Contacts of the strand formed by residues 278 - 285 (chain D) in PDB entry 4UI2
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 THR 278 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D LEU* 4.4 12.1 - - + -
220D PHE* 5.7 0.2 - - + -
271D MET 3.7 0.9 - - - +
272D HIS* 3.9 0.5 - - - -
273D ALA* 2.9 33.0 + - + +
276D ILE* 2.4 47.7 + - + +
277D GLY* 1.3 74.2 - - - +
279D THR* 1.3 66.5 + - - +
280D VAL* 4.2 11.8 - - + +
293D ILE* 4.0 16.6 - - + -
294D ARG 3.3 12.1 - - - +
295D MET* 3.6 24.7 - - + +
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Residues in contact with THR 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D GLU* 3.8 14.1 - - - +
271D MET 3.4 8.5 - - - +
272D HIS* 4.1 15.8 + - + +
277D GLY 4.0 2.1 + - - -
278D THR* 1.3 75.2 + - - +
280D VAL* 1.3 66.3 + - - +
281D PHE* 3.4 33.0 - - + -
292D ALA 4.0 0.3 - - - +
293D ILE* 3.5 2.9 - - - +
294D ARG* 2.8 52.1 + - - +
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Residues in contact with VAL 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D LEU* 4.9 7.2 - - + -
197D VAL* 5.7 1.3 - - + -
218D ILE* 3.8 26.7 - - + -
220D PHE* 4.4 19.5 - - + -
269D VAL 4.1 0.2 - - - +
270D GLU* 3.2 4.2 - - - +
271D MET* 2.7 49.3 + - + +
278D THR* 4.2 17.0 - - + -
279D THR* 1.3 79.7 - - - +
281D PHE* 1.3 67.9 + - - +
291D LEU* 4.0 15.9 - - + -
292D ALA 3.4 9.6 - - - +
293D ILE* 4.2 11.4 - - + -
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Residues in contact with PHE 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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162C PHE* 6.0 3.4 - + - -
268D TYR* 3.7 22.4 - + + -
269D VAL 3.5 5.4 - - - +
270D GLU* 3.3 35.7 - - + -
279D THR* 3.4 31.6 - - + -
280D VAL* 1.3 76.0 - - - +
282D VAL* 1.3 69.5 + - - +
283D ARG* 6.2 1.1 - - + -
290D THR 4.7 0.2 - - - -
291D LEU* 3.5 6.2 - - - +
292D ALA* 2.8 56.6 + - + +
294D ARG* 5.4 7.9 - - + -
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Residues in contact with VAL 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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216D ILE* 4.0 39.5 - - + -
218D ILE* 4.3 5.4 - - + -
232D TYR* 4.3 7.2 - - + -
234D ALA* 4.3 10.5 - - + -
239D LEU* 3.6 22.8 - - + +
268D TYR* 3.1 3.3 - - - +
269D VAL* 2.9 43.8 + - + +
271D MET* 4.1 20.2 - - + -
280D VAL* 4.8 0.2 - - + -
281D PHE* 1.3 79.3 - - - +
283D ARG* 1.3 65.3 + - - +
289D LEU* 4.6 3.1 - - + -
290D THR 3.6 3.1 - - - +
291D LEU* 4.4 4.0 - - + -
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Residues in contact with ARG 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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239D LEU* 4.4 1.8 - - - -
264D GLU* 2.7 41.5 + - - -
267D HIS* 3.6 11.8 + - - +
268D TYR* 3.2 31.9 - - + +
281D PHE* 5.8 1.1 - - + -
282D VAL* 1.3 76.5 - - - +
284D GLN* 1.3 73.9 + - - +
285D VAL* 3.8 17.7 - - + -
289D LEU* 3.1 12.7 - - - +
290D THR* 2.9 44.0 + - - +
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Residues in contact with GLN 284 (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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236D THR* 3.7 12.7 - - - +
237D ASP* 3.2 51.3 + - - +
238D ASP 4.5 0.5 + - - -
239D LEU* 4.0 19.5 - - + +
267D HIS* 3.2 25.1 + - + +
283D ARG* 1.3 86.4 + - - +
285D VAL* 1.3 62.0 + - - +
286D GLY 2.9 28.8 + - - +
287D ARG 4.1 3.0 - - - -
288D TYR 3.4 6.3 + - - +
289D LEU* 3.9 8.7 - - + -
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Residues in contact with VAL 285 (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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167C GLY* 6.0 2.5 - - - -
168C ASP* 4.3 17.9 - - - +
283D ARG* 3.8 22.6 + - + +
284D GLN* 1.3 76.8 - - - +
286D GLY* 1.3 69.3 + - - +
287D ARG 3.0 1.0 + - - -
288D TYR* 2.8 28.9 + - + +
290D THR* 3.8 24.7 - - + -
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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