Contacts of the helix formed by residues 292 - 301 (chain N) in PDB entry 3H1I
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 SER 292 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275N ALA 5.7 0.4 - - - -
276N ILE 3.8 14.5 + - - -
277N ILE 2.9 28.7 + - - -
278N GLY* 4.7 4.7 - - - -
279N ARG 5.3 2.5 - - - -
290N LEU* 3.3 4.6 - - - +
291N SER* 1.3 76.6 - - - +
293N ARG* 1.3 65.7 + - - +
294N LEU 3.8 2.1 + - - -
295N ALA* 2.7 38.1 + - - +
296N ALA* 2.9 11.3 + - - +
307N PHE* 4.1 0.4 - - - -
356N ARG* 4.4 1.3 - - - +
90O GLU* 4.3 1.4 + - - -
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Residues in contact with ARG 293 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276N ILE* 4.6 6.8 + - + -
277N ILE* 5.7 1.1 - - - +
291N SER 3.2 7.8 + - - +
292N SER* 1.3 73.1 + - - +
294N LEU* 1.3 63.3 + - - +
296N ALA* 2.9 22.1 + - - +
297N LEU* 3.3 22.7 + - + +
341N GLU* 3.0 29.5 + - - +
344N ARG* 3.4 35.5 - - - +
353N GLU* 3.5 25.7 + - - +
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Residues in contact with LEU 294 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277N ILE* 3.9 19.9 - - + +
292N SER* 3.3 1.2 + - - +
293N ARG* 1.3 79.1 - - - +
295N ALA* 1.3 57.0 + - - +
297N LEU* 4.1 4.9 - - - +
298N ALA* 2.8 31.5 + - - +
303N LEU* 5.1 1.3 - - + -
307N PHE* 3.4 44.6 - - + -
322N PHE* 6.1 4.5 - - + -
334N MET* 3.2 31.2 - - + -
337N CYS* 4.0 13.0 - - + +
338N ALA* 3.6 28.9 - - + +
341N GLU* 3.9 14.6 - - + +
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Residues in contact with ALA 295 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279N ARG 5.2 2.5 - - - +
280N TYR* 4.0 12.7 - - + -
290N LEU* 3.9 26.2 - - + -
292N SER* 2.7 36.8 + - - +
294N LEU* 1.3 73.7 - - - +
296N ALA* 1.3 60.4 + - - +
298N ALA* 2.9 16.9 - - - +
299N VAL* 2.9 16.3 + - - +
307N PHE* 3.7 12.3 - - + -
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Residues in contact with ALA 296 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287N GLY 5.1 2.9 - - - -
288N LYS* 4.4 17.6 - - - +
290N LEU* 4.6 11.5 - - - +
292N SER 2.9 8.9 + - - +
293N ARG* 2.9 13.4 + - - +
295N ALA* 1.3 71.5 - - - +
297N LEU* 1.3 63.8 + - + +
299N VAL* 2.6 31.5 + - - +
300N GLU* 2.8 15.6 + - - +
87O ARG* 5.8 2.2 - - - +
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Residues in contact with LEU 297 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293N ARG* 3.5 25.8 - - + +
294N LEU* 4.1 4.9 - - - +
296N ALA* 1.3 78.9 - - + +
298N ALA* 1.3 65.7 + - - +
299N VAL 2.8 1.6 + - - -
300N GLU* 2.9 30.0 + - - +
301N HIS* 3.0 24.9 + - + +
303N LEU* 3.5 17.1 - - + +
337N CYS* 3.8 29.2 - - + -
341N GLU* 4.5 13.0 - - - +
3P PRO* 6.3 0.4 - - + -
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Residues in contact with ALA 298 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280N TYR* 4.0 20.5 - - + -
294N LEU* 2.8 24.3 + - + +
295N ALA* 2.9 15.0 - - - +
297N LEU* 1.3 75.3 - - - +
299N VAL* 1.3 56.2 + - - +
302N LYS* 3.3 3.3 + - - -
303N LEU* 2.7 42.1 + - + +
304N CYS* 4.1 14.5 + - - +
307N PHE* 4.2 7.0 - - + -
334N MET* 5.1 0.7 - - - -
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Residues in contact with VAL 299 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280N TYR* 3.5 39.7 - - + +
287N GLY* 3.8 20.6 - - - +
288N LYS* 3.3 32.5 - - + +
290N LEU* 4.6 0.4 - - + -
295N ALA 2.9 9.3 + - - +
296N ALA 2.6 14.0 + - - +
298N ALA* 1.3 70.9 - - - +
300N GLU* 1.3 69.7 + - - +
302N LYS* 3.0 22.9 + - - +
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Residues in contact with GLU 300 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288N LYS* 5.9 5.4 - - + -
296N ALA* 2.8 14.6 + - - +
297N LEU* 3.6 18.7 + - - +
299N VAL* 1.3 78.2 - - - +
301N HIS* 1.3 89.7 + - + +
302N LYS* 3.5 10.6 + - - +
2P ALA* 5.7 1.0 - - - +
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Residues in contact with HIS 301 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297N LEU* 3.0 28.7 + - + +
300N GLU* 1.3 112.5 + - + +
302N LYS* 1.3 73.1 + - - +
303N LEU* 3.1 21.5 + - + +
330N SER* 5.7 1.6 - - - -
2P ALA* 4.2 24.7 + - + -
3P PRO* 4.0 34.0 - - + +
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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