Contacts of the helix formed by residues 287 - 295 (chain B) in PDB entry 2R5N
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 PRO 287 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B TRP* 4.8 0.9 - - + -
281B TYR* 3.5 50.6 - - + +
285B GLU* 4.9 1.8 - - + +
286B ILE* 1.4 92.5 - - + +
288B SER* 1.3 67.4 + - - +
289B GLU* 4.4 6.1 - - + +
290B ILE* 3.1 40.9 + - + +
291B TYR* 3.3 10.5 + - - -
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Residues in contact with SER 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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286B ILE 3.9 0.6 + - - -
287B PRO* 1.3 73.0 - - - +
289B GLU* 1.3 59.1 + - - +
291B TYR* 3.3 11.9 + - - +
292B ALA* 2.8 30.2 + - - +
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Residues in contact with GLU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B SER* 2.9 34.3 + - - +
287B PRO* 3.3 5.4 - - + +
288B SER* 1.3 82.9 + - - +
290B ILE* 1.3 62.2 + - + +
292B ALA* 3.4 7.9 + - + +
293B GLN* 2.9 39.8 + - + +
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Residues in contact with ILE 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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2B SER* 3.8 16.4 - - - +
6B GLU* 3.9 20.0 - - + +
7B LEU* 4.0 8.7 - - + -
10B ALA* 4.0 11.7 - - + -
77B LEU* 4.7 0.4 - - + -
279B TRP* 3.7 31.4 - - + -
281B TYR* 4.3 2.0 - - + +
286B ILE* 3.8 15.0 - - + -
287B PRO* 3.1 31.9 + - + +
289B GLU* 1.3 75.6 - - + +
291B TYR* 1.3 65.0 + - - +
293B GLN* 3.3 6.2 + - - +
294B TRP* 3.0 43.8 + - + +
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Residues in contact with TYR 291 (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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76B HIS* 2.6 46.2 + + - -
77B LEU* 4.2 21.0 - - + +
84B MET* 3.3 16.3 - - - +
286B ILE* 3.4 45.2 + - + +
287B PRO 3.3 10.4 + - - -
288B SER* 3.6 9.6 - - - +
290B ILE* 1.3 77.7 - - - +
292B ALA* 1.3 56.8 + - - +
294B TRP* 4.5 2.9 - - - +
295B ASP* 2.7 40.5 + - + +
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Residues in contact with ALA 292 (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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288B SER 2.8 20.5 + - - +
289B GLU* 3.5 10.3 - - + +
290B ILE 3.2 0.4 - - - -
291B TYR* 1.3 75.6 - - - +
293B GLN* 1.3 61.3 + - + +
295B ASP* 4.0 12.1 + - - +
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Residues in contact with GLN 293 (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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2B SER* 2.8 61.6 + - - +
7B LEU* 3.7 21.8 - - + +
42B ARG* 2.8 38.2 + - - +
289B GLU* 2.9 29.3 + - + +
290B ILE 3.3 0.2 + - - -
291B TYR 3.2 0.2 - - - -
292B ALA* 1.3 77.5 - - + +
294B TRP* 1.3 61.5 + - - +
295B ASP 4.6 2.5 - - - +
678B EDO 4.8 3.5 + - - -
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Residues in contact with TRP 294 (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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7B LEU* 2.9 39.2 + - + +
10B ALA* 4.2 0.8 - - - +
11B ILE* 3.7 16.6 - - + -
38B GLU* 3.7 34.1 - - + -
41B TRP* 4.2 5.8 - - + -
42B ARG* 3.7 26.8 - - + +
74B LEU* 3.7 30.1 - - + -
77B LEU* 3.4 40.9 - - + +
78B THR* 3.5 39.7 - - + +
290B ILE* 3.0 37.8 + - + +
291B TYR* 3.9 2.2 - - - +
293B GLN* 1.3 78.6 - - - +
295B ASP* 1.3 66.0 + - - +
296B ALA* 3.4 4.0 + - - +
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Residues in contact with ASP 295 (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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77B LEU 3.7 8.9 - - - +
78B THR 3.8 0.6 - - - -
79B GLY* 3.5 14.0 - - - -
291B TYR* 2.7 24.7 + - + +
292B ALA* 4.0 10.3 + - - +
293B GLN 3.5 2.7 - - - +
294B TRP* 1.3 73.9 - - - +
296B ALA* 1.3 59.8 + - - +
297B LYS* 2.6 59.4 + - - +
298B GLU* 4.4 4.2 + - - +
299B ALA* 6.0 0.3 - - - +
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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