Contacts of the helix formed by residues 275 - 285 (chain A) in PDB entry 5UM9
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 LEU 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A LEU* 3.8 25.6 - - + -
234A TYR 5.2 3.6 - - - +
235A CYS* 3.9 13.6 - - + +
273A ASN* 3.6 15.0 - - + +
274A TRP* 1.3 88.4 - - - +
276A HIS* 1.3 63.9 + - - +
277A LYS 3.2 3.4 - - - -
278A GLU* 3.1 27.5 + - + +
279A ALA* 3.0 22.0 + - - +
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Residues in contact with HIS 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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225A ASP* 5.4 0.6 + - - -
228A ILE* 3.6 14.4 - - + +
235A CYS* 4.0 10.8 - - - -
256A ILE* 3.4 36.9 - - + +
257A GLU* 4.5 10.5 - - + -
260A VAL* 5.5 3.2 - - + +
274A TRP* 3.6 49.6 - + + +
275A LEU* 1.3 76.2 - - - +
277A LYS* 1.3 95.2 + - + +
280A HIS* 2.9 29.9 + - - +
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Residues in contact with LYS 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A GLU* 4.8 23.8 + - - +
275A LEU 3.2 0.8 - - - -
276A HIS* 1.3 107.8 - - + +
278A GLU* 1.3 70.9 + - - +
280A HIS* 3.5 7.4 + - - +
281A GLN* 2.9 28.2 + - - +
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Residues in contact with GLU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 3.6 24.6 - - + +
274A TRP 4.2 1.4 - - - +
275A LEU* 3.1 44.2 + - + +
277A LYS* 1.3 87.6 - - - +
279A ALA* 1.3 60.6 + - - +
281A GLN* 3.6 6.6 + - - +
282A LEU* 2.9 28.2 + - - +
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Residues in contact with ALA 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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92A LEU* 4.0 7.8 - - + +
228A ILE* 3.9 10.1 - - + -
232A SER* 5.0 1.3 - - - +
234A TYR* 4.3 15.9 - - + -
235A CYS* 3.7 33.9 - - + -
275A LEU 3.0 9.6 + - - +
276A HIS 3.9 2.0 - - - +
278A GLU* 1.3 76.2 - - - +
280A HIS* 1.3 67.3 + - - +
282A LEU* 3.2 4.3 + - - +
283A PHE* 2.9 31.7 + - + +
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Residues in contact with HIS 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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221A GLU* 3.3 32.8 - - + +
224A VAL* 3.6 13.5 - - + +
225A ASP* 2.7 32.9 + - - +
228A ILE* 3.4 10.1 - - + +
276A HIS* 2.9 20.1 + - - +
277A LYS* 3.5 9.0 - - - +
279A ALA* 1.3 76.3 - - - +
281A GLN* 1.3 62.8 - - - +
283A PHE* 3.4 1.6 + - - +
284A LEU* 3.0 62.2 + - + +
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Residues in contact with GLN 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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277A LYS 2.9 18.2 + - - +
278A GLU* 3.7 8.5 - - - +
280A HIS* 1.3 78.5 - - - +
282A LEU* 1.3 63.8 + - - +
284A LEU* 3.3 4.5 + - - +
285A GLU* 2.5 68.0 + - - +
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Residues in contact with LEU 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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90A PRO* 3.9 26.7 - - + -
92A LEU* 4.0 14.4 - - + -
185A PHE* 4.0 6.4 - - + -
234A TYR* 3.6 41.3 - - + -
278A GLU 2.9 18.7 + - - +
279A ALA* 3.2 5.1 + - - +
281A GLN* 1.3 77.8 - - - +
283A PHE* 1.3 64.4 + - + +
285A GLU 4.5 3.4 - - - +
286A PRO* 3.3 37.6 - - + +
287A GLU* 5.2 4.0 - - + +
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Residues in contact with PHE 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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2A GLY 6.0 0.4 - - - -
3A ILE* 5.3 1.6 - - + -
181A ASP* 4.2 9.6 - - + -
184A THR* 2.9 51.9 - - + +
185A PHE* 3.6 45.2 - + - -
224A VAL* 3.7 27.1 - - + -
227A CYS* 5.5 2.9 - - + -
228A ILE* 4.4 8.7 - - + -
232A SER* 3.8 26.7 - - - -
233A ASP 5.3 0.2 - - - -
234A TYR* 3.5 28.3 - + - -
279A ALA* 2.9 25.6 + - + +
282A LEU* 1.3 80.8 - - + +
284A LEU* 1.3 62.6 + - - +
285A GLU 3.4 0.3 + - - -
286A PRO* 3.7 8.5 - - - +
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Residues in contact with LEU 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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184A THR 5.3 0.2 - - - -
220A GLN* 3.9 25.8 - - + +
221A GLU* 3.9 19.1 - - + +
224A VAL* 3.7 24.9 - - + -
280A HIS* 3.0 51.2 + - + +
281A GLN* 4.1 5.2 - - - +
283A PHE* 1.3 77.0 - - - +
285A GLU* 1.3 70.6 + - + +
286A PRO* 3.6 4.4 - - - +
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Residues in contact with GLU 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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281A GLN* 2.5 51.6 + - - +
282A LEU* 3.6 7.1 - - - +
284A LEU* 1.3 91.1 - - + +
286A PRO* 1.3 67.9 - - - +
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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