Contacts of the strand formed by residues 270 - 283 (chain A) in PDB entry 3URF
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 PHE 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A HIS 3.2 9.6 - - - +
225A HIS* 3.7 23.8 - + + +
268A SER* 2.9 26.4 + - - -
269A GLU* 1.3 89.3 - - + +
271A HIS* 1.3 74.1 + - - +
272A PHE* 6.4 0.4 - - + -
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Residues in contact with HIS 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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223A ARG* 3.2 4.2 - - - +
224A HIS* 2.8 31.4 + - + +
226A GLU* 3.0 28.1 + - - -
231A LEU* 4.9 1.1 - - + -
263A TYR 5.2 0.2 - - - -
264A TRP* 3.2 69.5 + + + +
265A SER* 3.2 24.3 + - - -
268A SER* 2.8 29.0 + - - -
270A PHE* 1.3 92.4 + - - +
272A PHE* 1.3 62.6 + - - +
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Residues in contact with PHE 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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221A CYS* 3.6 27.4 - - + -
222A PHE 3.3 11.9 - - - -
223A ARG* 3.9 23.3 - - + -
262A LYS* 5.0 3.8 + - - -
264A TRP* 4.1 5.1 + - - +
270A PHE* 6.4 0.4 - - + -
271A HIS* 1.3 77.4 - - - +
273A TYR* 1.3 89.3 + - - +
274A SER* 4.1 10.5 - - - -
300A ASP* 3.6 22.7 - - - -
305A ALA* 5.6 0.7 - - + -
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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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221A CYS* 3.5 1.2 - - - -
222A PHE* 2.8 42.8 + + - +
238A LEU* 3.8 29.6 - - + -
259A GLY* 3.1 15.9 + - - -
260A SER* 3.1 30.5 - - - -
262A LYS* 3.2 37.0 - - + -
264A TRP* 4.1 9.4 - - + -
272A PHE* 1.3 83.5 - - - +
274A SER* 1.3 79.5 + - - +
275A ILE* 3.4 22.2 - - + +
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Residues in contact with SER 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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219A ASN* 4.7 8.5 + - - -
220A ILE 3.2 3.6 - - - -
221A CYS* 3.4 28.3 - - - -
272A PHE* 4.1 9.0 - - - -
273A TYR* 1.3 96.8 + - - +
275A ILE* 1.3 65.5 + - - +
276A ASN* 6.0 0.3 - - - +
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Residues in contact with ILE 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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218A ALA 3.7 0.5 - - - +
219A ASN* 3.2 8.5 + - - -
220A ILE* 2.8 38.1 + - + +
222A PHE* 3.6 23.3 - - + -
238A LEU 3.5 23.3 - - - +
239A MET 3.8 0.2 - - - -
240A VAL* 3.6 38.8 - - + +
258A GLY* 3.7 5.2 - - - -
259A GLY* 3.6 22.9 - - - +
273A TYR* 3.4 24.5 - - + +
274A SER* 1.3 74.3 - - - +
276A ASN* 1.3 70.6 + - - +
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Residues in contact with ASN 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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217A TYR* 5.6 3.3 - - - +
218A ALA 3.2 10.6 + - - +
219A ASN* 3.2 25.4 + - - +
274A SER* 6.0 0.2 - - - +
275A ILE* 1.3 78.0 - - - +
277A VAL* 1.3 78.4 + - - +
278A GLY* 4.9 0.6 - - - +
307A TYR* 4.8 3.6 + - - -
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Residues in contact with VAL 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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217A TYR* 3.1 4.3 - - - +
218A ALA* 2.9 54.7 + - + +
240A VAL* 4.4 14.1 - - + -
242A VAL* 4.0 17.0 - - + -
256A MET* 4.1 14.4 - - + -
257A LYS 3.6 32.5 - - - +
258A GLY* 4.1 8.7 - - - +
275A ILE* 4.7 0.2 - - + -
276A ASN* 1.3 88.2 + - - +
278A GLY* 1.3 58.9 + - - +
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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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215A TYR* 3.4 20.0 - - - -
216A LEU 3.0 13.2 - - - -
217A TYR* 4.0 1.8 - - - -
256A MET* 3.2 12.1 - - - +
276A ASN* 4.9 1.3 - - - +
277A VAL* 1.3 77.0 - - - +
279A GLY* 1.3 58.1 + - - -
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Residues in contact with GLY 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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215A TYR* 3.3 16.4 - - - -
216A LEU 2.8 33.7 + - - +
256A MET* 3.5 1.1 - - - -
278A GLY* 1.3 73.9 - - - -
280A PHE* 1.3 58.1 - - - -
281A PHE* 3.3 24.2 - - - -
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Residues in contact with PHE 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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213A PHE* 3.3 43.7 - + + -
214A TYR 3.5 11.0 - - - -
215A TYR* 4.4 11.6 - + + -
279A GLY* 1.3 70.5 - - - -
281A PHE* 1.3 74.8 + - - +
313A VAL* 3.9 35.2 - - + -
314A ARG* 4.8 9.0 - - + -
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Residues in contact with PHE 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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213A PHE* 3.4 5.0 - - - -
214A TYR 2.9 37.9 + - - +
216A LEU* 3.7 26.5 - - + -
244A LYS* 5.4 1.6 - - - +
255A LEU* 3.9 35.0 - - + -
256A MET* 3.6 35.4 - - + -
279A GLY* 3.3 34.1 - - - -
280A PHE* 1.3 82.7 - - - +
282A LYS* 1.3 62.0 + - - +
283A LEU* 3.4 14.8 + - + +
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Residues in contact with LYS 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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212A GLY 3.7 0.4 - - - -
213A PHE* 3.5 33.2 - - + -
244A LYS* 3.6 12.5 + - - -
281A PHE* 1.3 70.4 - - - +
283A LEU* 1.3 71.8 + - - +
284A ARG* 3.8 29.0 - - - +
287A GLU* 3.9 2.9 - - - +
316A ILE* 3.8 35.9 - - + +
58Z GLU* 3.9 12.5 + - - -
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Residues in contact with LEU 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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199A MET* 5.8 0.9 - - + -
208A VAL* 3.8 28.0 - - + -
211A ASP* 3.4 1.8 - - - -
212A GLY 2.8 36.1 + - - +
214A TYR* 3.9 35.0 - - + -
216A LEU* 4.1 18.2 - - + -
244A LYS* 3.7 21.5 - - + +
255A LEU* 5.2 0.9 - - + -
281A PHE* 3.8 16.6 - - + +
282A LYS* 1.3 86.3 - - - +
284A ARG* 1.3 63.5 + - - +
287A GLU* 3.7 7.2 - - + +
289A ILE* 4.1 21.8 - - + -
310A ALA* 5.8 0.2 - - + -
316A ILE* 3.8 5.4 - - - +
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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