7.8 + - - +
268A GLY* 1.3 75.8 - - - +
270A CYS* 1.3 62.4 + - - +
272A TYR* 3.3 4.7 + - - +
273A GLU* 3.0 22.0 + - - +
279A THR* 4.0 5.4 - - - +
280A PRO* 3.9 20.4 - - + -
281A PHE* 4.4 2.7 - - + -
321A ILE* 3.9 17.0 - - + -
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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
----------------------------------------------------------
161A LEU* 6.1 0.9 - - + -
181A ILE* 4.8 5.6 - - + -
184A MET* 4.2 24.7 - - + -
201A ILE* 4.5 0.4 - - - -
202A LYS* 3.8 14.6 - - - -
203A PRO* 3.7 33.2 - - + +
242A TYR* 3.9 9.9 - - - -
266A SER 3.0 19.1 + - - -
267A LEU* 3.4 8.7 - - - +
269A VAL* 1.3 75.5 - - - +
271A MET* 1.3 59.8 + - - +
273A GLU* 3.4 6.9 + - - +
274A MET* 2.9 35.9 + - + +
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Residues in contact with MET 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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177A ALA* 6.0 0.4 - - + -
181A ILE* 3.8 33.4 - - + -
267A LEU 2.9 12.8 + - - +
268A GLY* 3.6 9.2 - - - +
269A VAL 3.2 0.2 - - - -
270A CYS* 1.3 78.6 - - - +
272A TYR* 1.3 62.6 + - - +
274A MET* 3.1 5.8 + - + +
275A LEU* 3.1 31.5 + - + +
313A ALA* 3.4 38.1 - - + +
316A LEU* 3.7 29.2 - - + -
317A ILE* 4.0 12.1 - - + -
320A LEU* 4.9 4.7 - - + -
341A PHE* 3.7 29.2 - - + -
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Residues in contact with TYR 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A GLY 2.9 16.6 + - - +
269A VAL* 3.6 5.4 - - - +
271A MET* 1.3 79.2 - - - +
273A GLU* 1.3 56.1 + - - +
275A LEU 3.2 0.3 + - - -
276A TYR* 2.9 49.1 + + + +
278A GLU* 3.2 24.2 - - + -
279A THR 4.1 2.1 + - - -
280A PRO* 3.5 30.8 + - + +
300A PHE* 3.6 37.5 - + - -
301A GLN 3.3 11.5 + - - -
302A PHE* 3.9 14.1 - + - -
303A PRO* 3.1 29.4 - - + +
317A ILE* 3.9 19.7 - - + +
321A ILE* 4.5 2.2 - - + -
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Residues in contact with GLU 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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165A LEU* 5.6 6.6 - - + +
170A ASP 3.2 9.9 - - - +
203A PRO* 4.2 8.8 - - + +
241A ASP* 4.6 1.9 - - - +
242A TYR* 2.5 45.6 + - - -
269A VAL* 3.0 18.2 + - - +
270A CYS* 3.7 4.3 - - - +
272A TYR* 1.3 76.2 - - - +
274A MET* 1.3 58.3 + - - +
277A GLY* 2.8 25.3 + - - -
278A GLU 3.4 20.9 - - - +
279A THR* 2.4 37.6 + - - +
280A PRO* 4.4 0.4 - - + -
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Residues in contact with MET 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 3.8 26.9 - - + -
165A LEU* 4.3 26.4 - - + +
171A LYS* 3.2 7.1 - - - -
172A LEU* 2.9 36.6 + - + +
177A ALA* 3.6 35.0 - - + -
180A TYR* 3.6 25.4 - - + -
181A ILE* 3.6 28.0 - - + +
184A MET* 4.7 2.0 - - - -
203A PRO* 6.5 0.2 - - + -
270A CYS* 2.9 25.5 + - + +
271A MET* 3.1 7.6 + - - +
273A GLU* 1.3 74.8 - - - +
275A LEU* 1.3 59.6 + - + +
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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
----------------------------------------------------------
171A LYS* 3.4 16.8 + - - +
172A LEU 3.8 13.6 - - - +
174A GLU* 3.6 25.4 - - + +
177A ALA* 3.8 24.2 - - + -
271A MET* 3.1 34.5 + - + +
272A TYR 4.2 1.3 - - - +
274A MET* 1.3 79.8 - - + +
276A TYR* 1.3 66.4 + - + +
306A VAL* 5.6 0.5 - - - +
308A ASP* 5.0 1.2 - - - +
309A VAL* 3.7 31.2 - - + +
313A ALA* 3.8 29.2 - - + -
317A ILE* 4.4 5.2 - - + -
341A PHE* 4.9 1.6 - - + -
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Residues in contact with TYR 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LYS* 3.8 11.1 - - - +
272A TYR* 2.9 45.6 + + + +
275A LEU* 1.3 82.5 - - + +
277A GLY* 1.3 60.4 + - - +
278A GLU* 3.1 16.1 + - + +
302A PHE* 3.3 39.1 - + + +
303A PRO* 3.3 31.9 - - + -
306A VAL* 3.6 27.1 - - + -
309A VAL* 3.6 37.0 - - + +
314A LYS* 3.6 14.7 + - - +
317A ILE* 4.2 12.8 - - + -
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Residues in contact with GLY 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ASP* 3.3 33.9 - - - +
171A LYS* 3.8 7.9 - - - +
273A GLU* 2.8 19.7 + - - -
275A LEU 3.7 0.4 - - - -
276A TYR* 1.3 79.3 - - - +
278A GLU* 1.3 65.3 + - - +
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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