Contacts of the strand formed by residues 250 - 272 (chain A) in PDB entry 4IYT
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 250 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A TYR* 4.1 17.0 - - + +
182A LYS* 6.3 0.7 - - - -
183A PRO* 5.1 0.4 - - - -
240A THR 3.6 0.2 - - - +
241A ARG* 3.5 4.3 - - - +
242A ARG* 2.8 70.3 + - + +
243A THR 4.3 1.3 - - - -
244A THR* 3.6 36.6 - - - -
248A ASN 4.6 0.7 - - - +
249A SER* 1.3 74.3 - - - +
251A LEU* 1.3 75.2 + - - +
252A GLU* 3.6 27.7 + - + +
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Residues in contact with LEU 251 (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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179A VAL* 3.7 12.8 - - + +
180A GLY* 3.3 28.2 - - - +
181A TYR* 3.9 6.0 + - - +
182A LYS 4.3 0.2 - - - -
183A PRO* 4.0 27.4 - - + -
191A TYR* 3.2 68.4 - - + +
239A ALA* 4.8 2.7 - - + -
240A THR 3.4 2.2 - - - -
241A ARG* 3.8 18.4 - - + +
250A TYR* 1.3 86.1 - - - +
252A GLU* 1.3 62.6 + - - +
253A GLY 4.2 0.2 - - - -
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Residues in contact with GLU 252 (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 ASN* 3.8 17.7 + - - +
179A VAL* 4.4 2.5 - - - -
238A HIS 3.6 2.9 - - - +
239A ALA* 3.7 0.2 - - - -
240A THR* 3.0 39.5 + - - +
242A ARG* 3.4 37.9 - - - +
250A TYR* 3.6 20.4 + - + +
251A LEU* 1.3 76.2 - - - +
253A GLY* 1.3 66.9 + - - +
254A SER* 5.3 0.2 - - - -
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Residues in contact with GLY 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A PRO* 3.6 17.2 - - - +
176A ASN* 3.7 18.6 + - - +
179A VAL* 3.6 24.0 - - - +
238A HIS 3.5 7.0 - - - -
252A GLU* 1.3 81.8 - - - +
254A SER* 1.3 61.0 + - - -
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Residues in contact with SER 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A PRO* 3.6 9.1 + - - -
236A VAL 4.0 0.2 - - - +
237A THR* 3.5 5.4 - - - +
238A HIS* 2.8 55.1 + - - +
240A THR* 5.2 5.8 - - - +
252A GLU 5.3 0.4 - - - -
253A GLY* 1.3 73.9 - - - -
255A ARG* 1.3 59.5 + - - +
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Residues in contact with ARG 255 (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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74A TRP* 3.4 15.2 - - - -
76A PHE* 4.0 3.8 - - - -
172A GLY 3.0 29.7 + - - -
173A HIS* 3.5 12.6 + - - +
174A ASP 2.7 31.0 + - - -
175A PRO* 3.9 20.6 + - + +
177A LEU* 3.6 14.3 - - - +
235A ASP* 2.7 46.9 + - - +
236A VAL 3.5 6.1 - - - -
237A THR* 3.5 23.3 + - - -
254A SER* 1.3 76.4 - - - +
256A ILE* 1.3 64.3 + - - +
257A HIS* 3.8 17.0 + - + +
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Residues in contact with ILE 256 (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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235A ASP* 3.5 5.5 - - - -
236A VAL* 2.9 34.5 + - + +
238A HIS* 3.9 27.8 - - + +
255A ARG* 1.3 73.5 - - - +
257A HIS* 1.3 65.1 + - - +
259A ALA* 3.7 26.0 - - + +
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Residues in contact with HIS 257 (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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76A PHE* 3.4 38.8 - + - -
173A HIS* 5.9 4.0 - - + +
235A ASP* 2.9 34.5 - - - +
255A ARG* 3.7 14.7 + - + +
256A ILE* 1.3 74.0 - - - +
258A ASN* 1.4 97.9 + - - +
259A ALA* 4.4 0.3 - - - -
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Residues in contact with ASN 258 (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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76A PHE* 4.7 5.7 - - - -
233A ASN* 4.4 16.7 - - - +
234A MET 4.0 2.9 - - - -
235A ASP* 2.9 15.3 + - - -
257A HIS* 1.4 102.7 + - - +
259A ALA* 1.4 65.2 + - - +
260A PHE 3.4 2.4 + - - -
261A VAL* 3.5 31.9 + - + +
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Residues in contact with ALA 259 (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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234A MET 3.0 11.8 + - - +
236A VAL* 3.8 18.8 - - + +
256A ILE* 3.7 31.4 - - + +
257A HIS 3.3 0.8 - - - -
258A ASN* 1.4 78.6 - - - +
260A PHE* 1.3 84.6 + - + +
261A VAL 4.5 0.2 + - - -
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Residues in contact with PHE 260 (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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61A TYR* 5.6 1.6 - - - -
73A ARG* 4.1 33.4 - - - -
233A ASN* 3.5 1.7 - - - -
234A MET* 2.7 42.2 + - + -
236A VAL* 4.1 10.3 - - + -
259A ALA* 1.3 96.9 - - + +
261A VAL* 1.3 61.0 + - - +
263A ARG* 3.7 31.0 - - + +
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Residues in contact with VAL 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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233A ASN* 3.6 16.2 - - + +
258A ASN* 3.5 47.3 - - + +
259A ALA 4.2 0.4 - - - -
260A PHE* 1.3 74.0 - - - +
262A ASN* 1.3 85.0 + - + +
263A ARG* 3.4 8.1 + - - -
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Residues in contact with ASN 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TRP* 5.0 3.1 - - - -
79A ASN* 3.9 5.5 + - - -
155A GLN* 5.0 4.9 + - - -
233A ASN* 2.8 25.6 + - - +
261A VAL* 1.3 89.4 - - - +
263A ARG* 1.3 62.0 + - - +
264A ASN* 3.0 33.2 + - - +
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Residues in contact with ARG 263 (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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25A TRP* 3.7 42.1 - - + +
27A VAL* 5.9 0.2 - - - +
231A GLY* 3.2 3.3 - - - -
232A ARG* 2.8 61.2 + - + +
234A MET* 4.2 10.3 - - + -
260A PHE* 3.7 39.9 - - + +
261A VAL 4.0 8.2 + - - -
262A ASN* 1.3 70.3 + - - +
264A ASN* 1.3 55.0 + - - +
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Residues in contact with ASN 264 (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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25A TRP* 3.6 14.3 - - - -
79A ASN* 2.9 36.7 + - - +
155A GLN* 5.0 2.6 - - - +
229A THR* 3.3 27.7 + - - +
230A TYR 3.4 5.8 - - - +
231A GLY* 3.1 16.1 - - - -
262A ASN* 3.0 29.0 + - - +
263A ARG* 1.3 76.6 + - - +
265A TYR* 1.3 57.9 + - - +
266A THR* 3.7 3.2 + - - +
284A ASN* 2.9 23.4 + - - -
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Residues in contact with TYR 265 (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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20A THR* 3.0 39.3 + - + -
21A SER 3.5 13.0 + - - -
22A SER* 3.5 26.9 - - - -
25A TRP* 3.7 24.9 - + + +
27A VAL* 3.7 26.2 - - + -
29A GLN* 3.2 12.0 + - + -
230A TYR 2.8 35.2 + - - +
264A ASN* 1.3 71.1 - - - +
266A THR* 1.3 58.5 + - - +
267A VAL* 3.5 21.5 - - + +
283A HIS* 3.6 23.6 + - + -
284A ASN* 3.4 29.2 - - - -
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Residues in contact with THR 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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227A GLU* 3.2 44.9 - - + +
228A ILE 3.4 5.2 - - - +
229A THR* 2.9 23.9 + - - -
264A ASN* 4.2 5.9 + - - +
265A TYR* 1.3 72.1 - - - +
267A VAL* 1.3 61.3 + - - +
268A LYS* 6.2 0.2 - - + -
283A HIS* 3.1 24.6 - - - +
284A ASN* 2.8 24.7 + - - +
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Residues in contact with VAL 267 (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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20A THR* 3.7 10.8 - - + +
29A GLN* 3.7 22.0 - - - +
226A PHE 3.7 1.4 - - - +
227A GLU* 3.3 3.3 - - - -
228A ILE 2.8 32.8 + - - -
265A TYR* 3.5 38.1 - - + +
266A THR* 1.3 80.4 - - - +
268A LYS* 1.3 62.5 - - - +
269A TYR* 3.5 24.5 - - + +
280A VAL* 3.7 21.1 - - + -
282A GLY 3.5 11.0 - - - +
283A HIS* 3.9 3.4 - - + -
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Residues in contact with LYS 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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225A GLU* 3.4 36.9 + - + +
226A PHE 3.4 8.7 - - - +
227A GLU* 4.3 21.3 - - + +
266A THR* 5.3 0.2 - - - +
267A VAL* 1.3 72.3 - - - +
269A TYR* 1.3 61.3 + - - +
280A VAL* 3.5 6.2 - - - +
281A LYS* 2.8 41.7 + - + -
282A GLY* 2.8 23.1 + - - +
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Residues in contact with TYR 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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18A GLU* 3.9 22.8 - - + +
20A THR* 3.2 18.1 - - + +
29A GLN* 2.7 29.0 + - - -
31A ILE* 3.5 14.4 - - + +
33A PHE* 3.8 26.0 - + + -
224A SER 3.8 0.3 - - - +
225A GLU* 3.2 5.3 - - - +
226A PHE* 2.6 47.9 + - + +
228A ILE* 3.7 24.9 - - + -
267A VAL* 3.5 25.1 - - + -
268A LYS* 1.3 73.7 - - - +
270A GLU* 1.3 63.2 + - - +
271A VAL* 5.3 1.1 - - + -
278A ILE* 4.6 1.6 - - + -
279A LYS 3.4 7.4 - - - +
280A VAL* 3.8 29.2 - - + -
281A LYS* 4.7 2.7 - - - -
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Residues in contact with GLU 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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223A THR* 3.7 34.6 + - - +
224A SER 3.3 12.8 - - - +
225A GLU* 4.1 16.6 - - + +
269A TYR* 1.3 75.0 - - - +
271A VAL* 1.3 65.3 + - - +
272A ASN* 5.7 1.2 + - - +
277A GLU 4.0 0.2 - - - +
278A ILE* 3.4 6.6 - - - +
279A LYS* 2.8 61.3 + - + +
281A LYS* 3.8 21.6 - - + +
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Residues in contact with VAL 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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33A PHE* 4.2 13.2 - - + -
35A PHE* 3.9 16.8 - - + -
46A LEU* 4.0 14.1 - - + -
222A ASP 3.7 0.3 - - - +
223A THR* 3.1 9.0 - - - -
224A SER 2.9 32.8 + - - +
226A PHE* 3.9 25.8 - - + -
269A TYR* 5.3 0.9 - - + -
270A GLU* 1.3 80.4 - - - +
272A ASN* 1.3 59.7 + - - +
273A TRP* 3.7 40.2 - - + +
277A GLU 3.7 3.4 - - - -
278A ILE* 4.1 13.9 - - + -
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Residues in contact with ASN 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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35A PHE* 4.0 4.8 - - - -
222A ASP* 3.3 14.7 + - - +
223A THR* 3.9 17.5 - - + +
270A GLU* 5.7 1.3 + - - +
271A VAL* 1.3 72.5 - - - +
273A TRP* 1.3 56.5 + - - +
274A LYS* 3.1 15.8 + - - +
275A THR* 2.9 48.6 + - - +
276A HIS* 2.9 31.2 + - - -
277A GLU* 3.0 22.6 + - + +
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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