Contacts of the helix formed by residues 269 - 288 (chain A) in PDB entry 1UW9
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 TYR 269 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A HIS* 3.3 13.1 + - - -
268A ASP* 1.3 73.3 - - - +
270A LEU* 1.3 85.1 + - + +
273A GLY* 2.8 30.7 + - - -
274A PHE* 3.5 33.8 + + - -
277A ASN* 3.5 25.1 - - - +
293A ILE* 3.1 22.0 - - + -
294A HIS 3.3 10.6 + - - -
295A ARG* 3.8 11.7 - - + -
311A PHE* 4.1 9.5 - - - -
314A LEU* 2.9 35.7 + - - +
318A LEU* 3.6 25.6 - - + +
326A LEU* 3.7 18.6 - - + +
1483A EDO 4.5 0.2 + - - -
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Residues in contact with LEU 270 (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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117A PHE* 6.0 0.2 - - + -
268A ASP 3.3 0.4 - - - -
269A TYR* 1.3 118.0 - - + +
271A THR* 1.3 64.0 + - - +
273A GLY* 3.7 3.3 + - - -
274A PHE* 4.1 15.0 - - + -
295A ARG 3.9 5.6 - - - +
296A ALA 3.4 11.8 + - - +
297A MET* 3.9 11.0 - - + -
298A HIS* 3.7 40.6 - - + +
301A ILE* 4.8 5.2 - - + -
314A LEU* 4.4 17.3 - - + -
1483A EDO 2.8 45.5 + - - +
274B PHE* 5.8 0.2 - - - -
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Residues in contact with THR 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ASP* 3.1 21.9 - - - +
270A LEU* 1.3 74.7 - - - +
272A GLY* 1.3 62.5 + - - +
296A ALA* 3.7 19.9 + - + +
297A MET* 3.8 23.3 - - + -
114B THR* 2.9 29.7 + - - +
117B PHE* 4.3 7.4 - - + -
118B THR* 2.9 41.8 + - - +
274B PHE* 3.9 16.8 + - - +
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Residues in contact with GLY 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A HIS* 4.0 12.8 - - - -
268A ASP 2.8 15.8 + - - -
271A THR* 1.3 78.7 + - - +
273A GLY* 1.3 58.8 + - - +
276A ALA* 4.1 2.4 - - - +
114B THR* 3.7 7.5 - - - +
273B GLY* 3.8 1.6 - - - -
274B PHE 3.6 3.8 + - - -
275B THR* 3.1 46.3 + - - -
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Residues in contact with GLY 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A HIS* 4.0 0.9 + - - -
269A TYR 2.8 21.7 + - - -
270A LEU 4.0 7.4 - - - -
271A THR 3.5 1.0 - - - -
272A GLY* 1.3 76.0 - - - +
274A PHE* 1.3 60.5 + - - -
275A THR 3.3 2.6 + - - -
276A ALA 3.5 2.8 + - - -
277A ASN* 2.8 29.1 + - - +
1483A EDO 4.3 3.8 - - - -
272B GLY 3.9 0.9 - - - -
273B GLY* 3.8 17.0 - - - -
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Residues in contact with PHE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A VAL* 3.6 25.4 - - + -
114A THR* 3.5 22.0 - - - +
117A PHE* 3.9 29.2 - + + -
269A TYR* 3.5 38.6 + + - -
270A LEU* 4.1 14.6 - - + -
273A GLY* 1.3 69.6 - - - -
275A THR* 1.3 58.0 + - - +
277A ASN* 4.1 2.9 - - + -
278A THR* 2.7 38.8 + - - +
314A LEU* 5.0 1.6 - - + -
317A ALA* 3.7 29.2 - - + -
321A SER* 4.0 14.4 - - - -
1483A EDO 4.6 10.3 + - - -
245B GLY 4.5 0.4 - - - -
271B THR* 4.0 13.3 + - - +
272B GLY 3.7 2.8 + - - -
297B MET* 6.1 0.9 - - - -
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Residues in contact with THR 275 (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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114A THR* 3.1 9.4 + - - -
274A PHE* 1.3 76.2 - - - +
276A ALA* 1.3 63.7 + - - +
278A THR 3.5 0.2 + - - -
279A SER* 3.3 23.4 + - - -
244B ALA 2.8 23.8 + - - +
245B GLY 3.5 7.1 - - - +
246B THR* 3.2 33.3 - - - +
247B CYS* 3.3 6.0 + - - +
250B MET* 4.7 8.1 - - + -
267B HIS* 5.0 1.1 - - + -
272B GLY* 3.1 24.1 + - - -
276B ALA* 3.8 17.9 - - + -
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Residues in contact with ALA 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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247A CYS* 4.0 14.8 - - - -
250A MET* 3.5 21.4 - - - +
267A HIS* 4.3 3.8 - - - +
272A GLY 4.1 3.1 - - - +
273A GLY 3.5 7.4 + - - +
275A THR* 1.3 78.4 - - - +
277A ASN* 1.3 59.1 + - - +
279A SER* 3.3 5.8 + - - -
280A LEU* 2.9 23.9 + - - +
272B GLY 4.3 1.0 + - - -
275B THR* 3.7 36.8 - - + -
276B ALA* 4.5 3.1 - - - +
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Residues in contact with ASN 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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267A HIS* 2.7 35.0 + - + +
269A TYR* 3.5 16.2 - - + +
273A GLY 2.8 21.8 + - - +
274A PHE* 3.7 6.7 - - - +
275A THR 3.3 0.2 - - - -
276A ALA* 1.3 75.4 - - - +
278A THR* 1.3 56.6 + - - +
280A LEU* 3.2 3.1 + - - +
281A ALA* 2.9 27.0 + - - +
291A LEU* 4.4 2.6 - - - +
293A ILE* 3.2 24.2 - - - +
318A LEU* 3.6 6.8 - - - +
321A SER* 3.0 19.0 + - - +
322A GLY 3.0 19.5 + - - +
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Residues in contact with THR 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLY 4.4 15.1 + - - +
113A VAL* 5.3 4.3 + - - +
148A PHE* 6.0 1.1 - - + -
149A VAL* 6.4 0.9 - - + -
274A PHE* 2.7 22.8 + - - +
277A ASN* 1.3 69.9 - - - +
279A SER* 1.3 65.1 + - - +
281A ALA* 3.3 2.3 + - - +
282A ILE* 3.0 37.6 + - + +
320A MET 5.6 0.4 - - - +
321A SER* 2.8 34.8 + - - +
245B GLY 3.2 26.2 + - - +
246B THR* 3.8 13.0 - - + -
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Residues in contact with SER 279 (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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250A MET* 4.5 0.7 - - - -
251A MET* 3.8 11.5 - - - +
275A THR 3.3 5.3 + - - -
276A ALA* 3.4 9.6 - - - -
278A THR* 1.3 78.1 - - - +
280A LEU* 1.3 62.4 + - - +
282A ILE* 3.3 8.3 + - - +
283A TYR* 3.0 22.3 + - - +
246B THR* 3.4 3.9 - - - +
247B CYS* 2.8 41.1 + - - -
248B GLU* 2.7 27.9 + - - +
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Residues in contact with LEU 280 (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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242A ALA* 4.1 9.0 - - + -
250A MET* 4.0 25.6 - - + -
251A MET* 4.1 10.5 - - - +
254A ALA* 3.8 29.8 - - + -
265A ILE* 3.9 15.0 - - + -
267A HIS* 3.6 34.5 - - + -
276A ALA 2.9 16.2 + - - +
277A ASN* 3.6 5.6 - - - +
279A SER* 1.3 76.4 - - - +
281A ALA* 1.3 57.1 + - - +
283A TYR* 3.2 5.0 + - + +
284A CYS* 2.9 29.1 + - - -
291A LEU* 3.7 17.3 - - + -
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Residues in contact with ALA 281 (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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149A VAL* 5.6 0.8 - - - +
150A GLY 4.5 4.9 - - - +
152A PRO* 3.5 15.7 - - + +
277A ASN 2.9 16.3 + - - +
278A THR 3.7 1.8 - - - +
280A LEU* 1.3 76.6 - - - +
282A ILE* 1.3 59.6 + - + +
284A CYS 3.3 1.0 + - - -
285A ARG* 2.9 27.0 + - - +
291A LEU* 3.7 13.8 - - + +
321A SER 3.6 21.3 - - - +
322A GLY* 3.8 22.0 - - - +
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Residues in contact with ILE 282 (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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149A VAL* 4.1 32.3 - - + -
278A THR* 3.0 27.4 + - + +
279A SER* 3.6 6.1 - - - +
281A ALA* 1.3 75.0 - - + +
283A TYR* 1.3 65.7 + - - +
285A ARG* 3.3 8.0 + - + +
286A ASP* 3.0 38.6 + - - +
246B THR* 3.9 24.2 - - + -
248B GLU* 5.7 4.0 - - - +
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Residues in contact with TYR 283 (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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251A MET* 4.2 23.3 - - + -
254A ALA* 3.8 32.5 - - + -
255A VAL* 3.5 34.2 - - + +
258A LYS* 3.3 24.9 - - - +
279A SER 3.0 13.5 + - - +
280A LEU* 3.2 9.4 + - - +
282A ILE* 1.3 77.1 - - - +
284A CYS* 1.3 62.7 + - - +
286A ASP* 3.2 3.6 + - - -
287A ASN* 2.9 60.0 + - + +
289A LEU* 4.1 11.9 - - + -
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Residues in contact with CYS 284 (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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152A PRO* 3.8 12.8 - - + -
153A HIS* 3.7 0.7 + - - -
265A ILE* 3.7 31.6 - - - -
280A LEU* 2.9 17.9 + - - +
281A ALA* 3.5 8.5 - - - +
283A TYR* 1.3 75.8 - - - +
285A ARG* 1.3 54.6 + - - +
288A GLY* 2.8 30.3 + - - -
289A LEU* 3.0 43.1 + - - +
290A PHE 4.4 0.2 - - - -
291A LEU* 4.0 17.3 - - - -
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Residues in contact with ARG 285 (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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149A VAL* 3.3 41.4 + - + +
151A HYP 2.8 24.9 + - - -
152A PRO* 2.8 31.8 + - + +
153A HIS* 4.7 5.2 - - - -
281A ALA 2.9 12.9 + - - +
282A ILE* 3.5 11.0 - - - +
284A CYS* 1.3 75.7 - - - +
286A ASP* 1.3 71.6 + - - +
287A ASN 3.4 0.7 + - - -
288A GLY* 3.7 5.9 + - - -
372A PRO* 4.9 6.9 - - - +
213K ARG* 3.6 48.8 - - - +
215K ARG* 3.7 16.4 - - - +
216K ASP* 6.0 1.6 - - - -
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Residues in contact with ASP 286 (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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282A ILE* 3.0 33.6 + - - +
283A TYR* 3.2 6.2 + - + +
285A ARG* 1.3 86.2 - - - +
287A ASN* 1.3 69.8 + - - +
288A GLY 3.7 0.2 - - - -
214K TRP* 5.3 9.8 + - - -
215K ARG* 3.0 19.3 + - - +
252K LYS* 3.5 34.1 + - - -
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Residues in contact with ASN 287 (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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258A LYS* 2.8 39.5 + - + +
283A TYR* 2.9 66.4 + - + +
284A CYS* 4.7 0.4 - - - +
286A ASP* 1.3 87.4 - - - +
288A GLY* 1.3 65.3 + - - +
289A LEU* 3.4 4.6 + - + +
63I VAL* 6.0 0.2 - - - -
65I CYS* 4.0 14.4 - - - +
215K ARG* 3.5 21.1 + - - +
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Residues in contact with GLY 288 (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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153A HIS* 3.7 19.3 - - - -
161A LYS* 4.1 5.3 + - - -
284A CYS 2.8 10.4 + - - -
285A ARG 3.7 4.3 + - - -
287A ASN* 1.3 78.8 - - - +
289A LEU* 1.3 57.1 + - - -
65I CYS* 3.6 14.6 - - - +
66I LEU* 3.4 20.1 - - - +
215K ARG* 3.5 17.5 - - - +
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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
------------------------------------------------------------
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