Contacts of the helix formed by residues 271 - 288 (chain B) in PDB entry 3SN5
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 271 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ARG* 4.5 1.3 + - - +
269B THR 3.9 0.8 + - - -
270B PHE* 1.3 76.4 - - - +
272B ASP* 1.3 66.3 - - - +
273B LEU* 3.4 11.6 + - - +
274B GLU* 3.0 56.9 + - - +
275B LYS* 3.0 22.5 + - - +
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Residues in contact with ASP 272 (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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243B ARG* 3.5 27.3 + - + +
244B HIS* 5.3 3.1 + - - +
271B ASP* 1.3 73.1 - - - +
273B LEU* 1.3 61.4 + - - +
275B LYS* 3.5 18.0 + - - +
276B ALA* 3.2 19.8 + - - +
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Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B GLU* 3.8 20.2 - - + +
239B ALA* 4.2 23.6 - - + -
240B GLU* 3.8 13.0 - - + +
243B ARG* 3.6 32.6 - - - +
271B ASP* 3.3 8.7 + - - +
272B ASP* 1.3 74.0 - - - +
274B GLU* 1.4 61.3 + - + +
276B ALA* 3.2 7.2 + - + +
277B LYS* 3.0 43.3 + - + +
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Residues in contact with GLU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B GLY 5.2 2.7 - - - +
111B HIS* 4.3 9.3 - - + +
112B ARG* 2.9 70.4 + - - +
270B PHE* 3.5 18.5 - - + -
271B ASP* 3.0 46.1 + - - +
273B LEU* 1.4 71.0 - - + +
275B LYS* 1.3 65.8 + - - +
277B LYS* 3.2 12.0 + - + +
278B THR* 3.0 27.7 + - - +
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Residues in contact with LYS 275 (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 HIS* 3.9 15.5 - - + +
264B ASN* 3.4 46.2 + - + +
265B ASP* 2.8 31.2 + - - +
268B SER* 4.1 4.1 + - - -
270B PHE* 3.3 29.9 + - + -
271B ASP 3.0 16.9 + - - +
272B ASP* 3.5 19.1 + - - +
274B GLU* 1.3 75.0 - - - +
276B ALA* 1.4 61.1 + - - +
278B THR* 2.6 25.6 + - - -
279B HIS* 3.3 12.3 - - - -
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Residues in contact with ALA 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ALA* 3.0 31.5 - - + +
242B LEU* 3.4 28.6 - - - +
243B ARG* 3.8 9.8 - - + +
272B ASP 3.2 10.9 + - - +
273B LEU* 3.3 12.1 - - + +
275B LYS* 1.4 78.0 - - - +
277B LYS* 1.3 57.8 + - - +
279B HIS* 3.2 8.0 + - - +
280B LEU* 3.1 21.7 + - - +
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Residues in contact with LYS 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B PHE* 3.4 23.7 - - + +
110B GLY* 3.0 26.8 + - - +
111B HIS* 4.3 9.9 - - + -
235B ARG* 3.8 10.3 - - - +
236B GLU* 3.5 37.5 + - - -
239B ALA* 4.0 15.7 - - + -
273B LEU* 3.0 33.1 + - + +
274B GLU* 3.2 11.2 + - + +
276B ALA* 1.3 73.2 - - - +
278B THR* 1.4 59.5 + - - +
280B LEU* 3.0 25.3 + - + +
281B VAL* 3.0 20.0 + - - +
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Residues in contact with THR 278 (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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111B HIS* 4.8 8.5 - - + -
114B ILE* 4.7 5.4 - - + -
260B ARG* 3.1 16.6 + - - +
264B ASN* 3.1 20.8 + - - +
270B PHE* 4.3 22.4 - - + -
274B GLU 3.0 20.9 + - - +
275B LYS* 2.6 19.5 + - - -
277B LYS* 1.4 75.9 - - - +
279B HIS* 1.3 60.0 + - - +
281B VAL* 3.6 12.6 - - - +
282B VAL* 3.5 22.5 + - - +
1429B K2B 4.0 20.0 - - + +
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Residues in contact with HIS 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B PHE* 3.4 23.8 - - + -
242B LEU* 3.5 30.1 - - + -
244B HIS* 3.0 27.5 + + - -
247B LEU* 3.6 9.9 - - + -
257B ILE* 3.9 17.1 - - + +
260B ARG* 4.0 21.2 + - + +
261B MET* 3.6 19.1 - - + +
264B ASN* 3.5 17.7 + - - -
275B LYS 3.3 15.0 + - - -
276B ALA 3.2 6.4 + - - +
277B LYS 3.2 0.4 - - - -
278B THR* 1.3 76.3 - - - +
280B LEU* 1.4 58.8 + - - +
282B VAL* 3.3 6.5 + - - +
283B LEU 2.9 22.7 + - - -
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Residues in contact with LEU 280 (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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109B PHE* 3.9 16.8 - - + +
209B PHE* 5.1 3.4 - - + -
212B PHE* 4.5 10.1 - - + -
235B ARG* 3.5 42.4 - - + +
238B LEU* 3.9 31.4 - - + -
239B ALA* 4.7 3.6 - - - +
242B LEU* 3.7 10.5 - - + +
276B ALA 3.1 11.5 + - - +
277B LYS* 3.0 21.6 + - + +
279B HIS* 1.4 74.1 - - - +
281B VAL* 1.4 63.6 + - - +
283B LEU* 3.2 15.7 + - + -
284B TRP* 2.9 23.3 + - - +
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Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B SER* 3.5 20.4 - - - +
109B PHE* 3.6 32.2 - - + -
111B HIS* 3.8 11.7 - - + +
277B LYS 3.0 15.5 + - - +
278B THR* 3.6 9.9 - - - +
279B HIS 3.3 0.4 - - - -
280B LEU* 1.4 75.4 - - - +
282B VAL* 1.4 56.5 + - - +
284B TRP* 3.4 3.5 + - - +
285B ALA* 2.9 29.3 + - - +
1429B K2B 3.4 50.5 - - + -
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Residues in contact with VAL 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B PHE* 4.0 29.4 - - + -
187B ILE* 4.3 9.2 - - + -
256B LEU* 3.8 20.6 - - + -
257B ILE* 3.7 25.8 - - + -
260B ARG* 4.5 13.9 - - - -
278B THR 3.5 11.6 + - - +
279B HIS 3.3 8.1 + - - +
280B LEU 3.3 0.2 - - - -
281B VAL* 1.4 74.0 - - - +
283B LEU* 1.4 64.2 + - - +
285B ALA* 3.4 7.2 + - - +
286B SER* 2.9 22.7 + - - -
601B HEM 4.8 7.6 - - + -
1429B K2B 4.8 5.6 - - + -
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Residues in contact with LEU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B PHE* 4.2 5.6 - - + -
184B TYR* 3.7 37.0 - - + -
187B ILE* 6.2 0.2 - - + -
188B PHE* 3.7 23.3 - - + -
209B PHE* 4.1 12.8 - - + -
238B LEU* 4.0 27.1 - - + -
242B LEU* 4.3 7.4 - - + -
279B HIS 2.9 10.8 + - - +
280B LEU* 3.2 20.6 + - + +
282B VAL* 1.4 74.2 - - - +
284B TRP* 1.4 61.2 + - - +
286B SER* 2.7 22.2 + - - +
287B GLN* 3.1 35.2 + - + +
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Residues in contact with TRP 284 (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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109B PHE* 3.6 25.6 - + + -
209B PHE* 3.7 28.9 - + + -
212B PHE* 4.0 20.2 - + + -
213B ASP* 3.0 20.4 + - - -
216B PHE* 3.4 41.3 - + - -
280B LEU* 2.9 15.8 + - + +
281B VAL 3.6 1.3 - - - +
283B LEU* 1.4 74.0 - - - +
285B ALA* 1.4 65.7 + - - +
287B GLN 3.0 0.9 + - - -
288B ALA* 2.8 51.4 + - + +
289B ASN* 5.1 1.6 - - - -
483B ARG* 3.7 11.2 - - - -
486B LEU* 4.3 11.4 - - + -
1429B K2B 3.8 49.6 - - + -
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Residues in contact with ALA 285 (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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281B VAL 2.9 20.0 + - - +
282B VAL* 3.5 7.4 - - - +
284B TRP* 1.4 83.6 - - - +
286B SER* 1.3 59.5 + - - +
287B GLN 3.6 0.2 + - - -
288B ALA 4.6 1.7 + - - -
289B ASN* 4.8 8.1 + - - +
601B HEM 3.4 46.9 + - + +
1429B K2B 3.6 29.8 - - + +
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Residues in contact with SER 286 (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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183B GLY* 5.4 0.8 + - - -
187B ILE* 4.3 22.8 - - - +
282B VAL* 2.9 14.6 + - - -
283B LEU* 2.7 24.6 + - - +
285B ALA* 1.3 75.8 - - - +
287B GLN* 1.4 67.8 + - - +
290B THR* 2.9 23.2 + - - +
449B PHE* 5.7 1.3 - - - -
453B GLU* 4.3 3.5 - - - +
601B HEM 3.6 34.4 - - - +
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Residues in contact with GLN 287 (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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179B MET* 3.5 6.5 - - - +
180B PHE* 3.1 53.4 + - + -
183B GLY* 3.5 10.6 - - - -
184B TYR* 3.4 16.6 - - - +
209B PHE* 3.8 17.7 - - + -
283B LEU* 3.1 29.4 + - + +
284B TRP 3.0 1.8 + - - -
286B SER* 1.4 84.1 + - - +
288B ALA* 1.4 65.5 + - - +
289B ASN 3.2 3.5 + - - -
290B THR* 4.0 3.0 - - - +
291B ILE* 3.1 44.1 + - + +
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B PHE* 4.2 7.3 - - + -
213B ASP* 4.4 9.7 - - - +
284B TRP* 2.8 64.2 + - + +
285B ALA 5.3 0.4 - - - +
287B GLN* 1.4 70.8 - - - +
289B ASN* 1.3 62.8 + - - +
291B ILE* 5.4 0.9 - - - -
292B PRO* 3.3 19.8 - - - +
483B ARG* 4.7 8.1 + - - +
486B LEU 5.8 0.2 - - - +
488B ILE 5.0 1.0 - - - +
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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
------------------------------------------------------------
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