Contacts of the helix formed by residues 280 - 297 (chain B) in PDB entry 3SSB
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 ASN 280 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B GLU* 3.3 24.0 - - + +
164B ILE* 3.3 11.1 - - - +
278B THR 3.2 3.7 + - - +
279B SER* 1.3 72.5 - - - +
281B PHE* 1.3 53.2 + - - +
282B SER* 3.1 12.2 + - - -
283B GLN* 2.9 45.5 + - - +
284B LEU 2.8 30.3 + - - -
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Residues in contact with PHE 281 (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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160B GLU* 3.0 50.3 + - + +
163B ALA* 3.6 16.6 - - + -
164B ILE* 3.7 13.7 - - + -
217B TYR* 3.7 27.1 - + + -
220B ARG* 5.8 0.4 - - + -
233B ASN* 3.4 32.5 - - + -
236B ILE* 4.0 22.7 - - + -
237B ILE* 3.8 25.8 - - + -
280B ASN* 1.3 71.2 - - - +
282B SER* 1.3 58.1 + - - +
284B LEU* 3.3 8.6 + - - +
285B ARG 3.0 22.7 + - - -
310B PHE* 4.5 1.6 - - - -
315B VAL* 3.4 25.4 - - + +
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Residues in contact with SER 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B GLU* 4.7 0.4 + - - -
280B ASN* 3.1 12.2 + - - -
281B PHE* 1.3 77.1 - - - +
283B GLN* 1.3 61.2 + - - +
285B ARG* 3.4 5.5 + - - +
286B ALA* 3.1 24.9 + - - +
315B VAL* 4.1 4.6 - - - +
316B LYS* 2.6 30.5 + - - +
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Residues in contact with GLN 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B LEU* 4.3 2.6 - - - +
278B THR* 3.6 5.6 + - - +
279B SER* 3.3 16.8 - - - +
280B ASN* 2.9 52.4 + - - +
282B SER* 1.3 76.6 - - - +
284B LEU* 1.3 60.1 + - - +
286B ALA* 3.3 8.2 + - + +
287B ALA* 2.9 30.6 + - - +
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Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ILE* 3.8 26.0 - - + -
168B ILE* 5.4 0.9 - - + -
237B ILE* 3.5 45.3 - - + -
267B PHE* 4.1 21.5 - - + -
270B ALA* 4.9 3.1 - - + -
275B LEU* 4.0 33.7 - - + +
280B ASN 2.8 16.8 + - - +
281B PHE 3.3 8.0 + - - +
283B GLN* 1.3 69.5 - - - +
285B ARG* 1.3 66.6 + - - +
287B ALA* 3.2 2.5 + - + +
288B ALA* 2.9 25.4 + - + +
310B PHE* 3.9 11.7 - - + -
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Residues in contact with ARG 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B PHE 3.0 13.3 + - - +
282B SER 3.5 8.5 - - - +
284B LEU* 1.3 78.1 - - - +
286B ALA* 1.3 55.9 + - - +
288B ALA* 3.7 0.9 - - - +
289B VAL* 2.8 46.1 + - + +
306B VAL 5.5 0.2 - - - +
307B LYS* 3.6 33.5 + - - +
310B PHE* 3.7 34.4 - - + +
311B ASP* 2.8 39.2 + - - +
315B VAL* 2.8 36.0 + - + -
316B LYS* 3.5 28.1 + - - +
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Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B SER 3.1 14.0 + - - +
283B GLN* 3.7 10.3 - - + +
284B LEU 3.2 0.2 - - - -
285B ARG* 1.3 77.6 - - - +
287B ALA* 1.3 57.7 + - - +
289B VAL* 3.8 5.9 - - - +
290B GLN* 2.8 31.8 + - - +
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Residues in contact with ALA 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ALA* 3.9 7.4 - - + -
274B TYR* 3.6 31.5 - - + +
275B LEU* 3.6 20.6 - - + -
283B GLN 2.9 16.8 + - - +
284B LEU 3.6 4.9 - - - +
286B ALA* 1.3 73.7 - - - +
288B ALA* 1.3 54.0 - - - +
290B GLN* 3.4 2.6 + - - +
291B SER* 2.8 40.2 + - - -
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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
----------------------------------------------------------
266B ILE* 3.5 19.4 - - + +
267B PHE* 4.5 10.5 - - + -
270B ALA* 4.1 5.7 - - + +
284B LEU* 2.9 22.4 + - + +
285B ARG 3.7 2.0 - - - +
287B ALA* 1.3 69.7 - - - +
289B VAL* 1.3 62.0 + - - +
291B SER* 3.4 1.5 + - - -
292B ALA* 2.9 31.2 + - - +
306B VAL* 3.6 20.8 - - + +
310B PHE* 4.0 12.6 - - + -
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Residues in contact with VAL 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ARG* 2.8 36.2 + - + +
286B ALA* 3.9 6.1 - - - +
288B ALA* 1.3 77.1 - - - +
290B GLN* 1.3 54.1 + - - +
292B ALA* 3.4 4.0 + - - +
293B THR* 2.7 43.2 + - - +
303B VAL* 4.2 7.6 - - + +
306B VAL* 3.8 19.1 - - + -
307B LYS* 3.6 43.5 - - + +
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Residues in contact with GLN 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B TYR* 3.4 33.2 + - + +
286B ALA 2.8 19.8 + - - +
287B ALA* 3.8 4.7 - - - +
289B VAL* 1.3 75.0 - - - +
291B SER* 1.3 59.6 + - - +
293B THR* 3.2 17.8 + - - +
294B ASP* 2.9 57.0 + - - +
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Residues in contact with SER 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ILE* 3.4 23.1 - - - -
269B ARG* 3.5 10.0 - - - +
270B ALA* 3.0 24.1 + - - -
274B TYR* 3.3 8.7 - - - -
287B ALA 2.8 26.0 + - - -
288B ALA 3.7 4.9 - - - -
289B VAL 3.3 0.2 - - - -
290B GLN* 1.3 73.6 - - - +
292B ALA* 1.3 57.4 + - - +
294B ASP* 3.4 12.2 + - - +
295B LEU* 3.1 35.3 + - - +
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ILE* 3.9 30.2 - - + +
288B ALA 2.9 18.8 + - - +
289B VAL* 3.8 1.8 - - - +
291B SER* 1.3 73.4 - - - +
293B THR* 1.3 59.8 + - - +
296B TYR* 3.0 37.8 + - + +
302B GLU 4.4 0.4 - - - -
303B VAL* 3.4 22.9 - - + +
306B VAL* 4.0 12.1 - - + -
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Residues in contact with THR 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B VAL* 2.7 29.5 + - - +
290B GLN* 3.2 20.3 + - - +
292B ALA* 1.3 74.1 - - - +
294B ASP* 1.3 63.0 + - - +
297B GLY* 2.8 27.2 + - - +
298B SER* 3.8 28.1 - - - +
303B VAL* 3.4 16.6 - - - +
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Residues in contact with ASP 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B ARG* 2.9 40.5 + - - +
274B TYR* 2.5 31.8 + - - -
290B GLN* 2.9 38.8 + - - +
291B SER 3.5 2.9 - - - +
293B THR* 1.3 75.1 - - - +
295B LEU* 1.3 62.7 + - - +
297B GLY 4.8 0.2 + - - -
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B LYS* 3.9 43.5 - - + +
266B ILE* 4.0 7.2 - - - +
269B ARG* 3.9 22.2 - - + +
291B SER 3.1 19.0 + - - +
293B THR 3.2 0.2 - - - -
294B ASP* 1.3 82.6 - - - +
296B TYR* 1.3 89.8 + - + +
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Residues in contact with TYR 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B LYS* 3.3 34.2 - - + +
265B LYS* 3.5 24.8 - - + +
266B ILE* 3.9 20.6 - - + -
292B ALA* 3.0 21.9 + - - +
295B LEU* 1.3 97.3 - - + +
297B GLY* 1.3 60.2 + - - +
300B SER* 3.3 26.6 - - - +
302B GLU* 3.4 41.7 - - + +
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Residues in contact with GLY 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ALA 3.7 0.8 + - - -
293B THR* 2.8 19.9 + - - -
294B ASP 4.8 0.2 + - - -
295B LEU 3.9 0.2 - - - -
296B TYR* 1.3 78.3 - - - +
298B SER* 1.3 63.6 + - - -
299B THR* 3.2 4.5 - - - -
300B SER* 2.7 27.3 + - - -
303B VAL* 3.3 5.2 - - - +
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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