Contacts of the helix formed by residues 293 - 309 (chain C) in PDB entry 3JCK
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 293 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259C CYS* 5.7 8.3 - - - -
290C THR 4.8 1.4 + - - -
291C TYR* 3.0 16.5 + - - -
292C GLN* 1.3 86.9 + - - +
294C ARG* 1.3 68.0 + - - +
295C GLY 3.0 7.3 + - - -
296C ILE* 3.3 18.9 + - - +
297C ASP* 3.7 7.3 + - - +
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Residues in contact with ARG 294 (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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293C SER* 1.3 76.4 - - - +
295C GLY* 1.3 55.1 + - - +
297C ASP* 2.6 37.3 + - - +
298C ALA* 3.7 0.3 - - - +
320C GLN 3.8 17.8 + - - -
321C TYR* 4.2 15.1 - - - -
323C LYS* 3.1 48.9 - - + +
324C GLU* 2.8 40.6 - - + +
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Residues in contact with GLY 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C CYS* 6.2 4.6 - - - -
262C LEU* 5.2 8.7 - - - -
263C LYS* 5.0 7.6 - - - -
293C SER* 3.0 6.0 + - - +
294C ARG* 1.3 79.6 - - - +
296C ILE* 1.3 65.9 + - - +
299C MET* 3.3 24.5 + - - +
324C GLU* 3.2 27.9 + - - +
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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
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262C LEU* 4.7 16.6 - - + -
266C LEU* 5.5 8.6 - - + +
282C LEU* 3.7 26.7 - - + +
287C THR* 5.2 10.1 - - + +
288C LYS* 4.2 16.6 - - + -
291C TYR 4.4 10.1 + - - +
292C GLN* 3.6 37.5 - - + -
293C SER 3.4 13.9 - - - +
295C GLY* 1.3 73.8 - - - +
297C ASP* 1.3 76.6 + - + +
298C ALA 3.2 0.2 + - - -
299C MET* 3.3 3.1 + - - +
300C LYS* 3.0 27.2 + - - +
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Residues in contact with ASP 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C SER 4.1 8.0 - - - +
294C ARG* 2.6 37.6 + - - +
296C ILE* 1.3 78.5 - - + +
298C ALA* 1.3 84.6 + - - +
300C LYS* 3.7 4.4 - - - +
301C ALA* 3.0 23.4 + - - +
321C TYR* 3.3 30.2 + - - +
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Residues in contact with ALA 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C ARG 3.7 3.6 - - - +
295C GLY 3.5 0.2 - - - +
296C ILE 3.1 0.2 - - - -
297C ASP* 1.3 83.6 + - - +
299C MET* 1.3 61.6 + - + +
301C ALA* 2.8 23.0 + - - +
302C VAL* 2.9 17.5 + - + +
321C TYR* 3.2 37.2 - - + -
324C GLU* 3.0 28.7 - - + +
325C LEU* 5.3 5.4 - - + -
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Residues in contact with MET 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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262C LEU* 5.3 1.3 - - - -
263C LYS* 3.2 54.3 - - - +
266C LEU* 3.4 27.1 - - + -
267C LEU* 3.3 23.8 - - + +
270C ILE* 3.6 17.9 - - + +
278C VAL* 5.9 0.7 - - - -
295C GLY 3.3 17.4 + - - +
296C ILE 4.4 0.7 - - - +
298C ALA* 1.3 82.5 - - + +
300C LYS* 1.3 62.2 + - - +
302C VAL* 4.3 7.6 - - - -
303C ALA* 2.9 24.5 + - - +
324C GLU* 4.7 5.4 - - - +
325C LEU* 5.5 1.1 - - + -
331C THR* 5.1 4.3 - - + -
335C PHE* 4.2 14.4 - - + -
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Residues in contact with LYS 300 (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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266C LEU* 5.5 2.0 - - - +
275C ILE* 4.6 0.7 - - - -
278C VAL* 3.9 21.3 - - + -
279C LYS* 4.0 37.3 - - - +
282C LEU* 3.6 33.0 - - + +
296C ILE 3.0 18.4 + - - +
297C ASP* 3.7 5.2 - - - +
299C MET* 1.3 76.4 - - - +
301C ALA* 1.3 54.7 + - - +
303C ALA* 2.4 28.3 + - - -
304C GLU* 2.6 39.8 + - - +
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Residues in contact with ALA 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C ASP 3.0 13.8 + - - +
298C ALA 2.8 4.4 + - - -
300C LYS* 1.3 76.2 - - - +
302C VAL* 1.3 49.9 + - - +
304C GLU* 3.1 15.1 - - - +
305C ALA* 2.4 40.5 + - - +
313C ASP* 4.4 5.8 - - - +
317C ALA* 4.6 6.3 - - + -
321C TYR* 3.4 26.0 - - + +
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Residues in contact with VAL 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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270C ILE* 4.8 4.7 - - + -
298C ALA* 2.9 20.2 + - + +
299C MET* 4.0 6.7 - - - +
301C ALA* 1.3 76.1 - - - +
303C ALA* 1.3 58.3 + - - +
305C ALA* 3.4 6.0 - - - +
306C TYR* 2.9 26.0 + - - +
314C PHE* 3.7 31.2 - - + +
317C ALA* 3.5 33.0 - - + +
318C LEU* 5.8 1.8 - - + -
321C TYR* 4.7 0.7 - - + -
325C LEU* 5.1 4.7 - - + -
335C PHE* 4.2 34.3 - - + -
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Residues in contact with ALA 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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270C ILE* 3.7 30.3 - - + -
275C ILE* 3.6 20.2 - - + -
278C VAL* 4.6 6.5 - - + -
299C MET 2.9 15.2 + - - +
300C LYS* 2.4 26.6 + - - +
302C VAL* 1.3 64.9 - - - +
304C GLU* 1.3 62.9 + - - +
306C TYR* 2.7 21.8 + - - +
307C ASN* 3.0 13.1 + - - +
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Residues in contact with GLU 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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275C ILE* 3.7 17.5 - - + +
279C LYS* 4.7 6.5 - - - +
300C LYS* 2.6 57.0 + - - +
301C ALA* 3.1 22.1 + - - +
303C ALA* 1.3 73.8 - - - +
305C ALA* 1.3 56.5 + - - +
307C ASN* 3.7 8.0 - - + +
308C ASN* 2.7 48.0 + - - +
313C ASP* 5.7 0.9 - - - +
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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 ALA 2.4 31.9 + - - +
302C VAL* 3.4 8.7 - - - +
304C GLU* 1.3 79.5 - - - +
306C TYR* 1.3 60.8 + - - +
308C ASN* 4.0 3.7 - - - +
309C ARG* 3.1 14.6 + - - -
310C SER* 3.7 13.2 + - - +
313C ASP* 3.3 34.1 - - - +
314C PHE* 4.3 17.3 - - - +
317C ALA* 5.3 0.7 - - + -
342C LEU* 5.1 0.3 - - - +
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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 ILE* 4.4 10.3 - - + -
273C ASN* 2.9 34.1 + - - -
302C VAL 2.9 13.1 + - - +
303C ALA* 2.7 17.6 + - - +
305C ALA* 1.3 67.6 - - - +
307C ASN* 1.3 72.4 + - - +
308C ASN 3.0 2.2 - - - -
309C ARG* 2.6 49.7 + - - +
314C PHE* 4.6 8.1 - + + -
338C LEU* 3.4 48.0 - - + +
341C THR* 5.3 4.3 + - - -
342C LEU* 4.0 39.1 - - + +
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Residues in contact with ASN 307 (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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273C ASN* 3.0 34.0 + - - +
274C LEU 4.5 0.2 - - - -
275C ILE* 3.1 38.2 - - + +
303C ALA* 3.0 10.4 + - - +
304C GLU* 4.1 7.6 - - + +
306C TYR* 1.3 93.5 - - - +
308C ASN* 1.3 60.8 + - - +
309C ARG* 3.0 25.7 + - - +
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Residues in contact with ASN 308 (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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304C GLU* 2.7 36.0 + - - +
305C ALA* 4.0 5.6 + - - +
307C ASN* 1.3 78.9 + - - +
309C ARG* 1.3 71.6 + - - +
310C SER* 3.5 13.7 + - - +
313C ASP* 5.0 2.6 - - - +
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Residues in contact with ARG 309 (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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273C ASN* 4.9 9.7 - - - +
305C ALA 3.1 5.2 + - - -
306C TYR* 2.6 47.1 + - + +
307C ASN* 3.0 32.2 + - - +
308C ASN* 1.3 74.2 - - - +
310C SER* 1.3 59.3 + - - +
311C LEU 3.9 1.5 + - - -
342C LEU* 3.6 32.8 - - + +
345C SER* 5.3 3.5 + - - -
346C ASN* 3.8 27.6 + - - +
349C LYS* 5.0 15.9 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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