Contacts of the helix formed by residues 283 - 294 (chain A) in PDB entry 6UPR
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 HIS 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A TYR* 3.8 16.1 + - + +
213A LEU* 3.8 21.7 - - + +
214A PRO* 3.4 39.0 - - + +
224A PHE* 5.2 14.0 - + - -
227A GLN* 5.9 0.4 + - - -
228A THR* 5.3 6.8 + - + +
231A LEU* 4.5 5.6 - - + +
279A MET* 3.1 33.1 + - + +
280A LEU 3.7 2.0 - - - -
282A THR* 1.3 103.0 + - - +
284A MET* 1.3 64.6 + - - +
285A GLN 3.3 2.2 - - - -
286A ASP* 3.3 8.6 + - - +
287A LEU* 2.9 29.3 + - + +
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Residues in contact with MET 284 (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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38A PHE* 3.6 43.3 - - + -
58A PHE* 4.3 15.3 - - + -
88A ILE* 5.3 1.1 - - + -
95A LEU* 4.2 33.9 - - + -
97A LEU* 4.9 6.5 - - + -
280A LEU* 3.0 41.7 + - + +
281A ILE* 3.5 18.6 + - - +
282A THR 3.6 0.2 - - - -
283A HIS* 1.3 77.2 - - - +
285A GLN* 1.3 64.3 + - - +
287A LEU* 3.1 5.9 + - - +
288A GLN* 3.0 29.4 + - - +
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Residues in contact with GLN 285 (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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36A PHE* 5.4 10.8 - - + -
282A THR 5.3 0.8 + - - -
283A HIS 3.3 0.6 - - - -
284A MET* 1.3 77.5 - - - +
286A ASP* 1.3 58.1 + - - +
288A GLN* 3.2 17.4 + - - +
289A GLU* 2.8 59.0 + - + +
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Residues in contact with ASP 286 (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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211A TYR* 2.7 31.7 + - - +
212A HIS 4.9 0.3 - - - +
214A PRO* 3.3 27.9 - - + +
283A HIS* 3.3 12.1 + - - +
284A MET 3.3 0.6 - - - -
285A GLN* 1.3 76.2 - - - +
287A LEU* 1.3 60.7 + - - +
289A GLU* 3.7 18.0 - - - +
290A VAL* 2.9 39.5 + - - +
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Residues in contact with LEU 287 (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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38A PHE* 4.1 14.1 - - + -
147A HIS* 3.8 10.5 - - - +
148A CYS* 4.3 14.4 - - + -
176A ASN* 3.4 20.7 + - + +
211A TYR* 3.6 44.9 - - + -
279A MET* 5.2 4.9 - - - -
280A LEU* 4.0 27.8 - - + +
283A HIS* 2.9 28.6 + - + +
284A MET* 3.1 5.6 + - - +
286A ASP* 1.3 77.8 - - - +
288A GLN* 1.3 54.8 + - - +
290A VAL* 4.8 0.2 - - - -
291A THR* 2.5 36.2 + - - -
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Residues in contact with GLN 288 (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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36A PHE* 3.3 44.1 - - - +
37A GLU 3.0 25.0 + - - -
38A PHE* 3.5 25.6 - - + +
95A LEU* 5.6 2.0 - - - +
143A ASP* 6.0 0.2 - - - +
147A HIS* 4.1 17.0 - - + +
284A MET* 3.0 21.6 + - - +
285A GLN* 3.2 14.6 + - + +
287A LEU* 1.3 76.8 - - - +
289A GLU* 1.3 62.4 + - + +
291A THR* 3.2 7.7 + - - -
292A GLN* 3.0 22.5 + - - +
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Residues in contact with GLU 289 (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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285A GLN* 2.8 55.1 + - + +
286A ASP* 3.2 19.2 + - - +
288A GLN* 1.3 74.3 - - + +
290A VAL* 1.3 57.7 + - + +
292A GLN* 3.2 4.8 + - - +
293A ASP* 2.8 45.1 + - - +
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Residues in contact with VAL 290 (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* 3.2 24.7 - - - +
211A TYR* 4.5 8.3 - - + -
286A ASP* 2.9 38.5 + - - +
287A LEU* 4.1 1.8 - - - +
289A GLU* 1.3 73.5 - - + +
291A THR* 1.3 61.0 + - - +
293A ASP* 4.5 3.1 - - - +
294A LEU* 2.9 55.9 + - + +
295A HIS* 3.5 3.0 + - - +
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Residues in contact with THR 291 (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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126A PHE* 4.5 11.4 - - + -
145A ARG* 4.3 15.9 - - + +
146A VAL 3.4 21.8 - - - +
147A HIS* 3.4 23.9 - - + -
174A LYS 5.4 0.2 - - - +
176A ASN* 3.0 12.8 + - - +
287A LEU 2.5 22.9 + - - -
288A GLN 3.4 7.9 - - - -
289A GLU 3.2 0.2 - - - -
290A VAL* 1.3 78.6 - - - +
292A GLN* 1.3 59.3 + - - +
295A HIS* 3.4 12.3 + - + -
296A TYR* 2.9 29.5 + - - +
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Residues in contact with GLN 292 (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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129A TYR* 3.8 14.3 + - - +
133A GLU* 4.5 3.4 + - - -
145A ARG* 3.2 38.2 - - - +
288A GLN 3.0 13.3 + - - +
289A GLU* 3.7 8.5 - - - +
291A THR* 1.3 78.5 - - - +
293A ASP* 1.3 74.8 + - - +
296A TYR* 3.5 23.2 - - - +
297A GLU* 3.4 29.7 + - - +
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Residues in contact with ASP 293 (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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289A GLU* 2.8 32.0 + - - +
290A VAL* 4.6 2.0 - - - +
292A GLN* 1.3 88.3 - - - +
294A LEU* 1.3 58.5 + - + +
297A GLU* 3.4 22.9 - - - +
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Residues in contact with LEU 294 (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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290A VAL* 2.9 28.6 + - + +
293A ASP* 1.3 79.8 - - + +
295A HIS* 1.3 85.4 + - + +
296A TYR 3.5 0.4 - - - -
298A ASN* 3.0 55.1 + - - +
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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