Contacts of the helix formed by residues 278 - 298 (chain B) in PDB entry 1JSC
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 SER 278 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B THR* 1.3 72.7 - - - +
279B ARG* 1.3 57.9 + - - +
280B ALA* 3.5 16.6 + - - +
281B GLN* 2.8 26.8 + - - +
282B ASP* 2.6 39.4 + - - +
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Residues in contact with ARG 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B SER* 1.3 75.3 - - - +
280B ALA* 1.3 56.8 + - - +
281B GLN 3.3 0.2 - - - -
282B ASP* 3.8 9.2 + - - -
283B GLU* 3.0 49.6 + - + +
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Residues in contact with ALA 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B SER* 3.1 11.1 + - - +
279B ARG* 1.3 80.5 - - - +
281B GLN* 1.3 61.1 + - + +
283B GLU* 4.2 4.7 - - - +
284B PHE* 3.7 20.4 + - - +
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Residues in contact with GLN 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B LEU 4.5 0.9 - - - +
277B THR* 3.0 30.5 - - + +
278B SER* 2.8 38.1 + - - +
280B ALA* 1.3 81.5 - - + +
282B ASP* 1.3 65.9 + - - +
284B PHE* 3.5 6.6 + - - +
285B VAL* 3.3 23.4 + - - +
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Residues in contact with ASP 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B THR* 2.9 22.4 + - - +
278B SER* 2.6 29.8 + - - +
279B ARG* 3.8 7.2 + - - +
281B GLN* 1.3 77.8 - - - +
283B GLU* 1.3 57.2 + - + +
285B VAL* 3.7 3.4 + - - +
286B MET* 3.1 31.3 + - - +
433B LYS* 4.8 13.0 + - - +
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Residues in contact with GLU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ARG* 3.0 36.3 + - + +
280B ALA* 4.5 4.4 - - - +
281B GLN 3.3 0.2 - - - -
282B ASP* 1.3 75.2 - - + +
284B PHE* 1.3 61.4 + - - +
286B MET* 3.8 4.7 - - - +
287B GLN* 2.8 33.5 + - - +
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Residues in contact with PHE 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ALA 3.7 16.7 + - - +
281B GLN* 3.5 7.5 + - - +
283B GLU* 1.3 78.9 - - - +
285B VAL* 1.3 66.5 + - + +
287B GLN* 3.4 15.7 - - + +
288B SER* 3.6 11.5 + - - -
424B GLU* 4.5 28.9 - - + -
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Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B GLN 3.3 14.1 + - - +
282B ASP* 4.1 2.9 - - - +
283B GLU 3.2 0.4 - - - -
284B PHE* 1.3 80.4 - - + +
286B MET* 1.3 67.3 + - - +
287B GLN 3.0 1.8 - - - -
288B SER* 2.7 26.4 + - - -
289B ILE* 2.9 18.3 + - + +
423B VAL* 6.4 0.7 - - + -
424B GLU 5.3 6.7 - - - +
430B ASN* 5.1 7.2 - - - +
433B LYS* 5.5 9.0 - - + +
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Residues in contact with MET 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ASP 3.1 19.1 + - - +
283B GLU* 3.8 5.2 - - - +
285B VAL* 1.3 78.4 - - - +
287B GLN* 1.3 61.1 + - - +
289B ILE* 3.2 40.4 + - + +
290B ASN* 2.8 62.0 + - - +
433B LYS* 3.6 15.9 - - - +
437B LYS* 6.3 0.9 - - + -
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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
----------------------------------------------------------
283B GLU 2.8 18.4 + - - +
284B PHE* 3.4 11.4 - - + +
286B MET* 1.3 77.4 - - - +
288B SER* 1.3 61.5 + - - +
290B ASN* 3.3 6.2 + - - +
291B LYS* 3.1 23.1 + - - +
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Residues in contact with SER 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B PHE* 3.6 10.9 + - - -
285B VAL* 2.7 25.3 + - - -
287B GLN* 1.3 74.2 - - - +
289B ILE* 1.3 63.5 + - - +
291B LYS* 3.9 6.5 - - - -
292B ALA* 3.0 26.2 + - - +
421B ILE* 3.8 8.1 - - - +
422B ALA 3.5 27.0 + - - -
423B VAL* 4.1 11.4 - - - +
424B GLU 5.0 1.2 + - - -
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Residues in contact with ILE 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B VAL* 2.9 22.9 + - + +
286B MET* 3.2 27.3 + - + +
288B SER* 1.3 78.0 - - - +
290B ASN* 1.3 57.4 + - - +
292B ALA* 4.6 0.2 - - - -
293B ALA* 2.8 23.8 + - + +
423B VAL* 4.0 20.0 - - + -
430B ASN* 4.0 17.5 - - - +
433B LYS* 3.0 52.3 - - + +
434B MET* 2.9 34.8 - - + +
437B LYS* 6.2 0.7 - - + -
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Residues in contact with ASN 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B MET* 2.8 53.1 + - - +
287B GLN* 3.8 6.3 - - - +
289B ILE* 1.3 74.3 - - - +
291B LYS* 1.3 68.1 + - - +
292B ALA 3.0 1.3 - - - -
293B ALA* 2.9 6.2 + - - +
294B ASP* 2.8 32.3 + - - +
437B LYS* 4.7 12.3 - - - +
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Residues in contact with LYS 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B GLN 3.1 15.8 + - - +
288B SER* 3.9 8.1 - - - +
290B ASN* 1.3 77.6 - - - +
292B ALA* 1.3 61.6 + - - +
294B ASP* 3.4 9.9 + - - +
295B LEU* 3.3 16.3 + - - +
421B ILE* 3.5 18.6 - - + +
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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
----------------------------------------------------------
288B SER 3.0 18.6 + - - +
290B ASN 3.0 0.2 - - - -
291B LYS* 1.3 74.6 - - - +
293B ALA* 1.3 66.5 + - - +
294B ASP 3.0 3.2 + - - -
295B LEU* 3.3 1.4 + - - -
296B ILE* 3.1 21.1 + - - +
404B ILE* 3.7 19.1 - - + +
421B ILE* 3.4 27.8 - - + +
423B VAL* 4.0 9.4 - - + -
434B MET* 3.5 17.7 - - + -
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Residues in contact with ALA 293 (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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289B ILE* 2.8 23.0 + - + +
290B ASN* 2.9 10.5 + - - +
292B ALA* 1.3 71.9 - - - +
294B ASP* 1.3 65.0 + - - +
296B ILE* 3.5 5.2 - - - +
297B ASN* 3.2 29.9 + - - -
434B MET* 3.3 25.3 - - + +
437B LYS* 4.0 23.3 - - + +
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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
----------------------------------------------------------
290B ASN* 2.8 21.8 + - - +
291B LYS* 3.6 11.8 - - - +
293B ALA* 1.3 76.1 - - - +
295B LEU* 1.3 55.8 + - - +
296B ILE 2.6 16.1 + - - -
297B ASN* 3.2 5.5 + - - +
298B LEU* 3.0 29.6 + - + +
439B PHE* 6.1 0.7 - - - -
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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
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291B LYS 3.3 9.0 + - - +
292B ALA 3.3 7.7 + - - +
294B ASP* 1.3 77.7 - - - +
296B ILE* 1.3 61.6 + - - +
298B LEU* 3.8 15.8 - - + +
299B ALA* 3.5 11.4 - - + +
369B LEU* 3.3 26.8 - - + +
395B ALA 3.4 23.6 - - - +
396B ALA* 3.4 34.8 - - + -
404B ILE* 4.8 3.8 - - + -
420B GLN* 4.6 4.9 - - + -
421B ILE* 3.9 24.5 - - + -
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Residues in contact with ILE 296 (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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292B ALA 3.1 11.7 + - - +
293B ALA* 3.5 13.9 - - - +
294B ASP 2.6 5.1 + - - -
295B LEU* 1.3 72.7 - - - +
297B ASN* 1.3 70.1 + - - +
298B LEU 2.9 1.9 + - - -
299B ALA* 3.0 20.6 + - - +
302B PRO* 5.4 5.5 - - + +
329B ILE* 6.3 2.5 - - + -
369B LEU* 3.9 10.2 - - + +
371B ILE* 5.4 7.4 - - + -
404B ILE* 4.6 8.5 - - + -
434B MET* 5.9 3.1 - - - -
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Residues in contact with ASN 297 (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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293B ALA 3.2 18.5 + - - +
294B ASP* 3.2 5.5 + - - +
296B ILE* 1.3 78.9 - - - +
298B LEU* 1.3 52.5 + - + +
299B ALA 2.8 18.2 + - - +
327B ALA* 5.5 6.0 - - - +
437B LYS 3.0 26.9 + - - -
438B ILE* 4.0 3.5 - - - +
439B PHE* 3.0 53.2 + - + +
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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
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294B ASP* 3.0 21.2 + - + +
295B LEU* 3.8 14.0 - - + +
296B ILE 2.9 0.4 + - - -
297B ASN* 1.3 72.8 - - - +
299B ALA* 1.3 63.7 + - - +
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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
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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