Contacts of the helix formed by residues 332 - 343 (chain B) in PDB entry 1H3F
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 332 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298B ALA* 4.9 1.8 - - + -
317B LEU* 3.3 35.3 - - + +
319B TYR* 4.0 8.1 - - + +
331B GLY* 1.3 92.0 - - - +
333B GLU* 1.3 62.0 + - - +
334B GLU* 4.8 1.8 - - + +
335B VAL* 3.3 32.1 - - + +
336B ARG* 3.0 24.5 + - - +
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Residues in contact with GLU 333 (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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332B PRO* 1.3 71.8 - - - +
334B GLU* 1.3 62.5 + - + +
336B ARG* 3.3 24.4 + - - +
337B ARG* 2.7 69.5 + - - +
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Residues in contact with GLU 334 (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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247B PRO* 3.3 37.5 - - + +
301B ALA* 4.5 14.2 - - + +
332B PRO* 4.8 2.1 - - + +
333B GLU* 1.3 79.7 - - + +
335B VAL* 1.3 56.6 + - + +
337B ARG* 3.5 7.3 - - - +
338B ALA* 2.6 40.6 + - - +
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Residues in contact with VAL 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B PHE* 4.3 7.5 - - + -
294B ARG* 3.8 27.6 - - + +
297B THR* 4.3 9.4 - - + -
298B ALA* 3.8 32.3 - - + +
301B ALA* 6.1 1.1 - - + -
319B TYR* 3.0 24.5 - - + +
332B PRO* 3.3 28.0 - - + -
333B GLU 3.2 0.8 - - - -
334B GLU* 1.3 77.5 - - + +
336B ARG* 1.3 56.8 + - - +
337B ARG 3.1 0.3 + - - -
338B ALA* 3.1 6.2 + - - +
339B GLU* 2.8 30.9 + - - +
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Residues in contact with ARG 336 (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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319B TYR* 4.0 4.5 + - - -
328B LYS 4.8 9.1 - - - +
329B GLU* 3.8 32.3 + - - +
330B ALA* 3.2 18.6 - - - +
331B GLY 4.4 3.1 + - - -
332B PRO 3.0 20.6 + - - +
333B GLU* 3.7 27.2 + - - +
335B VAL* 1.3 78.4 - - - +
337B ARG* 1.3 72.6 + - + +
339B GLU* 3.6 9.0 + - - +
340B ALA* 3.2 19.2 + - - +
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Residues in contact with ARG 337 (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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333B GLU* 2.7 58.5 + - - +
334B GLU* 3.5 6.7 - - - +
336B ARG* 1.3 80.0 - - + +
338B ALA* 1.3 57.7 + - - +
339B GLU 3.1 1.1 - - - -
340B ALA* 2.7 27.6 + - - +
341B ARG* 2.9 45.4 + - - +
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Residues in contact with ALA 338 (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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247B PRO* 4.2 5.2 - - + +
248B GLU* 4.1 23.4 - - + +
251B PHE* 4.1 25.6 - - + +
297B THR* 5.1 1.6 - - + -
334B GLU 2.6 23.0 + - - +
335B VAL* 3.6 5.4 - - - +
337B ARG* 1.3 71.7 - - - +
339B GLU* 1.3 62.1 + - - +
341B ARG* 3.3 12.7 + - - +
342B TYR* 3.2 21.8 + - - +
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Residues in contact with GLU 339 (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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251B PHE* 3.4 27.3 - - + -
290B ARG* 2.8 32.5 + - - +
294B ARG* 2.6 52.1 + - - +
319B TYR* 4.2 5.4 + - - -
328B LYS* 2.9 18.9 - - + +
335B VAL 2.8 16.0 + - - +
336B ARG* 3.7 6.5 - - - +
338B ALA* 1.3 78.1 - - - +
340B ALA* 1.3 57.8 + - - +
342B TYR* 3.5 2.3 + - - +
343B ASP* 3.0 37.1 + - - +
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Residues in contact with ALA 340 (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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328B LYS* 6.4 0.9 - - - +
336B ARG 3.2 13.8 + - - +
337B ARG* 2.7 13.0 + - - +
339B GLU* 1.3 74.2 - - - +
341B ARG* 1.3 68.0 - - + +
342B TYR 3.0 2.7 + - - -
343B ASP* 3.1 24.9 + - - +
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Residues in contact with ARG 341 (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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248B GLU* 2.7 53.2 + - + +
337B ARG* 2.9 54.3 + - - +
338B ALA* 3.6 9.0 - - - +
340B ALA* 1.3 79.0 - - - +
342B TYR* 1.3 61.9 + - - +
343B ASP 4.7 1.2 - - - -
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Residues in contact with TYR 342 (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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251B PHE* 4.4 10.5 - + + -
252B LYS* 4.2 35.7 - - + -
255B MET* 3.5 59.9 + - + +
256B ARG* 4.5 16.1 + - - +
290B ARG* 5.5 0.7 - - - -
338B ALA 3.2 12.4 + - - +
339B GLU 3.6 7.6 - - - +
340B ALA 3.0 0.6 - - - -
341B ARG* 1.3 78.8 - - - +
343B ASP* 1.3 76.7 + - - +
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Residues in contact with ASP 343 (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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290B ARG* 2.7 42.1 + - - -
328B LYS* 3.4 26.1 - - - +
339B GLU* 3.0 23.2 + - - +
340B ALA* 3.1 17.1 + - - +
341B ARG 4.7 1.3 - - - -
342B TYR* 1.3 91.3 - - - +
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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