Contacts of the strand formed by residues 274 - 283 (chain D) in PDB entry 1UHG
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 GLU 274 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218D ARG* 4.0 3.8 - - - +
219D VAL* 3.0 33.1 + - - +
270D SER 5.2 2.9 - - - +
271D ASN 5.3 4.7 - - - +
272D VAL 4.3 8.5 - - - +
273D MET* 1.3 80.0 - - - +
275D GLU* 1.3 69.9 + - - +
276D ARG* 2.8 49.3 + - - +
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Residues in contact with GLU 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D LEU* 3.5 35.9 - - + +
217D PHE* 3.4 21.4 + - - -
218D ARG* 3.5 25.9 + - + +
274D GLU* 1.3 74.6 - - - +
276D ARG* 1.3 65.7 + - - +
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Residues in contact with ARG 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D GLY 3.4 0.5 - - - +
216D LEU* 3.5 8.2 - - - +
217D PHE 2.8 30.4 + - - +
219D VAL* 3.9 21.2 + - + +
220D ALA* 6.2 0.8 - - - +
272D VAL 5.7 1.0 + - - -
274D GLU* 2.8 51.1 + - + +
275D GLU* 1.3 80.4 - - - +
277D LYS* 1.3 68.4 + - - +
278D ILE* 3.4 4.2 + - + +
356D GLU* 3.3 28.6 + - - +
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Residues in contact with LYS 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D ILE* 5.2 0.4 - - + -
215D GLY* 3.2 9.2 - - - +
216D LEU* 3.8 39.7 - - + +
276D ARG* 1.3 76.1 - - - +
278D ILE* 1.3 58.4 + - - +
342D VAL* 6.1 1.4 - - - +
346D GLU* 3.8 13.9 + - - +
350D ASP* 3.6 34.2 + - - +
353D SER* 6.0 0.4 - - - +
354D VAL* 3.4 33.7 - - + +
356D GLU* 4.7 7.6 - - - +
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Residues in contact with ILE 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D ILE* 3.4 2.2 - - - -
215D GLY 2.9 37.0 + - - +
217D PHE* 4.0 14.8 - - + +
219D VAL* 4.3 19.1 - - + -
228D LYS* 5.9 1.6 - - + -
230D LEU* 4.6 4.5 - - + -
276D ARG* 3.9 9.9 - - + +
277D LYS* 1.3 75.2 - - - +
279D LYS* 1.3 73.2 + - - +
280D VAL* 3.7 16.8 + - + +
354D VAL* 3.7 6.7 - - - +
356D GLU* 3.3 36.8 - - + +
357D GLU* 3.6 21.8 - - - +
358D PHE* 3.7 13.2 - - + +
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Residues in contact with LYS 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D TYR* 2.7 41.8 + - + +
213D GLN 3.5 5.8 - - - -
214D ILE* 3.6 18.3 - - + +
278D ILE* 1.3 73.0 - - - +
280D VAL* 1.3 60.1 + - - +
281D TYR* 4.4 7.7 + - + +
351D ALA 5.2 3.2 + - - -
354D VAL* 3.8 29.3 + - + +
355D SER* 4.6 7.2 - - - +
356D GLU 3.0 19.1 + - - +
357D GLU* 3.7 20.4 - - + +
358D PHE 2.8 27.4 + - - +
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Residues in contact with VAL 280 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188D PHE* 4.1 20.8 - - + -
211D MET 3.7 0.2 - - - +
212D TYR* 3.2 8.5 - - - -
213D GLN* 2.7 41.3 + - + +
217D PHE* 3.9 30.1 - - + -
230D LEU* 3.8 30.7 - - + -
232D LEU* 4.7 4.7 - - + -
278D ILE* 4.0 12.6 - - + +
279D LYS* 1.3 77.3 - - - +
281D TYR* 1.3 69.5 + - - +
282D LEU* 4.5 5.6 - - + -
358D PHE* 3.6 6.5 - - + +
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Residues in contact with TYR 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D GLN* 5.9 2.7 - - + -
196D MET* 3.5 29.6 - - + -
210D MET* 3.7 16.8 - - + -
211D MET 3.2 4.9 - - - -
212D TYR* 3.4 44.3 + + + -
279D LYS* 4.4 14.1 + - + +
280D VAL* 1.3 76.3 - - - +
282D LEU* 1.3 60.3 + - - +
357D GLU* 3.8 9.4 - - - -
358D PHE* 2.9 12.2 + - - +
359D ARG* 3.6 58.5 + - + -
360D ALA* 3.0 24.6 + - - +
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Residues in contact with LEU 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D TRP* 4.2 14.1 - - + -
188D PHE* 4.3 11.4 - - + -
210D MET* 3.4 4.2 - - - -
211D MET* 2.8 55.0 + - + +
230D LEU* 6.0 0.2 - - + -
232D LEU* 3.8 26.9 - - + -
241D MET* 4.9 4.7 - - - -
243D VAL* 4.3 21.1 - - + -
280D VAL* 4.1 6.4 - - + +
281D TYR* 1.3 73.9 - - - +
283D PRO* 1.3 84.5 - - + +
285D MET* 5.0 2.5 - - - -
334D ILE* 4.2 7.6 - - + -
358D PHE* 5.2 2.9 - - + -
360D ALA* 4.2 13.5 - - + -
364D PHE* 4.4 11.9 - - + -
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Residues in contact with PRO 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D PHE* 4.3 0.9 - - + -
208D VAL* 3.8 20.2 - - + -
209D GLN 3.4 7.4 - - - +
210D MET* 3.7 11.4 - - + -
211D MET* 3.8 7.9 - - - +
282D LEU* 1.3 97.3 - - + +
284D ARG* 1.3 70.3 + - - +
285D MET* 3.4 14.9 + - + +
334D ILE* 4.4 0.9 - - - +
360D ALA* 3.4 23.1 - - + +
364D PHE* 4.0 18.4 - - + -
385D PRO* 3.9 18.8 - - + -
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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