Contacts of the helix formed by residues 332 - 347 (chain B) in PDB entry 4BN2
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 CYS 332 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B GLN* 3.6 31.2 - - - +
327B HIS* 3.5 50.5 - - - +
329B GLY 3.1 7.6 + - - +
331B ARG* 1.3 79.7 - - - +
333B PHE* 1.3 66.8 + - - +
334B GLY 3.1 3.0 + - - -
335B GLU* 3.2 4.4 + - - +
336B THR* 2.8 25.3 + - - +
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Residues in contact with PHE 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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36B CYS* 4.2 29.8 - - + -
47B LEU* 4.0 22.9 - - + -
48B HIS 4.4 3.4 - - - -
49B SER* 3.8 41.5 - - - -
329B GLY 3.8 1.6 + - - -
330B SER 3.3 19.0 + - - +
331B ARG 3.3 1.2 - - - -
332B CYS* 1.3 78.0 - - - +
334B GLY* 1.3 63.5 + - - +
336B THR* 3.5 2.1 - - - +
337B LEU* 2.8 49.8 + - + +
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Residues in contact with GLY 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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331B ARG 5.1 1.0 + - - -
332B CYS 3.2 1.2 - - - -
333B PHE* 1.3 87.0 - - - +
335B GLU* 1.3 59.3 + - - +
337B LEU* 3.3 7.2 + - - +
338B SER* 3.0 29.3 + - - -
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Residues in contact with GLU 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLN* 3.5 42.6 - - + +
255B SER* 4.0 7.6 + - - +
256B GLU* 3.2 26.1 + - + +
257B ARG* 2.8 33.5 + - - +
332B CYS* 3.2 5.5 + - - +
334B GLY* 1.3 74.6 - - - +
336B THR* 1.3 61.0 + - - +
338B SER* 3.3 14.5 + - - -
339B THR* 2.9 32.9 + - - -
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Residues in contact with THR 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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36B CYS* 4.9 2.7 - - - -
37B LEU* 4.3 12.1 - - + -
47B LEU* 4.2 13.0 - - + -
96B GLN* 4.4 2.2 + - - -
326B VAL* 3.9 26.8 - - + +
327B HIS 3.3 22.1 + - - +
332B CYS* 2.8 22.4 + - - +
333B PHE* 3.5 6.3 - - - -
335B GLU* 1.3 76.3 - - - +
337B LEU* 1.3 60.3 + - - +
339B THR* 3.3 1.2 + - - -
340B LEU* 2.9 54.0 + - + +
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Residues in contact with LEU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 3.8 27.5 - - + +
54B LYS* 4.4 22.9 - - + +
56B PHE* 4.5 8.7 - - + -
333B PHE* 2.8 41.6 + - + +
334B GLY* 3.5 6.7 - - - +
336B THR* 1.3 74.5 - - - +
338B SER* 1.3 59.0 + - - +
340B LEU* 3.8 1.5 - - - -
341B ASN* 2.9 52.3 + - - +
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Residues in contact with SER 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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94B TYR* 5.6 1.3 - - - -
255B SER 6.0 0.9 - - - -
257B ARG* 6.1 0.9 - - - +
334B GLY 3.0 15.8 + - - -
335B GLU* 3.7 19.4 + - - -
337B LEU* 1.3 77.6 - - - +
339B THR* 1.3 65.5 + - - +
341B ASN* 3.1 9.8 + - - +
342B PHE* 2.8 24.6 + - - +
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Residues in contact with THR 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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94B TYR* 4.1 19.5 - - + +
95B GLY* 3.8 17.0 - - - -
96B GLN* 4.1 3.6 + - - +
255B SER* 4.0 9.2 + - - -
324B ALA* 3.8 24.9 - - + -
325B ASN 4.0 6.6 + - - +
326B VAL* 3.6 24.1 - - + +
335B GLU 2.9 22.2 + - - -
336B THR 3.7 4.0 - - - -
338B SER* 1.3 73.0 - - - +
340B LEU* 1.3 65.1 + - + +
342B PHE* 3.1 3.3 + - - +
343B ALA* 2.9 21.7 + - - +
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Residues in contact with LEU 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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17B VAL* 4.2 19.5 - - + -
37B LEU* 4.3 8.1 - - + -
45B LEU* 4.2 21.5 - - + -
47B LEU* 4.2 16.4 - - + -
56B PHE* 3.7 38.7 - - + -
58B PHE* 4.2 7.2 - - + -
326B VAL* 4.4 15.7 - - + -
336B THR* 2.9 41.2 + - + +
337B LEU* 3.9 2.0 - - - +
339B THR* 1.3 74.4 - - + +
341B ASN* 1.3 64.5 + - - +
343B ALA* 3.3 4.7 + - + +
344B GLN* 2.9 25.6 + - - +
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Residues in contact with ASN 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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54B LYS* 6.1 0.2 - - - +
56B PHE* 4.0 12.6 - - - -
337B LEU* 2.9 46.6 + - - +
338B SER* 3.5 7.1 - - - +
340B LEU* 1.3 77.3 - - - +
342B PHE* 1.3 65.1 + - - +
344B GLN* 3.4 12.9 + - - +
345B ARG* 3.4 41.9 + - - +
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Residues in contact with PHE 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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92B PHE* 5.0 1.3 - + - -
94B TYR* 3.7 63.0 - + + +
278B LEU 5.6 0.2 - - - -
281B LEU* 4.2 17.5 - - + -
282B GLY* 4.4 16.4 - - - -
285B ILE* 3.7 35.1 - - + +
322B ILE* 4.6 15.5 - - + -
338B SER 2.8 16.3 + - - +
339B THR 3.5 6.5 - - - +
341B ASN* 1.3 73.1 - - - +
343B ALA* 1.3 69.8 + - + +
345B ARG* 3.3 15.4 + - - +
346B ALA* 3.0 28.5 + - + +
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Residues in contact with ALA 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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15B VAL* 3.7 16.5 - - + +
17B VAL* 5.1 0.2 - - + -
58B PHE* 3.7 22.0 - - + -
322B ILE* 5.7 1.6 - - + -
324B ALA* 4.1 18.8 - - + -
339B THR 2.9 16.2 + - - +
340B LEU* 3.8 3.1 - - - +
342B PHE* 1.3 85.5 - - + +
344B GLN* 1.3 63.0 + - - +
346B ALA* 3.2 8.2 + - - +
347B LYS* 3.0 23.9 + - - +
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Residues in contact with GLN 344 (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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55B THR 5.1 4.0 + - - -
56B PHE* 3.8 32.5 - - + +
57B THR 5.8 1.0 - - - +
58B PHE* 3.8 9.5 - - + -
340B LEU 2.9 16.6 + - - +
341B ASN* 3.5 14.1 - - - +
343B ALA* 1.3 78.4 - - - +
345B ARG* 1.3 63.9 + - + +
347B LYS* 3.4 14.5 + - - +
348B LEU* 3.8 12.9 - - + +
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Residues in contact with ARG 345 (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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285B ILE* 3.9 15.7 - - + -
286B THR* 4.3 24.7 + - - +
289B VAL* 3.9 14.1 - - + +
341B ASN* 3.4 40.4 + - - +
342B PHE* 3.3 12.5 + - - +
343B ALA 3.3 0.2 - - - -
344B GLN* 1.3 75.6 - - + +
346B ALA* 1.3 59.7 + - - +
347B LYS 3.0 1.6 - - - -
348B LEU* 2.6 45.0 + - + +
349B ILE 3.6 2.3 + - - -
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Residues in contact with ALA 346 (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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13B ILE* 3.2 19.4 - - + +
15B VAL* 4.4 2.7 - - + -
285B ILE* 3.8 16.3 - - + +
322B ILE* 3.8 28.9 - - + -
342B PHE* 3.0 17.8 + - + +
343B ALA* 3.3 14.4 - - - +
345B ARG* 1.3 80.9 - - - +
347B LYS* 1.3 61.2 + - - +
348B LEU 3.0 1.7 + - - -
349B ILE* 3.1 15.3 + - - +
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Residues in contact with LYS 347 (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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12B ALA* 3.9 28.5 + - - +
13B ILE* 2.7 31.2 + - - -
14B LYS* 4.3 2.0 - - - +
15B VAL* 3.2 29.8 - - + +
57B THR 5.2 7.6 - - - +
58B PHE* 5.0 7.2 - - + -
59B ASP* 2.9 35.1 + - - +
343B ALA 3.0 9.3 + - - +
344B GLN* 3.7 12.1 - - - +
345B ARG 3.0 0.8 + - - -
346B ALA* 1.3 75.9 - - - +
348B LEU* 1.3 64.4 + - + +
349B ILE 4.5 0.4 - - - -
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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