Contacts of the helix formed by residues 290 - 306 (chain C) in PDB entry 1G3J
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 290 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C PHE* 3.1 21.9 - - + -
288C LYS* 3.7 2.9 - - + +
289C THR* 1.3 79.0 - - + +
291C VAL* 1.3 57.4 + - - +
292C LYS* 3.3 16.2 - - - +
293C PHE* 2.9 20.1 + - + +
294C LEU* 2.8 34.6 + - - +
48D LEU* 3.1 27.2 - - - +
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Residues in contact with VAL 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C THR 3.1 3.8 + - - +
290C ASN* 1.3 74.8 - - - +
292C LYS* 1.3 61.7 + - + +
294C LEU* 3.8 2.3 - - - +
295C ALA* 2.9 32.1 + - - +
331C TYR* 3.4 36.6 - - + -
333C TYR* 3.6 45.4 - - + -
336C LEU* 4.2 10.8 - - + +
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Residues in contact with LYS 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C ASN* 3.2 13.1 - - - +
291C VAL* 1.3 84.1 - - + +
293C PHE* 1.3 59.3 + - - +
295C ALA* 3.7 0.6 - - - +
296C ILE* 3.1 30.1 + - - +
333C TYR* 4.5 5.4 - - + +
44D VAL* 3.5 24.5 - - + +
47D SER* 5.9 1.6 - - - -
48D LEU* 3.7 24.1 - - + +
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Residues in contact with PHE 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C LEU* 4.2 19.1 - - + -
253C PHE* 3.7 24.7 - + + -
256C ILE* 3.7 25.4 - - + -
285C LEU* 3.6 51.1 - - + -
288C LYS* 3.9 22.7 - - + -
290C ASN* 2.9 25.9 + - + +
292C LYS* 1.3 78.0 - - - +
294C LEU* 1.3 69.1 + - - +
296C ILE* 3.1 5.0 + - - +
297C THR* 3.0 43.8 + - - -
48D LEU* 4.0 9.2 - - + +
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Residues in contact with LEU 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C LEU 3.8 11.4 - - - +
286C LEU* 3.5 35.7 - - + +
288C LYS* 3.5 27.8 - - + +
290C ASN 2.8 22.8 + - - +
291C VAL* 3.8 3.1 - - - +
293C PHE* 1.3 74.1 - - + +
295C ALA* 1.3 56.7 + - - +
297C THR* 3.8 4.6 - - - +
298C THR* 2.9 36.4 + - - +
327C ILE* 4.5 8.5 - - + -
331C TYR* 3.5 34.1 - - + -
336C LEU* 3.5 23.3 - - + -
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Residues in contact with ALA 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C VAL 2.9 18.2 + - - +
292C LYS 3.7 6.7 - - - +
294C LEU* 1.3 76.5 - - - +
296C ILE* 1.3 61.5 + - + +
298C THR* 2.9 18.6 + - - -
299C ASP* 3.3 12.1 + - - +
333C TYR* 4.4 5.8 - - + -
335C LYS* 4.5 4.3 - - + +
336C LEU* 3.5 23.7 - - - +
339C THR* 3.5 12.4 + - + +
41D LEU* 4.6 2.0 - - + +
44D VAL* 4.2 14.6 - - + -
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Residues in contact with ILE 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C ILE* 4.1 19.5 - - + +
257C THR* 4.5 2.2 - - + +
260C HIS* 4.0 28.6 + - + -
292C LYS 3.1 16.2 - - - +
293C PHE* 3.1 6.1 + - - +
295C ALA* 1.3 75.0 - - + +
297C THR* 1.3 66.3 + - - +
299C ASP* 3.4 6.0 + - - +
300C CYS* 3.1 27.9 + - - -
41D LEU* 4.3 16.6 - - + -
44D VAL* 3.6 25.6 - - + -
45D LYS* 3.5 30.3 - - + -
48D LEU* 4.3 11.7 - - + -
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Residues in contact with THR 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C ILE* 4.7 5.0 - - - +
282C MET* 3.5 44.2 - - + +
285C LEU* 4.7 7.9 - - + -
286C LEU* 4.1 13.2 - - + -
293C PHE* 3.0 41.0 + - + -
294C LEU* 3.8 5.4 - - - -
296C ILE* 1.3 75.1 - - - +
298C THR* 1.3 65.4 + - - +
300C CYS* 3.0 12.1 + - - +
301C LEU* 3.0 21.6 + - + +
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Residues in contact with THR 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C LEU* 3.8 20.0 - - + -
294C LEU 2.9 19.6 + - - +
295C ALA 2.9 10.9 + - - -
297C THR* 1.3 74.5 - - - +
299C ASP* 1.3 55.2 + - - +
301C LEU* 3.0 10.1 + - - +
302C GLN 2.9 24.9 + - - -
324C LEU* 4.2 12.1 - - + -
327C ILE* 4.3 3.4 - - + -
336C LEU* 4.2 2.5 - - + -
339C THR* 2.7 27.5 + - - -
340C THR* 3.5 21.1 - - - +
343C VAL* 3.1 22.2 - - - +
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Residues in contact with ASP 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C HIS* 2.9 27.2 - - + -
264C LEU* 4.8 1.7 - - - +
295C ALA 3.3 13.8 + - - +
296C ILE 3.7 4.7 - - - +
297C THR 3.3 0.4 - - - -
298C THR* 1.3 82.2 + - - +
300C CYS* 1.3 56.9 + - - +
302C GLN* 3.3 17.7 + - - +
303C ILE* 3.0 42.5 + - - +
339C THR* 4.2 14.0 - - + +
342C ARG* 5.7 1.4 - - - +
41D LEU* 3.5 22.9 - - + +
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Residues in contact with CYS 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C ILE* 4.2 10.8 - - - -
259C LEU* 5.0 1.8 - - - -
260C HIS* 3.7 34.5 - - - -
263C LEU* 4.0 14.7 - - + +
282C MET* 3.5 21.5 - - - -
296C ILE 3.1 24.7 + - - -
297C THR* 3.0 12.9 + - - +
299C ASP* 1.3 78.2 - - - +
301C LEU* 1.3 56.4 + - - +
303C ILE* 3.3 6.9 + - - +
304C LEU* 3.0 35.7 + - - +
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Residues in contact with LEU 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C LEU* 4.1 21.1 - - + +
282C MET* 3.7 26.0 - - + -
283C VAL* 4.0 23.8 - - + +
286C LEU* 3.8 32.1 - - + -
297C THR 3.0 17.1 + - - +
298C THR* 3.0 14.9 + - - +
300C CYS* 1.3 74.2 - - - +
302C GLN* 1.3 55.4 + - - +
304C LEU* 3.2 4.2 + - - +
305C ALA* 2.7 40.6 + - - +
315C ILE* 4.3 11.5 - - + +
324C LEU* 4.7 9.2 - - + -
343C VAL* 4.2 11.2 - - + -
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Residues in contact with GLN 302 (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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298C THR 2.9 6.3 + - - +
299C ASP* 3.4 20.8 + - - +
301C LEU* 1.3 77.1 - - - +
303C ILE* 1.3 89.5 + - - +
305C ALA* 4.1 2.0 - - - +
306C TYR* 3.0 36.9 + - - +
339C THR 4.8 0.7 - - - +
342C ARG* 3.9 35.6 - - + +
343C VAL* 3.6 23.5 - - + +
346C VAL* 4.1 13.6 - - + +
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Residues in contact with ILE 303 (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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260C HIS* 3.9 11.4 - - + +
263C LEU* 3.9 32.1 - - + +
264C LEU* 3.5 32.1 - - + -
270C LYS* 3.7 26.1 + - + +
274C ARG* 4.7 0.5 + - - -
299C ASP* 3.0 29.5 + - - +
300C CYS* 3.6 5.8 - - - +
302C GLN* 1.3 91.1 - - - +
304C LEU* 1.3 60.3 + - - +
306C TYR* 4.0 11.6 + - - +
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Residues in contact with LEU 304 (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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263C LEU* 3.6 30.3 - - + -
270C LYS* 3.8 27.4 - - + +
273C VAL* 4.0 11.0 - - + -
274C ARG* 2.9 32.6 + - + +
279C LEU* 3.9 23.8 - - + -
282C MET* 3.5 35.9 - - + -
300C CYS 3.0 21.2 + - - +
301C LEU* 3.7 4.0 - - - +
303C ILE* 1.3 78.4 - - - +
305C ALA* 1.3 60.7 + - - +
306C TYR 3.5 0.6 - - - +
308C ASN* 3.8 1.0 - - - +
311C SER* 3.6 10.9 + - - -
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Residues in contact with ALA 305 (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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301C LEU 2.7 22.2 + - - +
302C GLN* 4.1 1.8 - - - +
304C LEU* 1.3 74.1 - - - +
306C TYR* 1.3 64.7 + - - +
307C GLY 3.2 1.2 + - - -
308C ASN 3.0 14.8 + - - +
311C SER* 4.2 8.3 - - - -
312C LYS* 3.3 20.9 - - + -
315C ILE* 3.7 22.9 - - + +
343C VAL* 5.3 2.2 - - + -
346C VAL* 3.8 15.9 - - + -
347C LEU* 4.6 5.6 - - + -
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Residues in contact with TYR 306 (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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270C LYS* 5.3 5.1 + - - +
274C ARG* 5.0 1.7 + - - -
302C GLN* 3.0 26.0 + - - +
303C ILE* 4.2 9.6 - - - +
304C LEU 3.5 2.4 - - - +
305C ALA* 1.3 74.2 - - - +
307C GLY* 1.3 66.2 + - - +
308C ASN* 2.9 11.1 + - - +
346C VAL* 3.8 24.4 - - + +
24D GLU* 4.1 34.5 + - + +
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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