Contacts of the helix formed by residues 293 - 303 (chain B) in PDB entry 3L73
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 293 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B LEU 2.9 20.1 + - - -
280B GLY* 3.0 19.4 + - - -
290B SER* 3.6 18.5 + - - -
291B VAL 2.9 3.8 - - - -
292B THR* 1.3 77.0 - - - +
294B LYS* 1.3 58.7 + - - +
295B LEU* 4.4 0.2 - - - +
296B TYR* 3.2 25.8 + - - +
297B GLN* 2.9 33.8 + - - +
309B ALA 5.1 1.6 + - - -
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Residues in contact with LYS 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B VAL* 3.4 27.5 + - + +
279B LEU* 3.2 9.3 + - + +
291B VAL 5.0 2.0 - - - +
292B THR 5.0 2.9 - - - +
293B SER* 1.3 69.7 - - - +
295B LEU* 1.3 57.7 + - - +
297B GLN* 3.6 4.9 - - - +
298B GLY* 2.6 34.7 + - - -
343B GLN* 3.5 27.1 - - - +
347B ALA* 5.9 5.2 - - + -
351B GLY 3.0 27.2 + - - +
352B VAL* 4.2 1.0 - - + +
353B THR* 4.3 2.2 + - - +
356B ASP* 2.8 40.0 + - - -
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B LEU* 2.7 41.5 + - + +
280B GLY 4.9 0.7 - - - +
293B SER* 4.4 0.7 - - - +
294B LYS* 1.3 74.1 - - - +
296B TYR* 1.3 64.2 + - - +
298B GLY* 3.7 0.7 - - - -
299B VAL* 3.0 26.5 + - + +
309B ALA* 4.3 10.1 - - + +
310B SER* 3.4 38.4 - - - +
311B ALA* 4.0 5.2 - - - +
324B PHE* 3.7 14.6 - - + -
340B ALA* 3.4 47.3 - - + +
343B GLN* 4.3 10.9 - - + +
344B LEU* 5.5 0.9 - - + -
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Residues in contact with TYR 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B PRO* 5.9 3.8 - - + -
288B GLY 4.8 7.9 + - - -
289B SER* 5.2 9.2 - - - -
290B SER* 4.0 35.0 - - - +
293B SER* 3.2 24.4 + - - +
294B LYS 3.3 0.6 - - - -
295B LEU* 1.3 77.9 - - - +
297B GLN* 1.3 56.5 + - - +
299B VAL* 2.9 9.2 + - - +
300B ALA* 2.8 36.5 + - + -
307B PHE* 3.5 33.6 + + - -
308B ASP* 3.9 17.5 - - - -
309B ALA* 4.4 19.6 + - - +
52I ARG* 4.0 36.4 + - - +
56I SER* 4.9 9.4 - - - -
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Residues in contact with GLN 297 (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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289B SER* 3.2 21.0 + - - -
290B SER 2.9 28.1 + - - +
291B VAL* 3.2 36.8 - - + +
293B SER 2.9 15.6 + - - +
294B LYS* 3.7 4.7 - - - +
296B TYR* 1.3 78.4 - - - +
298B GLY* 1.3 62.3 + - - +
300B ALA* 3.5 12.2 - - - +
301B LYS* 3.1 46.5 + - - +
343B GLN* 5.8 0.2 - - - +
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Residues in contact with GLY 298 (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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294B LYS 2.6 21.0 + - - -
295B LEU 3.7 1.1 - - - -
296B TYR 3.0 0.2 - - - -
297B GLN* 1.3 74.6 - - - +
299B VAL* 1.3 61.1 + - - +
301B LYS* 3.2 20.8 + - - +
302B ALA* 3.2 10.9 + - - +
339B ALA* 4.4 5.9 - - - +
343B GLN* 3.7 23.5 + - - -
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Residues in contact with VAL 299 (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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295B LEU 3.0 16.2 - - - +
296B TYR 2.9 5.5 + - - +
298B GLY* 1.3 72.4 - - - +
300B ALA* 1.3 67.3 + - - +
302B ALA* 2.9 10.0 + - - +
303B THR* 3.0 15.0 + - + +
307B PHE* 3.5 22.4 - - + -
309B ALA* 4.1 15.5 - - + -
336B VAL* 3.3 42.2 - - + +
339B ALA* 3.9 8.3 - - + -
340B ALA* 3.9 28.0 - - + +
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Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B TYR* 2.8 17.7 + - + +
297B GLN* 3.5 21.5 - - - +
298B GLY 3.2 0.2 - - - -
299B VAL* 1.3 76.7 - - - +
301B LYS* 1.3 57.8 + - + +
303B THR 2.7 26.9 - - - +
307B PHE* 3.6 16.5 - - + -
52I ARG* 3.9 21.5 + - - +
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Residues in contact with LYS 301 (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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297B GLN* 3.1 35.3 + - - +
298B GLY* 3.2 9.1 + - - +
300B ALA* 1.3 76.0 - - + +
302B ALA* 1.3 61.9 + - - +
303B THR 4.2 1.6 - - - +
343B GLN* 5.9 1.3 - - - -
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Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B GLY 3.2 3.4 + - - +
299B VAL* 2.9 12.4 + - + +
301B LYS* 1.3 82.2 - - - +
303B THR* 1.3 59.0 + - - +
304B THR* 5.2 0.5 + - - -
335B GLU* 2.9 25.2 - - + +
339B ALA* 3.5 31.0 - - + -
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Residues in contact with THR 303 (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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299B VAL* 3.0 16.7 + - + +
300B ALA 2.7 23.4 - - - +
301B LYS 4.2 1.7 - - - +
302B ALA* 1.3 75.7 - - - +
304B THR* 1.3 72.0 + - - +
305B GLN 3.4 13.6 + - - +
307B PHE* 3.5 33.9 - - + -
332B HIS* 4.0 19.2 - - - +
335B GLU* 3.1 15.0 + - - -
336B VAL* 3.8 24.0 - - + -
52I ARG* 4.0 2.9 + - - -
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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