Contacts of the helix formed by residues 281 - 292 (chain B) in PDB entry 6UPQ
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 ASN 281 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B TYR* 3.7 13.9 - - - +
214B PHE* 3.4 8.2 - - + -
215B PRO* 3.3 33.4 - - - +
276B MET* 2.9 56.1 + - - +
277B LEU 4.6 0.2 + - - -
280B VAL* 1.3 91.9 - - - +
282B MET* 1.3 63.3 + - - +
283B GLU 3.3 2.2 - - - -
284B ASP* 3.3 7.6 + - + +
285B LEU* 3.0 29.1 + - + +
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Residues in contact with MET 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PHE 6.1 2.0 - - - +
41B CYS 5.6 0.2 - - - +
42B PHE* 3.4 61.5 - - + -
62B PHE* 5.5 1.3 - - + -
89B GLU* 6.0 1.3 - - - -
92B VAL* 6.2 2.7 - - - -
94B LEU* 4.4 20.2 - - + -
277B LEU 3.6 7.8 + - - +
278B ILE* 3.5 51.1 + - + +
280B VAL 3.4 4.0 + - - +
281B ASN* 1.3 76.9 - - - +
283B GLU* 1.3 66.6 + - + +
285B LEU* 3.4 1.0 + - - -
286B ARG* 3.2 28.9 + - - +
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Residues in contact with GLU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B VAL 4.7 4.1 + - - +
281B ASN 3.3 0.4 - - - -
282B MET* 1.3 80.3 - - + +
284B ASP* 1.3 58.0 + - - +
286B ARG* 3.3 23.9 + - - +
287B GLU* 2.9 28.6 + - - +
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Residues in contact with ASP 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B TYR* 2.5 37.7 + - - +
213B GLN 4.5 0.7 - - - +
215B PRO* 3.4 25.0 - - + +
281B ASN* 3.3 11.1 + - + +
283B GLU* 1.3 79.1 - - - +
285B LEU* 1.3 57.9 + - - +
287B GLU* 3.2 6.4 + - - +
288B GLN* 2.8 48.8 + - - +
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PHE* 3.8 15.5 - - + -
148B HIS* 3.5 11.9 - - - +
149B ALA* 4.3 5.2 - - + -
177B ASN* 3.0 29.1 + - + +
179B ILE* 4.5 4.9 - - + -
212B TYR* 3.5 43.3 - - + -
214B PHE* 5.2 0.2 - - + -
276B MET 4.9 0.2 - - - +
277B LEU* 3.6 38.8 - - + +
281B ASN* 3.0 23.7 + - + +
282B MET 3.7 4.5 - - - +
284B ASP* 1.3 76.0 - - - +
286B ARG* 1.3 56.0 + - - +
289B THR* 2.7 30.9 + - - -
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Residues in contact with ARG 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PHE* 5.3 9.6 - - - +
41B CYS* 3.4 28.5 + - - +
42B PHE* 3.9 7.9 - - + -
144B ASP* 5.5 2.8 + - - +
146B ARG* 5.1 1.7 + - - -
148B HIS* 3.6 37.5 + - + +
282B MET* 3.2 21.5 + - - +
283B GLU* 3.6 23.4 + - - +
284B ASP 3.3 0.2 - - - -
285B LEU* 1.3 77.3 - - - +
287B GLU* 1.3 57.9 + - - +
289B THR* 3.3 4.7 + - - -
290B HIS* 3.0 27.2 + - - +
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Residues in contact with GLU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B GLU 2.9 17.2 + - - +
284B ASP* 3.8 9.6 - - - +
286B ARG* 1.3 76.3 + - - +
288B GLN* 1.3 63.4 + - - +
290B HIS* 3.1 12.3 + - - +
291B THR* 2.8 60.7 + - + +
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Residues in contact with GLN 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B ASN* 3.7 20.6 - - - +
212B TYR* 4.2 7.4 - - + -
284B ASP* 2.8 44.4 + - - +
287B GLU* 1.3 75.6 - - - +
289B THR* 1.3 65.6 + - - +
291B THR* 3.9 8.3 + - - -
292B ARG* 3.0 66.6 + - - +
293B HIS* 3.3 5.8 + - - -
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Residues in contact with THR 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B PHE* 4.5 10.3 - - + -
146B ARG* 4.1 19.7 - - + +
147B ILE 3.4 20.6 + - - +
148B HIS* 3.3 25.0 - - + -
175B LYS 5.7 0.2 - - - +
177B ASN* 3.2 11.3 + - - +
285B LEU 2.7 20.7 + - - -
286B ARG 3.3 10.1 - - - -
287B GLU 3.2 0.2 - - - -
288B GLN* 1.3 78.0 - - - +
290B HIS* 1.3 55.4 + - - +
293B HIS* 4.0 12.4 - - + -
294B TYR* 2.7 34.7 + - - +
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Residues in contact with HIS 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B TYR* 4.0 21.1 - + - -
132B GLU* 4.2 6.5 - - - -
146B ARG* 2.9 40.4 + - - +
286B ARG 3.0 15.5 + - - +
287B GLU* 3.7 14.8 - - - +
289B THR* 1.3 80.1 - - - +
291B THR* 1.3 70.6 + - + +
294B TYR* 3.6 16.7 - + - +
295B GLU* 3.2 34.4 + - - +
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Residues in contact with THR 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B GLU* 2.8 57.8 + - + +
288B GLN* 3.9 11.1 + - - -
290B HIS* 1.3 83.6 - - + +
292B ARG* 1.3 57.9 + - - +
295B GLU* 3.2 23.1 - - - +
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Residues in contact with ARG 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ASN* 3.9 19.6 + - - -
211B ILE 5.6 0.8 + - - -
212B TYR* 4.6 13.1 - - - +
213B GLN* 5.4 4.2 - - - +
288B GLN* 3.0 43.0 + - - +
290B HIS 3.4 0.2 - - - -
291B THR* 1.3 79.7 + - - +
293B HIS* 1.3 84.9 + - + +
294B TYR 3.5 0.7 - - - -
295B GLU* 3.4 2.6 + - - +
296B LEU* 3.0 24.3 + - - +
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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