Contacts of the helix formed by residues 290 - 308 (chain B) in PDB entry 4BOS
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 ASP 290 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B ARG* 3.1 17.2 + - - -
273B ARG* 3.1 28.6 + - - -
286B PHE* 4.0 6.1 - - - +
287B SER* 3.1 30.0 + - - +
288B SER 3.5 0.8 - - - -
289B ASN* 1.3 71.8 - - - +
291B ASP* 1.3 58.9 + - - +
292B ILE* 3.0 13.5 + - - +
293B VAL* 2.9 37.3 + - + +
294B LEU 3.9 0.5 + - - -
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Residues in contact with ASP 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B ARG* 5.2 0.9 + - - -
289B ASN* 3.2 12.8 + - - +
290B ASP* 1.3 70.6 - - - +
292B ILE* 1.3 68.8 + - + +
294B LEU* 2.9 31.3 + - + +
295B VAL* 3.2 17.1 + - + +
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Residues in contact with ILE 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B GLY* 4.7 12.6 - - - +
273B ARG* 4.3 4.3 - - - +
290B ASP* 3.0 8.8 + - - +
291B ASP* 1.3 79.3 - - + +
293B VAL* 1.3 57.5 + - - +
295B VAL* 3.0 11.1 + - + +
296B GLN* 2.9 47.8 + - + +
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Residues in contact with VAL 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LEU* 3.6 18.8 - - + +
258B ARG* 4.0 22.2 - - - -
260B LEU* 3.8 11.7 - - + +
273B ARG* 3.3 18.1 - - - +
286B PHE* 3.6 38.8 - - + -
290B ASP* 2.9 36.9 + - + +
291B ASP 3.2 0.2 - - - -
292B ILE* 1.3 72.7 - - - +
294B LEU* 1.3 66.0 + - - +
296B GLN* 3.6 3.5 + - - -
297B ALA* 3.1 23.0 + - - +
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Residues in contact with LEU 294 (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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237B CYS* 4.3 14.8 - - + -
246B ILE* 3.8 20.3 - - + +
248B ARG* 3.5 39.3 - - - +
258B ARG* 3.7 41.3 - - - +
260B LEU* 4.4 10.8 - - + -
291B ASP* 2.9 24.5 + - + +
293B VAL* 1.3 78.1 - - - +
295B VAL* 1.3 58.4 + - + +
297B ALA* 3.3 4.9 + - - +
298B LEU* 2.9 31.8 + - - +
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Residues in contact with VAL 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B GLY 4.7 10.5 - - - +
291B ASP* 3.2 13.2 + - + +
292B ILE* 3.0 13.5 + - + +
294B LEU* 1.3 73.6 - - + +
296B GLN* 1.3 65.8 + - - +
297B ALA 3.0 1.9 + - - -
298B LEU* 3.1 6.4 + - - +
299B GLU* 2.9 47.8 + - + +
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Residues in contact with GLN 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B GLY* 4.5 9.4 - - - +
147B PRO* 2.7 46.6 + - - +
148B VAL* 3.4 9.4 + - - +
149B LEU* 3.0 39.0 + - + +
273B ARG* 2.7 48.6 + - - +
292B ILE* 2.9 29.3 + - + +
293B VAL* 3.8 2.3 - - - +
295B VAL* 1.3 73.3 - - - +
297B ALA* 1.3 60.2 + - - +
299B GLU* 3.9 14.2 - - - +
300B LEU* 4.1 2.4 - - - +
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LEU* 3.5 11.9 - - + +
239B VAL* 3.5 29.8 - - + +
246B ILE* 5.1 0.7 - - + -
260B LEU* 3.5 19.7 - - + -
271B LEU* 4.1 3.1 - - + -
293B VAL 3.1 17.2 + - - +
294B LEU 3.6 3.4 - - - +
295B VAL 3.0 0.6 - - - -
296B GLN* 1.3 76.0 - - - +
298B LEU* 1.3 65.2 + - - +
299B GLU 3.1 1.8 - - - -
300B LEU* 3.1 26.7 + - - +
301B ALA 3.8 1.4 + - - -
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Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B VAL* 4.6 2.0 - - + -
244B VAL* 4.6 3.8 - - + +
245B ARG* 4.0 22.7 - - - +
246B ILE* 3.8 30.3 - - + +
294B LEU 2.9 17.7 + - - +
295B VAL* 4.0 4.9 - - - +
297B ALA* 1.3 74.7 - - - +
299B GLU* 1.3 65.5 + - - +
301B ALA* 3.0 15.3 + - + +
302B ASP* 3.0 35.1 + - - +
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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
----------------------------------------------------------
146B GLY 3.0 28.8 + - - +
148B VAL* 3.7 26.0 + - + +
295B VAL* 2.9 39.4 + - + +
296B GLN* 3.9 8.2 - - - +
297B ALA 3.1 0.2 - - - -
298B LEU* 1.3 76.7 - - - +
300B LEU* 1.3 56.3 + - - +
302B ASP* 3.2 11.1 + - - +
303B GLU* 2.8 33.2 + - - +
306B ARG* 5.6 0.3 + - - -
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Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B VAL* 4.2 15.2 - - + +
149B LEU* 3.7 26.7 - - + +
151B ARG* 5.8 8.3 - - + +
241B THR* 4.5 3.4 - - - +
262B ILE* 3.9 19.7 - - + -
271B LEU* 4.0 30.7 - - + -
296B GLN 4.1 11.4 + - - +
297B ALA 3.1 14.9 + - - +
299B GLU* 1.3 77.5 - - - +
301B ALA* 1.3 58.3 + - - +
303B GLU* 3.6 6.3 + - + +
304B ALA* 3.1 25.8 + - - +
307B ARG* 4.7 2.8 + - - -
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Residues in contact with ALA 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B VAL* 3.7 23.7 - - + +
240B ASP 3.9 16.4 - - - +
241B THR* 4.1 12.2 - - - +
244B VAL* 4.0 18.5 - - + +
297B ALA 3.8 0.6 + - - -
298B LEU* 3.0 15.9 + - + +
300B LEU* 1.3 78.2 - - - +
302B ASP* 1.3 65.1 + - - +
304B ALA* 3.2 3.2 + - - +
305B ARG* 3.1 23.4 + - - +
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Residues in contact with ASP 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B VAL* 3.6 8.9 - - - +
298B LEU* 3.0 29.8 + - - +
299B GLU* 3.7 13.4 - - + +
301B ALA* 1.3 76.2 - - - +
303B GLU* 1.3 56.8 + - - +
305B ARG* 3.2 29.5 + - - +
306B ARG* 3.0 52.0 + - - +
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Residues in contact with GLU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B GLU 2.8 21.6 + - - +
300B LEU* 3.9 6.5 - - - +
302B ASP* 1.3 70.2 - - - +
304B ALA* 1.3 65.2 + - - +
306B ARG* 3.3 32.9 + - - +
307B ARG* 3.0 51.8 + - - +
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Residues in contact with ALA 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B THR* 4.2 22.2 - - + -
300B LEU 3.1 16.3 + - - +
301B ALA 3.2 5.6 + - - +
303B GLU* 1.3 77.9 - - - +
305B ARG* 1.3 62.0 + - - +
307B ARG* 3.1 37.4 + - - +
308B ARG* 3.2 26.8 + - - +
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Residues in contact with ARG 305 (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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244B VAL* 3.3 31.0 + - + +
301B ALA 3.1 12.1 + - - +
302B ASP* 3.2 29.7 + - - +
304B ALA* 1.3 78.0 - - - +
306B ARG* 1.3 63.6 + - - +
308B ARG* 3.0 41.7 + - + +
309B GLN* 3.5 29.4 + - + +
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Residues in contact with ARG 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B GLU 5.6 0.4 + - - -
302B ASP* 3.0 41.1 + - - +
303B GLU* 3.4 36.7 + - - +
304B ALA 3.2 0.2 - - - -
305B ARG* 1.3 76.6 - - - +
307B ARG* 1.3 61.4 + - - +
309B GLN* 3.2 32.4 + - - +
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Residues in contact with ARG 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B LEU 4.7 3.0 + - - -
303B GLU* 3.0 52.3 + - - +
304B ALA* 3.1 36.8 + - - +
306B ARG* 1.3 73.6 - - - +
308B ARG* 1.3 60.3 + - + +
309B GLN 3.1 13.6 + - - +
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Residues in contact with ARG 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B THR* 2.4 39.4 + - - -
242B GLN* 3.6 17.6 + - - +
244B VAL* 4.2 3.0 - - - +
304B ALA* 3.2 18.3 + - - +
305B ARG* 3.0 38.0 + - + +
307B ARG* 1.3 75.8 - - + +
309B GLN* 1.3 61.8 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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