Contacts of the helix formed by residues 270 - 288 (chain B) in PDB entry 3SF4
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 270 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ALA* 2.8 17.4 + - - +
266B ARG* 5.7 0.2 - - - -
268B LEU* 3.1 15.1 + - + +
269B LYS* 1.3 74.8 - - - +
271B ARG* 1.3 60.9 + - - +
272B ALA* 3.3 8.0 + - - +
273B VAL* 3.0 44.5 + - + +
274B GLU* 3.2 25.1 + - - +
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Residues in contact with ARG 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ARG* 5.8 0.2 - - - +
269B LYS* 3.7 9.6 + - - +
270B ASP* 1.3 72.2 + - - +
272B ALA* 1.3 68.0 + - - +
274B GLU* 2.8 38.5 + - - +
275B ALA* 2.9 24.6 + - - +
304B ILE* 3.4 31.9 - - + +
307B GLU* 2.9 41.9 + - - +
308B LEU* 4.3 14.1 - - + -
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Residues in contact with ALA 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ASP* 3.3 7.0 + - - +
271B ARG* 1.3 77.4 - - - +
273B VAL* 1.3 60.5 + - + +
275B ALA* 3.0 8.5 + - - +
276B GLN* 2.9 26.9 + - - +
308B LEU* 3.9 19.7 - - + +
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Residues in contact with VAL 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ARG* 3.7 51.8 - - + +
239B SER* 5.5 0.2 - - - +
265B ALA* 3.8 12.1 - - + -
270B ASP* 3.0 33.7 + - + +
272B ALA* 1.3 78.8 - - + +
274B GLU* 1.3 63.1 + - - +
276B GLN* 3.3 14.1 + - - +
277B SER* 2.9 31.5 + - - +
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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
----------------------------------------------------------
262B LEU* 3.7 15.7 - - + +
265B ALA* 3.7 12.3 - - + +
266B ARG* 2.7 44.0 + - + +
270B ASP 3.2 19.8 + - - +
271B ARG* 2.8 45.2 + - - +
273B VAL* 1.3 77.4 - - - +
275B ALA* 1.3 61.9 + - - +
277B SER* 3.3 6.8 + - - -
278B CYS* 3.1 22.3 + - - -
304B ILE* 3.5 15.5 - - + +
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Residues in contact with ALA 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ARG 2.9 5.4 + - - +
272B ALA* 3.4 10.1 - - - +
274B GLU* 1.3 75.1 - - - +
276B GLN* 1.3 66.0 + - - +
278B CYS* 3.0 7.0 + - - +
279B TYR 2.9 19.1 + - - -
301B HIS* 3.2 29.0 - - + +
304B ILE* 3.5 37.2 - - + +
305B ALA* 4.9 2.7 - - - +
308B LEU* 5.8 0.7 - - + -
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Residues in contact with GLN 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ARG* 4.1 9.0 + - - -
239B SER* 4.8 4.2 + - - -
272B ALA 2.9 13.6 + - - +
273B VAL* 3.5 16.3 - - - +
275B ALA* 1.3 75.9 - - - +
277B SER* 1.3 63.1 + - - +
279B TYR* 3.1 9.5 + - + +
280B SER* 2.9 30.7 + - - +
301B HIS* 4.9 1.6 - - - -
38E MET* 3.5 29.9 - - + +
40E GLU* 3.9 18.9 + - - +
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Residues in contact with SER 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B SER* 5.4 0.5 + - - -
258B TYR* 4.2 5.3 - - - +
261B THR* 3.0 31.4 + - - -
262B LEU* 3.8 24.6 + - - -
273B VAL* 2.9 18.0 + - - +
274B GLU* 3.4 9.1 - - - -
276B GLN* 1.3 76.9 + - - +
278B CYS* 1.3 53.1 + - - +
280B SER* 3.0 9.9 + - - -
281B LEU* 2.8 38.7 + - - +
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Residues in contact with CYS 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B LEU* 3.9 17.2 - - - +
266B ARG* 4.5 2.7 - - - -
274B GLU* 3.1 18.0 + - - +
275B ALA* 3.0 10.6 + - - +
277B SER* 1.3 80.3 - - - +
279B TYR* 1.3 56.4 + - - +
281B LEU* 3.3 6.5 + - - -
282B GLY* 2.9 23.2 + - - -
297B TYR* 3.3 35.4 - - - +
300B LYS* 3.7 33.9 - - - -
301B HIS* 4.0 8.5 - - + +
304B ILE* 5.1 2.2 - - - -
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Residues in contact with TYR 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ALA 2.9 12.4 + - - +
276B GLN* 3.5 10.5 - - + +
278B CYS* 1.3 73.7 - - - +
280B SER* 1.3 65.3 + - - +
282B GLY* 3.3 1.4 + - - +
283B ASN* 2.8 51.5 + - - -
298B HIS* 3.5 18.1 - + - -
301B HIS* 3.4 34.9 - + + +
316B ARG* 3.0 54.9 + - + +
317B ALA* 4.1 0.4 - - - -
319B TRP* 5.2 0.9 - - - -
320B SER* 2.6 29.9 + - - -
27E SER* 4.8 6.8 + - - -
31E TRP* 3.9 19.5 - + + -
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Residues in contact with SER 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B ASN* 5.0 1.9 + - - -
258B TYR* 3.9 28.2 - - - -
276B GLN* 2.9 21.4 + - - +
277B SER* 3.4 9.4 - - - -
279B TYR* 1.3 77.4 - - - +
281B LEU* 1.3 56.7 + - - +
283B ASN* 3.4 2.6 + - - +
284B THR* 2.8 34.8 + - - -
31E TRP* 3.7 31.6 + - - +
35E LEU* 5.1 2.4 - - - +
38E MET* 6.0 1.6 - - - +
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B SER* 3.6 22.7 - - - +
258B TYR* 3.5 34.8 - - + +
259B LYS* 4.1 8.1 - - + +
262B LEU* 3.9 17.5 - - + -
277B SER 2.8 19.5 + - - +
278B CYS 3.7 5.6 - - - +
280B SER* 1.3 77.1 - - - +
282B GLY* 1.3 61.6 + - - +
284B THR* 3.9 2.6 - - - -
285B TYR* 3.0 50.9 + - + -
297B TYR* 3.4 38.6 - - + -
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Residues in contact with GLY 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B CYS 2.9 15.7 + - - -
279B TYR 3.3 0.4 + - - -
280B SER 3.2 0.4 - - - -
281B LEU* 1.3 78.7 - - - +
283B ASN* 1.3 59.8 + - - +
285B TYR 3.4 0.9 + - - -
286B THR* 3.1 24.9 + - - -
294B ALA* 3.6 12.2 - - - +
297B TYR* 3.8 10.0 - - - +
298B HIS* 3.3 27.1 - - - -
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Residues in contact with ASN 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B TYR* 2.8 53.7 + - - +
280B SER 3.8 0.2 - - - +
282B GLY* 1.3 73.0 - - - +
284B THR* 1.3 65.7 + - - +
286B THR* 3.1 9.0 + - - -
287B LEU* 3.0 27.6 + - - +
298B HIS* 3.8 9.7 + - - -
320B SER* 4.8 3.1 + - - -
27E SER* 4.0 2.1 + - - +
28E VAL* 3.4 25.6 + - + +
31E TRP* 3.3 50.0 - - + +
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Residues in contact with THR 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ILE* 3.4 16.0 - - + +
251B PHE* 3.5 27.6 - - + +
255B SER* 3.9 21.5 - - - +
258B TYR* 3.3 20.4 - - - -
280B SER 2.8 21.6 + - - -
281B LEU* 3.9 7.6 - - - -
283B ASN* 1.3 78.9 - - - +
285B TYR* 1.3 57.9 + - - +
287B LEU* 3.2 12.8 + - - +
288B LEU* 2.9 29.8 + - + +
31E TRP* 3.8 1.6 - - - -
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Residues in contact with TYR 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B GLU* 5.3 4.3 + - - -
255B SER* 3.9 14.4 + - - -
259B LYS* 3.0 32.1 + - - -
281B LEU* 3.0 40.7 + - + +
282B GLY 4.0 1.6 - - - +
284B THR* 1.3 74.5 - - - +
286B THR* 1.3 60.3 + - - +
288B LEU* 3.2 23.8 + - + -
289B GLN 2.9 7.3 + - - -
290B ASP* 2.8 52.4 + - + +
293B LYS* 3.8 34.1 + - + -
294B ALA* 4.0 10.3 - - - +
297B TYR* 3.5 32.8 - + - -
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Residues in contact with THR 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B GLY 3.1 15.3 + - - -
283B ASN* 3.1 10.2 + - - -
285B TYR* 1.3 75.6 - - - +
287B LEU* 1.3 57.3 + - - +
289B GLN* 2.7 27.4 + - - +
291B TYR* 4.0 26.8 + - + +
294B ALA* 3.7 11.8 - - - +
298B HIS* 4.7 4.3 + - - -
324B ALA* 5.3 4.7 - - - +
24E GLN* 4.0 13.7 + - - +
25E VAL* 5.5 6.1 - - + -
28E VAL* 3.5 27.3 - - + +
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ILE* 4.1 7.0 - - + -
251B PHE* 3.6 51.8 - - + -
283B ASN 3.0 17.7 + - - +
284B THR* 3.4 8.1 - - - +
286B THR* 1.3 78.1 - - - +
288B LEU* 1.3 59.1 + - - +
289B GLN* 3.4 8.1 + - - +
20E LEU* 4.2 12.6 - - + +
24E GLN* 3.0 36.3 + - + +
28E VAL* 3.8 16.8 - - + -
31E TRP* 4.1 22.0 - - + -
32E MET* 4.4 12.1 - - + -
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Residues in contact with LEU 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B PHE* 3.6 44.0 - - + +
252B GLU* 4.1 25.8 - - + +
255B SER* 4.5 2.5 - - - +
284B THR* 2.9 21.6 + - + +
285B TYR* 3.6 33.7 - - + +
286B THR 3.1 0.8 - - - -
287B LEU* 1.3 75.8 - - - +
289B GLN* 1.3 71.0 + - - +
290B ASP* 3.2 5.1 + - + +
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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