Contacts of the helix formed by residues 290 - 308 (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 290 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B TYR* 2.8 34.0 + - + +
288B LEU* 3.2 5.8 - - + +
289B GLN* 1.3 71.3 - - - +
291B TYR* 1.3 62.0 + - - +
292B GLU* 3.5 11.6 + - - +
293B LYS* 3.2 44.9 + - - +
294B ALA* 3.2 15.6 + - - +
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Residues in contact with TYR 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B THR* 4.0 35.7 + - + +
289B GLN* 3.6 40.5 + - + +
290B ASP* 1.3 71.4 - - - +
292B GLU* 1.3 59.8 + - - +
294B ALA* 3.3 6.8 - - + +
295B ILE* 2.9 35.8 + - - +
324B ALA* 4.3 8.7 - - - +
327B ALA* 3.4 41.3 - - + -
328B LEU* 3.8 24.7 - - + -
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Residues in contact with GLU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ASP* 3.2 9.0 - - - +
291B TYR* 1.3 78.9 - - - +
293B LYS* 1.3 62.2 + - + +
295B ILE* 3.6 9.5 + - - +
296B ASP* 3.0 26.9 + - - +
328B LEU* 4.0 26.5 - - + +
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Residues in contact with LYS 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B LYS* 4.8 7.3 - - - +
285B TYR* 3.8 46.0 + - + +
290B ASP* 3.2 28.9 + - - +
291B TYR 3.2 0.4 - - - -
292B GLU* 1.3 76.1 - - + +
294B ALA* 1.3 66.8 + - - +
296B ASP* 3.4 11.5 + - - +
297B TYR* 3.2 36.0 + - + +
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Residues in contact with ALA 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B GLY* 3.6 25.4 - - - +
285B TYR* 4.0 3.3 - - - +
286B THR* 3.7 17.7 - - - +
290B ASP 3.2 12.9 + - - +
291B TYR* 3.1 15.4 + - + +
293B LYS* 1.3 79.8 - - - +
295B ILE* 1.3 63.4 + - - +
297B TYR* 3.9 0.5 - - - -
298B HIS* 3.0 35.2 + - + -
324B ALA* 4.7 7.2 - - + -
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Residues in contact with ILE 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B TYR 2.9 15.4 + - - +
292B GLU* 3.7 7.2 - - - +
294B ALA* 1.3 75.8 - - - +
296B ASP* 1.3 55.6 + - - +
298B HIS* 3.0 2.8 + - - +
299B LEU* 2.7 51.5 + - + +
321B LEU* 4.3 6.1 - - + -
324B ALA* 3.2 43.3 - - + +
325B TYR* 3.2 47.8 - - + +
328B LEU* 4.0 15.3 - - + -
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Residues in contact with ASP 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B GLU* 3.0 16.8 + - - +
293B LYS* 3.4 16.4 + - - +
294B ALA 3.3 0.2 - - - -
295B ILE* 1.3 83.0 - - - +
297B TYR* 1.3 66.0 + - + +
299B LEU* 3.3 10.5 + - - +
300B LYS* 3.1 41.3 + - - +
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Residues in contact with TYR 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B LYS* 3.8 21.7 - - - +
262B LEU* 4.1 12.3 - - + +
278B CYS* 3.3 35.9 - - - +
281B LEU* 3.4 32.0 - - + +
282B GLY* 3.8 8.3 - - - +
285B TYR* 3.5 33.7 - + - -
293B LYS* 3.2 32.8 + - + +
296B ASP* 1.3 83.0 - - + +
298B HIS* 1.3 61.3 + - - +
300B LYS* 4.0 26.0 - - + -
301B HIS* 3.1 18.0 + - - +
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Residues in contact with HIS 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B TYR* 3.5 39.1 - + - -
282B GLY* 3.3 24.8 + - - -
283B ASN* 3.6 15.5 + - - -
286B THR* 4.7 3.7 + - - -
294B ALA* 3.0 31.6 + - + +
295B ILE 3.6 2.9 - - - +
297B TYR* 1.3 75.1 - - - +
299B LEU* 1.3 65.8 + - - +
301B HIS* 3.3 6.2 + - - +
302B LEU* 2.9 22.7 + - - +
317B ALA* 4.6 3.7 + - - +
320B SER* 3.3 35.7 - - - -
321B LEU* 3.8 22.4 - - + +
324B ALA* 5.0 4.0 - - + -
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Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ILE* 2.7 38.3 + - + +
296B ASP* 3.6 10.1 - - - +
298B HIS* 1.3 77.4 - - - +
300B LYS* 1.3 63.5 + - + +
302B LEU* 2.9 12.9 + - + +
303B ALA* 2.9 25.1 + - - +
321B LEU* 4.0 22.9 - - + -
325B TYR* 4.1 8.1 - - - +
337B PHE* 4.3 14.1 - - + -
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Residues in contact with LYS 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ARG* 4.1 16.5 - - - +
278B CYS* 3.7 27.6 - - - -
296B ASP* 3.1 27.9 + - - +
297B TYR* 3.8 25.1 - - + +
299B LEU* 1.3 75.6 - - + +
301B HIS* 1.3 62.6 + - - +
303B ALA* 3.5 6.5 + - - +
304B ILE* 3.1 31.0 + - + +
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Residues in contact with HIS 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ALA* 3.2 42.5 - - + +
276B GLN* 4.4 1.3 - - - -
278B CYS* 4.0 6.2 - - + +
279B TYR* 3.4 38.1 - + + +
297B TYR 3.1 19.1 + - - +
298B HIS* 3.6 5.6 + - - +
299B LEU 3.2 0.2 - - - -
300B LYS* 1.3 77.1 - - - +
302B LEU* 1.3 57.2 + - - +
304B ILE* 3.9 1.0 - - - +
305B ALA* 2.9 32.7 + - + +
310B ASP* 5.4 2.2 + - - -
313B GLY* 3.1 34.5 - - - -
316B ARG* 4.9 1.1 - - + -
317B ALA* 3.6 12.7 - - + +
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Residues in contact with LEU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B HIS 2.9 12.4 + - - +
299B LEU* 2.9 16.5 + - + +
301B HIS* 1.3 74.6 + - - +
303B ALA* 1.3 67.3 + - - +
305B ALA* 3.1 4.2 + - - +
306B GLN* 2.8 46.9 + - - +
314B GLU* 3.5 33.9 - - + +
317B ALA* 3.7 22.9 - - + -
318B CYS* 4.4 8.1 - - - -
321B LEU* 3.9 8.3 - - + -
337B PHE* 3.8 30.5 - - + -
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Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ARG* 5.8 0.4 - - - -
299B LEU 2.9 14.8 + - - +
300B LYS* 3.7 8.5 - - - +
302B LEU* 1.3 78.3 - - - +
304B ILE* 1.3 59.2 + - + +
306B GLN* 3.2 14.9 + - - +
307B GLU* 2.9 26.9 + - - +
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Residues in contact with ILE 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ARG* 3.4 39.5 - - + +
274B GLU* 3.5 41.7 - - + +
275B ALA* 3.5 32.1 - - + +
278B CYS* 5.1 3.8 - - - -
300B LYS* 3.1 20.2 + - + +
301B HIS 4.0 0.2 - - - +
303B ALA* 1.3 77.8 - - + +
305B ALA* 1.3 63.1 + - - +
307B GLU* 2.9 18.9 + - - +
308B LEU* 3.0 23.3 + - + +
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Residues in contact with ALA 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ALA* 5.5 1.6 - - + -
301B HIS* 2.9 37.4 + - + +
302B LEU* 3.4 6.7 - - - +
304B ILE* 1.3 78.1 - - - +
306B GLN* 1.3 62.5 + - - +
308B LEU* 3.3 3.9 + - - +
309B ASN 3.1 2.6 + - - -
310B ASP* 2.8 53.6 + - + +
313B GLY 4.4 7.0 - - - +
314B GLU* 4.4 4.9 - - + +
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Residues in contact with GLN 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B LEU* 2.8 39.3 + - - +
303B ALA* 3.5 15.4 - - - +
305B ALA* 1.3 74.0 - - - +
307B GLU* 1.3 65.7 - - - +
309B ASN* 2.9 23.9 + - - +
314B GLU* 3.3 40.5 + - + +
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Residues in contact with GLU 307 (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 45.9 + - - +
303B ALA 2.9 12.6 + - - +
304B ILE* 3.1 12.1 - - - +
306B GLN* 1.3 77.5 - - - +
308B LEU* 1.3 77.7 + - + +
309B ASN* 3.4 1.5 + - - +
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Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ARG* 4.3 8.3 - - + -
272B ALA* 3.9 37.2 - - + +
275B ALA* 5.8 0.7 - - + -
304B ILE* 3.0 24.3 + - + +
305B ALA* 3.3 4.7 + - - +
306B GLN 3.1 0.2 - - - -
307B GLU* 1.3 99.5 - - - +
309B ASN* 1.3 71.7 + - - +
310B ASP* 3.0 10.0 + - + +
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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