Contacts of the helix formed by residues 287 - 295 (chain B) in PDB entry 1NOZ
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 287 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112B ASP* 5.0 2.9 - - - +
213B TRP* 3.5 41.1 - - + +
286B SER* 1.3 73.1 - - - +
288B GLU* 1.3 76.0 + - + +
290B VAL* 3.9 0.2 - - - -
291B ALA* 2.9 24.6 + - + +
299B LYS* 6.0 0.2 - - - -
324B ASP* 3.3 42.4 - - + +
327B SER* 3.4 32.1 - - - +
328B VAL* 4.4 4.5 - - + -
331B ILE* 4.2 16.2 - - + -
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Residues in contact with GLU 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 SER* 3.7 17.1 - - - +
287B LEU* 1.3 87.3 + - + +
289B SER* 1.3 65.0 + - - +
291B ALA* 5.0 1.1 - - - -
292B GLN* 2.9 46.2 + - - +
299B LYS* 4.8 18.5 + - + +
324B ASP* 4.0 17.8 - - - +
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Residues in contact with SER 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B LEU* 4.8 5.7 - - - +
283B PRO* 5.0 4.5 - - - +
284B SER* 2.7 39.7 + - - -
286B SER* 3.0 19.5 + - - -
288B GLU* 1.3 82.0 - - - +
290B VAL* 1.3 62.6 + - - +
292B GLN* 3.2 6.8 + - - +
293B HIS* 3.0 21.2 + - - +
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Residues in contact with VAL 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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213B TRP* 3.4 37.2 - - + -
274B TYR* 3.6 35.0 - - + -
282B LEU* 4.2 7.2 - - + -
285B PHE* 3.8 17.5 - - - +
286B SER 3.0 17.5 + - - +
287B LEU 3.9 1.8 - - - +
289B SER* 1.3 76.1 - - - +
291B ALA* 1.3 54.3 + - - +
293B HIS* 3.0 9.3 + - - +
294B GLU* 2.7 34.4 + - + +
331B ILE* 3.6 13.7 - - + -
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Residues in contact with ALA 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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287B LEU* 2.9 21.6 + - + +
288B GLU* 4.0 2.5 - - - +
290B VAL* 1.3 70.1 - - - +
292B GLN* 1.3 69.7 + - - +
294B GLU 4.4 0.2 - - - +
295B THR* 2.5 39.2 + - + +
297B LYS 4.5 2.5 - - - +
327B SER* 3.7 28.9 - - - -
331B ILE* 3.8 18.4 - - + +
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Residues in contact with GLN 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 GLU* 2.9 42.5 + - - +
289B SER* 3.3 10.8 - - - +
291B ALA* 1.3 76.2 - - - +
293B HIS* 1.3 57.5 + - - +
296B LYS* 2.5 38.7 + - - +
297B LYS 4.1 9.0 + - - +
298B GLY* 3.2 34.9 - - - +
299B LYS* 3.7 10.6 + - - +
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Residues in contact with HIS 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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274B TYR* 3.6 9.6 + - - -
280B THR* 4.4 11.2 - - + -
282B LEU* 3.8 32.5 - - + +
289B SER 3.0 9.4 + - - +
290B VAL 3.0 8.9 + - - +
292B GLN* 1.3 80.3 - - - +
294B GLU* 1.3 88.6 + - - +
296B LYS* 3.8 13.6 - - - +
335B ARG* 4.9 2.7 - - - -
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Residues in contact with GLU 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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274B TYR* 2.6 30.2 + - + +
290B VAL* 2.7 31.2 + - + +
291B ALA 4.0 1.1 - - - +
293B HIS* 1.3 86.9 + - - +
295B THR* 1.3 60.3 + - + +
296B LYS* 3.3 2.6 + - - +
331B ILE* 4.1 19.3 - - + -
334B ILE* 3.3 35.4 - - + +
335B ARG* 2.9 40.5 + - - +
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Residues in contact with THR 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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291B ALA* 2.5 32.2 + - + +
294B GLU* 1.3 79.9 - - + +
296B LYS* 1.3 67.9 + - - +
297B LYS* 2.8 37.7 + - + +
327B SER* 5.1 1.3 - - - +
330B ALA* 3.9 30.1 - - + -
331B ILE* 4.8 2.2 - - + +
334B ILE* 4.3 11.9 - - + -
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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