Contacts of the helix formed by residues 282 - 300 (chain B) in PDB entry 4CQ8
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 GLY 282 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B THR 3.4 6.3 - - - -
252B PRO 4.0 1.3 - - - -
253B ARG 3.7 0.7 - - - -
254B GLY 3.5 15.9 - - - -
280B ASN* 2.9 20.8 + - - -
281B MET* 1.3 80.9 - - - +
283B CYS* 1.3 65.9 + - - -
284B ASP 3.2 3.2 + - - -
285B LYS 3.3 2.0 + - - -
286B VAL* 3.1 24.2 + - - +
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Residues in contact with CYS 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ILE* 3.9 21.2 - - + +
251B THR 2.8 18.2 + - - +
252B PRO* 3.3 17.7 + - + +
280B ASN* 4.3 0.2 + - - -
282B GLY* 1.3 70.5 - - - +
284B ASP* 1.3 54.2 + - - +
286B VAL* 3.6 1.3 + - - +
287B THR* 2.7 42.0 + - - -
327B TYR* 4.1 5.6 - - + -
328B CYS* 3.7 29.2 - - - -
331B LYS* 3.6 29.8 - - - -
332B ILE* 4.4 0.9 - - - -
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Residues in contact with ASP 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B PRO 4.1 6.1 + - - +
282B GLY 3.3 1.0 - - - -
283B CYS* 1.3 74.4 - - - +
285B LYS* 1.3 61.1 + - - +
287B THR* 3.4 4.4 + - - -
288B GLU* 3.3 27.0 + - - +
327B TYR* 2.6 34.1 + - - -
331B LYS* 2.8 42.8 + - - +
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Residues in contact with LYS 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B MET* 3.3 54.3 + - + +
282B GLY 3.3 2.2 + - - -
284B ASP* 1.3 74.3 - - - +
286B VAL* 1.4 64.2 + - - +
288B GLU* 3.2 13.0 + - + +
289B ASN* 3.1 32.1 + - - +
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Residues in contact with VAL 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B LYS 4.2 0.4 - - - +
230B ASN* 3.6 50.5 - - + +
247B ILE* 3.7 23.3 - - + -
250B ILE* 3.6 31.4 - - + -
280B ASN* 4.8 0.2 - - - +
281B MET* 4.3 4.0 - - + +
282B GLY 3.1 21.5 + - - +
283B CYS 4.1 2.5 - - - +
285B LYS* 1.4 71.7 - - - +
287B THR* 1.4 58.7 + - - +
289B ASN* 3.2 3.6 + - - +
290B LEU* 2.9 27.5 + - - +
332B ILE* 4.2 6.5 - - + -
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Residues in contact with THR 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B CYS* 2.7 25.7 + - - -
284B ASP 3.6 5.6 - - - -
285B LYS 3.3 0.2 - - - -
286B VAL* 1.4 75.3 - - - +
288B GLU* 1.4 57.0 + - - +
290B LEU* 3.1 4.0 + - - +
291B ILE* 2.8 38.4 + - + +
331B LYS* 3.4 46.1 - - - +
332B ILE* 3.4 27.8 - - - +
335B TYR* 3.8 22.0 - - + -
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Residues in contact with GLU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ASP 3.3 12.8 + - - +
285B LYS* 3.2 16.4 + - + +
287B THR* 1.4 75.0 - - - +
289B ASN* 1.3 63.5 + - - +
291B ILE* 3.4 27.6 + - - +
292B LEU* 3.1 31.0 + - + +
331B LYS* 4.5 14.6 + - - -
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Residues in contact with ASN 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ASN 2.9 21.2 + - - +
231B GLY* 3.5 22.4 - - - +
232B VAL* 3.7 14.0 - - - +
281B MET* 3.1 26.5 - - - +
285B LYS* 3.1 21.6 + - - +
286B VAL 3.2 8.7 + - - +
288B GLU* 1.3 77.1 - - - +
290B LEU* 1.4 59.8 + - - +
292B LEU* 3.5 17.1 + - - +
293B PHE* 3.2 19.2 + - - +
296B ARG* 4.8 2.3 + - - -
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Residues in contact with LEU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B ILE* 4.0 16.6 - - + +
247B ILE* 4.1 8.5 - - + +
286B VAL 2.9 13.3 + - - +
287B THR* 3.6 7.2 - - - +
289B ASN* 1.4 72.4 - - - +
291B ILE* 1.4 61.8 + - - +
293B PHE* 3.1 14.6 + - + -
294B ARG* 2.9 35.4 + - + +
308B VAL* 3.8 24.7 - - + -
310B VAL* 3.7 28.5 - - + -
332B ILE* 3.8 13.0 - - + -
335B TYR* 3.6 36.1 - - + +
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Residues in contact with ILE 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B THR* 2.8 29.6 + - + +
288B GLU* 3.7 27.8 - - - +
290B LEU* 1.4 75.5 - - - +
292B LEU* 1.4 63.5 + - + +
294B ARG* 3.1 10.1 + - - +
295B LYS* 3.0 45.9 + - + +
331B LYS* 5.9 0.4 - - - -
335B TYR* 3.6 46.9 - - + +
417B PHE* 4.7 6.3 - - + -
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B GLU* 3.1 22.0 + - + +
289B ASN* 3.6 20.9 - - - +
290B LEU 3.3 0.2 - - - -
291B ILE* 1.4 76.7 - - + +
293B PHE* 1.4 60.5 + - - +
295B LYS* 3.4 13.9 + - + +
296B ARG* 3.1 43.7 + - - +
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Residues in contact with PHE 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B ILE* 3.6 33.2 - - + -
235B ASP* 3.4 33.0 - - - -
238B LEU* 4.0 15.5 - - + -
289B ASN 3.2 8.6 + - - +
290B LEU* 3.1 18.6 + - + +
292B LEU* 1.4 78.6 - - - +
294B ARG* 1.4 59.0 + - - +
296B ARG* 3.1 18.2 + - - +
297B GLN* 2.8 65.9 + - + +
303B LEU* 4.1 17.7 - - + -
306B HIS* 5.3 1.3 - - + -
308B VAL* 3.6 25.4 - - + -
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Residues in contact with ARG 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B LEU* 2.9 24.2 + - + +
291B ILE 3.1 8.0 + - - +
293B PHE* 1.4 84.4 - - - +
295B LYS* 1.4 55.8 + - - +
297B GLN* 2.9 24.7 + - - +
298B GLU* 3.1 27.4 + - - +
308B VAL* 3.6 24.8 + - - +
335B TYR* 2.9 32.4 + - + +
337B ASP* 2.9 27.1 + - - +
417B PHE* 3.4 46.5 + - + +
418B ASN* 3.5 10.8 - - - +
419B THR* 2.9 30.1 + - - +
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Residues in contact with LYS 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ILE* 3.0 34.9 + - + +
292B LEU* 3.7 16.6 - - + +
294B ARG* 1.4 72.2 - - - +
296B ARG* 1.4 63.9 + - - +
298B GLU* 3.4 13.4 + - - +
299B GLU* 3.0 26.3 - - - +
417B PHE* 3.9 20.0 - - + -
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Residues in contact with ARG 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B GLY 5.7 2.2 + - - -
232B VAL 5.6 4.8 + - - -
233B CYS* 6.2 0.2 - - - +
234B ILE* 5.6 1.6 - - - +
235B ASP* 2.8 45.5 + - - +
289B ASN 4.8 2.2 + - - -
292B LEU* 3.1 40.0 + - - +
293B PHE* 3.1 24.7 + - - +
295B LYS* 1.4 71.7 - - + +
297B GLN* 1.4 60.7 + - - +
299B GLU* 3.1 8.7 + - - +
300B ASP* 3.0 29.9 + - - +
303B LEU* 5.4 1.6 - - + -
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Residues in contact with GLN 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 PHE* 2.8 30.0 + - + +
294B ARG* 2.9 36.2 + - - +
296B ARG* 1.4 75.6 - - - +
298B GLU* 1.3 60.1 + - - +
300B ASP* 2.9 25.4 + - - +
303B LEU* 2.8 42.8 + - + +
304B SER* 3.8 15.6 + - - +
306B HIS 3.3 6.5 + - - -
418B ASN 4.6 4.2 - - - +
419B THR* 2.9 25.1 + - - -
421B LYS* 6.2 0.9 - - - -
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ARG 3.1 12.8 + - - +
295B LYS* 3.5 14.9 - - - +
296B ARG 3.3 0.2 - - - -
297B GLN* 1.3 74.3 - - - +
299B GLU* 1.3 70.8 - - - +
300B ASP 3.6 0.4 - - - -
417B PHE* 3.6 30.7 - - + -
421B LYS* 6.0 1.9 - - - -
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Residues in contact with GLU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LYS* 3.0 23.7 + - - +
296B ARG* 3.1 10.1 + - - +
298B GLU* 1.3 92.7 - - - +
300B ASP* 1.3 57.7 + - - +
301B LYS* 4.0 6.1 + - - +
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Residues in contact with ASP 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B LYS* 3.4 23.4 + - - -
296B ARG* 3.0 15.5 + - + +
297B GLN 2.9 18.7 - - - +
299B GLU* 1.3 76.7 - - + +
301B LYS* 1.4 63.9 + - - +
302B LEU* 3.3 27.8 + - - +
303B LEU* 3.3 25.8 + - + +
304B SER* 3.7 3.6 + - - -
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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