Contacts of the helix formed by residues 286 - 300 (chain B) in PDB entry 4BUR
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 LYS 286 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165B ASP* 3.9 22.6 + - - +
166B PRO* 5.8 5.5 - - - +
170B TYR* 3.6 11.9 - - - +
172B ARG* 4.7 2.9 - - - +
175B LEU* 4.2 8.5 - - - +
284B PHE* 5.3 1.2 - - - -
285B ARG* 1.3 86.9 - - + +
287B ILE* 1.3 65.8 + - - +
288B GLY* 3.2 6.5 - - - +
289B ASP* 2.7 38.6 + - - +
290B PHE* 3.2 5.0 + - - +
1612B FAD 5.7 3.4 - - - +
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Residues in contact with ILE 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLU* 3.9 24.7 - - + +
170B TYR* 3.5 51.1 + - + +
175B LEU* 4.2 18.8 - - + -
191B LEU* 3.8 33.4 - - + -
203B ILE* 4.7 2.7 - - + -
204B TYR* 4.1 3.8 - - + +
286B LYS* 1.3 73.4 - - - +
288B GLY* 1.3 62.7 + - - +
290B PHE* 2.9 13.6 + - + +
291B ARG* 3.0 41.8 + - + +
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Residues in contact with GLY 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LYS* 3.2 4.7 - - - +
287B ILE* 1.3 79.3 - - - +
289B ASP* 1.3 61.8 + - - +
291B ARG* 3.0 21.5 + - - +
292B SER* 3.1 17.1 + - - -
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Residues in contact with ASP 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B THR* 4.3 6.4 - - + +
283B LEU 3.4 21.0 - - - +
284B PHE* 3.5 22.9 - - + -
285B ARG* 3.0 10.0 + - - +
286B LYS* 2.7 47.9 + - - +
288B GLY* 1.3 75.6 - - - +
290B PHE* 1.3 57.1 + - - -
292B SER* 3.7 6.4 + - - -
293B LEU* 3.4 26.5 + - - +
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Residues in contact with PHE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B LEU* 3.6 34.8 - - + -
179B LEU* 3.6 36.6 - - + -
180B TRP* 3.5 47.8 - + - -
187B VAL* 4.8 3.8 - - + -
188B THR* 4.3 31.0 - - + -
191B LEU* 4.6 11.9 - - + -
284B PHE* 4.0 12.3 - - + -
286B LYS 3.2 6.4 + - - +
287B ILE* 2.9 11.1 + - + +
289B ASP* 1.3 74.6 - - - +
291B ARG* 1.3 68.8 + - + +
293B LEU* 4.9 0.4 - - - -
294B GLU* 3.3 25.8 + - + +
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Residues in contact with ARG 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLU* 4.9 7.7 + - - -
188B THR* 2.6 39.7 + - - +
189B LYS* 3.7 14.3 + - - +
191B LEU* 3.7 21.2 - - - +
287B ILE* 3.0 37.9 + - + +
288B GLY* 3.0 11.0 + - - +
290B PHE* 1.3 84.5 - - + +
292B SER* 1.3 60.2 + - - +
294B GLU* 3.9 6.9 - - - +
295B LYS* 3.0 26.2 + - - +
298B ARG* 5.0 0.2 + - - -
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Residues in contact with SER 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B THR* 5.3 5.9 + - - +
288B GLY 3.1 15.8 + - - -
289B ASP* 3.7 8.3 + - - -
291B ARG* 1.3 77.2 - - - +
293B LEU* 1.3 58.2 + - - +
295B LYS* 3.2 14.7 + - - +
296B ILE* 2.8 36.6 + - - +
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Residues in contact with LEU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B TRP* 3.9 18.6 - - + -
282B THR* 4.6 7.4 + - - +
284B PHE* 3.8 27.4 - - + -
289B ASP 3.4 16.8 + - - +
290B PHE 4.5 0.4 - - - +
291B ARG 3.3 0.4 - - - -
292B SER* 1.3 76.2 + - - +
294B GLU* 1.3 67.1 + - - +
295B LYS 3.0 1.1 - - - -
296B ILE* 3.2 8.4 + - + +
297B SER* 2.9 23.6 + - - -
303B ILE* 4.7 9.9 - - + -
315B LEU* 4.3 10.8 - - + -
319B LEU* 4.4 12.8 - - + -
393B HIS* 4.2 18.8 - - + +
395B VAL* 3.6 31.6 - - + -
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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
----------------------------------------------------------
180B TRP* 3.5 30.1 - - + -
187B VAL* 6.1 1.1 - - + -
188B THR* 3.3 30.6 - - + +
290B PHE* 3.3 27.6 + - + +
291B ARG 3.9 4.3 - - - +
293B LEU* 1.3 78.0 - - - +
295B LYS* 1.3 61.2 + - - +
297B SER* 2.9 17.8 + - - +
298B ARG* 2.6 50.7 + - - +
322B LYS* 4.7 12.9 + - - +
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Residues in contact with LYS 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 ARG 3.0 15.5 + - - +
292B SER* 3.2 16.6 - - - +
293B LEU 3.0 0.6 - - - -
294B GLU* 1.3 74.2 + - - +
296B ILE* 1.3 68.0 + - + +
298B ARG* 3.1 36.4 + - - +
299B GLU* 3.0 43.2 + - - +
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Residues in contact with ILE 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B THR* 4.9 1.1 - - - +
292B SER* 2.8 28.9 + - - +
293B LEU* 3.2 9.2 + - + +
295B LYS* 1.3 76.3 - - + +
297B SER* 1.3 58.3 + - - +
299B GLU* 2.8 31.5 + - - +
300B VAL* 3.0 39.1 + - + +
303B ILE* 4.0 8.7 - - + -
393B HIS* 3.3 54.3 - - + +
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Residues in contact with SER 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B TRP* 4.1 5.4 - - - -
293B LEU 2.9 13.8 + - - -
294B GLU* 2.9 21.3 + - - +
296B ILE* 1.3 75.7 - - - +
298B ARG* 1.3 61.5 + - - +
299B GLU 3.6 0.3 + - - -
300B VAL* 4.3 6.7 - - - +
303B ILE* 3.8 15.4 - - - +
319B LEU* 3.9 24.2 - - - -
322B LYS* 4.9 14.1 + - - +
326B LEU* 3.6 22.9 - - - +
328B THR* 5.0 0.7 + - - -
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Residues in contact with ARG 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B THR* 5.2 1.6 + - - +
294B GLU* 2.6 43.9 + - - +
295B LYS* 3.1 42.2 + - - +
296B ILE 3.0 0.2 + - - -
297B SER* 1.3 82.9 + - - +
299B GLU* 1.3 61.8 + - + +
300B VAL 4.0 0.7 - - - -
326B LEU* 5.2 8.8 - - + +
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Residues in contact with GLU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LYS* 3.0 50.8 + - + +
296B ILE* 2.8 10.9 + - - +
298B ARG* 1.3 86.5 + - + +
300B VAL* 1.3 72.6 + - - +
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Residues in contact with VAL 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ILE* 3.0 41.5 + - + +
297B SER 4.3 7.8 - - - +
298B ARG 5.3 0.3 - - - -
299B GLU* 1.3 91.5 - - - +
301B LYS* 1.3 63.4 + - - +
302B SER 3.9 7.9 - - - +
303B ILE* 3.8 22.0 - - + +
326B LEU* 5.3 0.2 - - - +
328B THR* 3.6 14.4 + - - +
392B ASP* 3.8 19.3 - - + +
393B HIS* 4.9 2.0 - - + -
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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