Contacts of the helix formed by residues 282 - 300 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A THR 3.4 6.5 - - - -
252A PRO 4.0 1.3 - - - -
253A ARG 3.7 0.7 - - - -
254A GLY 3.5 16.6 - - - -
280A ASN* 2.9 20.4 + - - -
281A MET* 1.3 80.1 - - - +
283A CYS* 1.3 66.3 + - - -
284A ASP 3.2 3.1 + - - -
285A LYS 3.3 1.8 + - - -
286A VAL* 3.1 24.5 + - - +
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Residues in contact with CYS 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A ILE* 3.9 21.2 - - + +
251A THR 2.8 18.4 + - - +
252A PRO* 3.4 17.2 + - + +
280A ASN* 4.3 0.2 + - - -
282A GLY* 1.3 70.6 - - - -
284A ASP* 1.3 54.3 + - - +
286A VAL* 4.1 0.8 - - - +
287A THR* 2.7 42.3 + - - -
327A TYR* 4.1 6.1 - - + -
328A CYS* 3.7 29.2 - - - -
331A LYS* 3.6 29.4 - - - -
332A ILE* 4.5 0.7 - - - -
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Residues in contact with ASP 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A PRO 4.1 6.3 + - - +
282A GLY 3.2 1.2 + - - -
283A CYS* 1.3 75.2 - - - +
285A LYS* 1.3 61.2 + - - +
287A THR* 3.5 4.0 + - - -
288A GLU* 3.3 28.4 + - - +
327A TYR* 2.6 32.9 + - - -
331A LYS* 2.8 43.5 + - - +
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Residues in contact with LYS 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A MET* 3.3 53.8 + - + +
282A GLY 3.3 2.2 + - - -
284A ASP* 1.3 74.6 - - - +
286A VAL* 1.3 65.4 + - - +
288A GLU* 3.2 31.3 + - - +
289A ASN* 3.1 29.1 + - - +
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Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A LYS 4.3 0.4 - - - +
230A ASN* 3.6 51.1 - - + +
247A ILE* 3.8 23.1 - - + -
250A ILE* 3.6 31.4 - - + -
281A MET* 4.3 3.4 - - + +
282A GLY 3.1 22.1 + - - +
283A CYS* 4.1 2.7 - - - +
285A LYS* 1.3 71.5 - - - +
287A THR* 1.3 59.5 + - - +
289A ASN* 3.1 3.2 + - - +
290A LEU* 2.9 27.5 + - - +
332A ILE* 4.1 5.6 - - + -
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Residues in contact with THR 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A CYS* 2.7 24.9 + - - -
284A ASP 3.7 5.6 - - - -
286A VAL* 1.3 75.6 - - - +
288A GLU* 1.4 51.5 + - - +
290A LEU* 3.2 2.8 + - - +
291A ILE* 2.9 50.3 + - + +
331A LYS* 3.4 45.5 - - - +
332A ILE* 3.4 28.9 - - - +
335A TYR* 3.9 10.3 - - + -
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Residues in contact with GLU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ASP* 3.3 17.2 + - - +
285A LYS* 3.2 35.4 + - + +
287A THR* 1.4 73.9 - - - +
289A ASN* 1.4 65.2 + - - +
291A ILE* 3.3 11.3 + - + +
292A LEU* 3.1 33.0 + - + +
331A LYS* 6.2 0.7 - - - +
464B ASN* 6.1 1.3 - - - +
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Residues in contact with ASN 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ASN 2.8 21.9 + - - +
231A GLY* 3.4 23.5 - - - +
232A VAL* 3.7 12.8 - - - +
281A MET* 3.1 27.1 - - - +
285A LYS* 3.1 15.6 + - - +
286A VAL 3.1 7.9 + - - +
288A GLU* 1.4 80.5 - - - +
290A LEU* 1.3 61.4 + - - +
292A LEU* 3.4 17.8 + - - +
293A PHE* 3.2 19.9 + - - +
296A ARG* 4.8 2.3 + - - -
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Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ILE* 4.0 15.2 - - + +
247A ILE* 4.2 8.0 - - + +
286A VAL 2.9 15.8 + - - +
287A THR* 3.2 4.7 + - - +
289A ASN* 1.3 72.5 - - - +
291A ILE* 1.4 60.9 + - - +
293A PHE* 3.1 9.5 + - + +
294A ARG* 2.9 40.6 + - - +
308A VAL* 3.8 24.5 - - + -
310A VAL* 3.7 28.9 - - + -
332A ILE* 3.8 13.0 - - + -
335A TYR* 3.6 34.8 - - + +
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Residues in contact with ILE 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A THR* 2.9 30.4 + - + +
288A GLU* 3.3 9.2 + - + +
290A LEU* 1.4 73.9 - - - +
292A LEU* 1.3 63.3 + - + +
294A ARG* 3.1 10.1 + - - +
295A LYS* 3.0 38.9 + - + +
331A LYS* 5.8 2.5 - - - -
335A TYR* 3.6 46.9 - - + +
417A PHE* 4.7 6.3 - - + -
464B ASN* 3.9 41.5 - - + +
470B GLU* 4.4 5.6 - - + +
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A GLU* 3.1 23.9 + - + +
289A ASN* 3.6 18.8 - - - +
290A LEU 3.3 0.2 - - - -
291A ILE* 1.3 76.0 - - - +
293A PHE* 1.4 60.4 - - - +
295A LYS* 3.4 9.2 + - + +
296A ARG* 3.1 43.5 + - - +
464B ASN* 4.1 26.9 - - - +
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Residues in contact with PHE 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A ILE* 3.6 34.5 - - + -
235A ASP* 3.4 32.3 - - - -
238A LEU* 4.0 15.7 - - + -
289A ASN 3.2 11.2 + - - +
290A LEU* 3.1 18.4 + - + +
292A LEU* 1.4 76.4 - - - +
294A ARG* 1.4 63.9 + - - +
296A ARG* 3.1 17.3 + - - +
297A GLN* 2.8 60.9 + - + +
303A LEU* 4.1 16.6 - - + -
306A HIS* 5.3 1.1 - - + -
308A VAL* 3.6 24.9 - - + -
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Residues in contact with ARG 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A LEU* 2.9 24.3 + - + +
291A ILE* 3.1 8.3 + - - +
293A PHE* 1.4 82.9 - - - +
295A LYS* 1.3 57.4 - - - +
297A GLN* 2.9 25.5 + - - +
298A GLU* 3.1 27.4 + - - +
308A VAL* 3.6 25.5 + - - +
335A TYR* 2.9 31.9 + - + +
337A ASP* 2.9 26.7 + - - -
417A PHE* 3.4 45.4 + - + +
418A ASN* 3.5 10.4 - - - +
419A THR* 2.9 29.5 + - - +
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Residues in contact with LYS 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A ILE* 3.0 31.4 + - + +
292A LEU* 3.7 13.0 - - + +
293A PHE 3.3 0.2 - - - -
294A ARG* 1.3 73.0 - - - +
296A ARG* 1.4 65.0 + - + +
298A GLU* 3.4 13.3 + - - +
299A GLU* 3.0 25.8 - - - +
417A PHE* 3.9 14.8 - - + -
273B ILE* 6.2 2.4 - - - +
461B THR 4.6 6.2 + - - +
463B ILE 3.5 13.5 + - - -
464B ASN* 2.8 32.4 + - - +
469B PHE 5.3 2.2 + - - -
470B GLU* 4.2 24.6 + - - +
472B LYS 5.5 2.8 + - - -
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Residues in contact with ARG 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A GLY 5.7 2.6 + - - -
232A VAL 5.7 3.4 + - - -
233A CYS* 6.2 0.4 - - - +
234A ILE* 5.6 1.8 - - - +
235A ASP* 2.8 45.5 + - - +
289A ASN 4.8 2.4 + - - -
292A LEU* 3.1 34.0 + - - +
293A PHE* 3.5 28.1 - - - +
295A LYS* 1.4 71.9 - - + +
297A GLN* 1.3 60.5 + - - +
299A GLU* 3.1 8.5 + - - +
300A ASP* 3.0 29.8 + - + +
303A LEU* 5.4 2.0 - - + -
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Residues in contact with GLN 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A PHE* 2.8 30.9 + - + +
294A ARG* 2.9 36.3 + - - +
295A LYS 3.4 0.2 - - - -
296A ARG* 1.3 75.7 - - - +
298A GLU* 1.3 59.0 + - - +
300A ASP 2.9 25.2 - - - +
303A LEU* 2.8 43.5 + - + +
304A SER* 3.8 15.5 + - - +
306A HIS 3.3 6.5 + - - -
418A ASN 4.5 4.4 - - - +
419A THR* 2.9 24.7 + - - -
421A LYS* 6.2 0.7 - - - -
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Residues in contact with GLU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A ARG 3.1 12.8 + - - +
295A LYS* 3.5 13.8 - - - +
296A ARG 3.3 0.4 - - - -
297A GLN* 1.3 74.6 - - - +
299A GLU* 1.3 71.3 + - - +
417A PHE* 3.6 30.7 - - + -
421A LYS* 6.0 1.6 - - - -
470B GLU 4.4 3.1 - - - +
471B ASN* 3.7 22.0 - - - +
472B LYS 5.2 1.6 - - - +
473B LYS* 4.7 16.6 - - + +
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Residues in contact with GLU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LYS* 3.0 23.7 + - - +
296A ARG* 3.1 10.1 + - - +
298A GLU* 1.3 87.8 - - - +
300A ASP* 1.3 59.1 + - - +
301A LYS* 4.0 7.2 + - - +
473B LYS* 3.4 35.8 + - - +
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Residues in contact with ASP 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A LYS* 3.4 23.6 + - - -
296A ARG 3.0 14.8 + - - +
297A GLN 2.9 17.6 + - - +
298A GLU 5.2 0.2 - - - -
299A GLU* 1.3 76.4 - - + +
301A LYS* 1.3 64.0 + - - +
302A LEU* 3.3 29.0 + - - +
303A LEU* 3.3 26.2 + - + +
304A SER* 3.7 3.8 + - - -
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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