Contacts of the helix formed by residues 284 - 304 (chain C) in PDB entry 4JUO
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 284 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C ASP 3.6 3.6 + - - -
283C GLY* 1.3 74.6 - - - -
285C THR* 1.3 57.1 + - - -
286C HIS* 3.3 7.6 - - - -
287C GLU* 3.1 4.6 + - - +
288C THR* 2.7 32.2 + - - -
346C LYS* 3.9 13.6 - - - +
347C LEU 3.2 16.4 - - - -
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Residues in contact with THR 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C GLY* 1.3 71.4 - - - -
286C HIS* 1.3 61.0 + - - +
288C THR* 3.2 10.2 + - - -
289C GLY 2.8 23.6 + - - -
347C LEU* 3.0 20.2 + - - +
348C GLY* 3.5 24.2 - - - +
349C SER 2.8 20.8 + - - +
350C PRO* 4.7 3.8 - - + -
352C ALA* 3.1 9.9 - - - +
353C ARG* 3.4 24.0 - - - +
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Residues in contact with HIS 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C SER* 3.8 7.7 - - - -
274C PHE 4.7 1.1 - - - -
275C VAL* 3.6 14.7 + - + +
280C THR* 3.1 19.1 + - - -
283C GLY 3.0 33.2 - - - -
284C GLY 3.5 3.2 - - - -
285C THR* 1.3 77.8 + - - +
287C GLU* 1.3 68.4 + - - -
289C GLY 3.3 1.0 + - - -
290C LEU* 3.0 17.7 + - - +
328C LEU* 4.0 19.5 - - + +
330C ILE* 3.8 38.1 - - + -
347C LEU* 3.6 19.9 - - + +
352C ALA* 4.2 4.9 - - + -
356C VAL* 3.5 30.1 - - + +
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Residues in contact with GLU 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C ILE* 3.9 38.8 - - + +
273C SER* 2.7 31.7 + - - -
280C THR 4.5 0.2 - - - +
283C GLY* 3.1 19.4 - - - -
284C GLY 3.3 14.8 - - - +
286C HIS* 1.3 84.9 + - + +
288C THR* 1.3 57.3 + - - +
290C LEU* 2.8 13.0 + - + +
291C LYS* 2.8 30.8 + - + +
328C LEU* 4.5 4.9 - - + -
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Residues in contact with THR 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C GLY 2.7 18.7 + - - -
285C THR* 3.2 13.0 - - - -
287C GLU* 1.3 74.0 - - - +
289C GLY* 1.3 57.6 + - - +
291C LYS* 4.0 7.9 - - + +
292C SER* 3.1 31.5 + - - -
353C ARG* 4.1 16.0 - - - +
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Residues in contact with GLY 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C THR 2.8 12.4 + - - -
286C HIS 3.6 3.1 - - - -
287C GLU 3.0 0.4 - - - -
288C THR* 1.3 77.5 - - - +
290C LEU* 1.3 57.8 + - - +
292C SER* 4.8 0.2 - - - -
293C ALA* 3.1 14.4 + - - +
353C ARG* 3.5 31.6 - - - +
356C VAL* 4.5 0.4 - - - -
357C ASP* 3.1 32.1 - - - +
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Residues in contact with LEU 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C VAL* 3.8 22.2 - - + -
271C ILE* 4.3 26.9 - - + -
286C HIS 3.0 11.8 + - - +
287C GLU* 2.8 11.9 + - + +
289C GLY* 1.3 75.6 - - - +
291C LYS* 1.3 65.9 + - + +
293C ALA* 3.4 12.0 + - - +
294C ILE* 3.4 18.3 + - + +
324C LEU* 6.1 2.0 - - + -
326C ALA* 4.9 9.2 - - + -
328C LEU* 4.2 21.5 - - + -
356C VAL* 3.8 8.7 - - + +
360C VAL* 3.8 31.2 - - + -
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Residues in contact with LYS 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C ILE* 6.2 1.6 - - + -
287C GLU* 2.8 20.0 + - + +
288C THR* 4.4 7.6 - - + +
290C LEU* 1.3 74.4 - - + +
292C SER* 1.3 62.8 + - - +
293C ALA 3.1 1.4 + - - -
294C ILE* 3.2 28.6 - - - +
295C THR* 3.3 11.4 + - - +
321C ARG* 3.6 27.8 - - - +
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Residues in contact with SER 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C THR* 3.1 23.8 + - - -
289C GLY* 4.8 0.4 - - - -
291C LYS* 1.3 76.6 - - - +
293C ALA* 1.3 62.0 + - - +
295C THR* 3.9 8.3 + - - -
296C LYS* 3.6 21.8 + - - +
353C ARG* 5.7 6.5 - - - -
357C ASP* 3.4 13.5 - - - +
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Residues in contact with ALA 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C GLY 3.1 19.8 + - - +
290C LEU 3.5 8.1 - - - +
291C LYS 3.1 0.6 - - - -
292C SER* 1.3 79.3 - - - +
294C ILE* 1.3 57.7 + - - +
296C LYS* 3.8 1.1 - - - +
297C VAL* 2.9 33.3 + - - +
357C ASP* 3.3 21.8 - - - +
360C VAL* 3.9 22.7 - - + -
361C ALA* 4.1 11.6 - - + +
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Residues in contact with ILE 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C TYR* 6.1 0.2 - - - +
290C LEU* 3.4 15.7 - - + +
291C LYS* 3.2 23.1 - - - +
293C ALA* 1.3 75.7 - - - +
295C THR* 1.3 83.8 + - + +
296C LYS 2.9 3.8 + - - -
297C VAL* 3.4 5.4 - - + +
298C MET* 3.0 40.8 + - + +
320C TYR* 4.4 11.9 - - + +
321C ARG* 4.2 23.8 - - + -
324C LEU* 5.2 7.9 - - + -
360C VAL* 4.9 6.3 - - + -
364C LEU* 4.0 28.5 - - + -
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Residues in contact with THR 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C LYS 3.3 18.1 + - - +
292C SER* 3.9 9.0 + - - -
294C ILE* 1.3 87.1 - - + +
296C LYS* 1.3 58.7 + - - +
299C ASN* 3.3 29.5 + - - +
316C GLU 4.9 1.0 + - - -
317C GLY* 3.2 37.9 - - - +
320C TYR* 4.0 12.9 - - - -
321C ARG* 3.8 11.0 - - - +
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Residues in contact with LYS 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C SER 3.6 15.4 + - - +
293C ALA* 3.6 2.5 + - - +
294C ILE 3.0 0.4 - - - -
295C THR* 1.3 82.5 + - - +
297C VAL* 1.3 61.9 + - - +
298C MET 3.4 1.8 - - - -
299C ASN* 4.1 6.1 - - - +
300C ASP* 3.5 18.7 + - - +
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Residues in contact with VAL 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C ALA 2.9 21.5 + - - +
294C ILE* 3.0 12.5 + - - +
296C LYS* 1.3 77.0 - - - +
298C MET* 1.3 65.0 + - + +
300C ASP* 3.6 7.1 - - + +
301C TYR* 3.3 20.4 + - - +
361C ALA* 3.6 15.0 - - + +
364C LEU* 3.5 32.1 - - + +
365C THR* 3.1 47.3 - - + +
368C LEU* 4.4 1.0 - - - +
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Residues in contact with MET 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C TYR* 3.7 24.7 - - + +
294C ILE* 3.0 27.1 + - + +
297C VAL* 1.3 79.4 - - + +
299C ASN* 1.3 57.7 + - - +
300C ASP 3.1 1.1 - - - -
301C TYR* 2.8 8.7 + - + +
302C ALA* 2.6 36.0 + - - +
320C TYR* 3.4 34.3 - - + -
364C LEU* 4.6 13.5 - - + -
368C LEU* 3.5 28.7 - - + -
378C LEU* 4.1 24.0 - - + -
379C ILE* 4.0 14.0 - - + +
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Residues in contact with ASN 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295C THR 3.3 18.5 + - - +
296C LYS* 4.1 7.4 - - - +
298C MET* 1.3 77.6 - - - +
300C ASP* 1.3 56.3 + - - +
302C ALA* 3.3 4.9 + - - +
303C ARG* 2.8 48.3 + - + +
316C GLU 3.1 26.0 + - - +
320C TYR* 2.6 30.3 + - - -
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Residues in contact with ASP 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C LYS 3.5 13.8 + - - +
297C VAL* 3.6 11.7 - - - +
298C MET 3.1 0.4 - - - -
299C ASN* 1.3 79.0 - - - +
301C TYR* 1.3 62.4 + - - +
303C ARG* 3.3 8.5 + - - +
304C LYS* 3.0 26.7 + - - +
365C THR* 5.4 8.1 - - + -
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Residues in contact with TYR 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C VAL 3.3 6.4 + - - +
298C MET 2.8 7.8 + - - +
300C ASP* 1.3 79.6 - - - +
302C ALA* 1.3 63.7 + - - +
304C LYS* 3.9 11.2 + - + +
306C GLY* 4.1 12.6 + - - -
365C THR* 5.6 5.3 - - + +
368C LEU* 3.7 60.6 + - + -
369C MET* 4.1 12.5 + - + -
372C GLY* 3.8 12.5 - - - -
375C ALA* 3.4 23.3 - - + +
376C SER* 3.7 16.1 + - - -
379C ILE* 3.2 25.5 - - + +
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Residues in contact with ALA 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C MET 2.6 17.0 + - - +
299C ASN* 3.4 12.3 - - - +
301C TYR* 1.3 72.3 - - - +
303C ARG* 1.3 55.3 + - + +
304C LYS 2.7 25.5 + - - +
307C LEU 3.1 35.3 + - - +
308C LEU* 4.9 2.5 - - + -
320C TYR* 4.6 2.7 - - - +
379C ILE* 3.4 27.5 - - + +
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Residues in contact with ARG 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C ASN* 2.8 41.5 + - + +
300C ASP* 3.4 8.1 - - - +
302C ALA* 1.3 72.4 - - + +
304C LYS* 1.3 64.7 + - - +
306C GLY 4.6 1.2 - - - +
308C LEU* 3.6 23.2 - - - +
310C GLU* 3.2 42.3 + - - +
311C LYS 4.1 13.9 + - - +
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Residues in contact with LYS 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C ASP 3.0 15.9 + - - +
301C TYR* 4.2 11.4 - - + +
302C ALA 2.7 5.2 + - - +
303C ARG* 1.3 85.7 - - - +
305C THR* 1.3 54.8 - - - +
306C GLY* 2.2 27.9 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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