Contacts of the helix formed by residues 280 - 292 (chain C) in PDB entry 2JRI
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 THR 280 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278C SER 3.6 2.7 + - - +
279C ASP* 1.3 76.0 + - - +
281C ILE* 1.3 65.7 + - - +
282C GLU* 3.2 5.8 - - - +
283C ASN* 3.1 18.8 + - - +
284C VAL* 3.0 24.0 + - - +
310C ASP 4.1 10.1 - - - +
311C GLY* 4.8 4.5 - - - -
312C ARG 3.6 15.7 - - - +
313C THR* 3.9 18.8 - - + -
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Residues in contact with ILE 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C THR* 1.3 70.7 - - - +
282C GLU* 1.3 56.4 - - - +
284C VAL* 3.1 7.3 + - + +
285C LYS* 2.9 36.9 + - - +
301C LEU* 3.8 21.8 - - + -
308C LEU* 3.6 40.6 - - + +
309C GLU 3.1 31.2 - - - +
310C ASP* 3.6 8.0 + - - -
312C ARG 3.0 14.6 + - - +
314C LEU* 3.5 27.8 - - + -
317C TYR* 3.9 8.3 - - + -
325C LEU* 5.2 1.1 - - + -
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Residues in contact with GLU 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C THR* 3.2 4.9 - - - +
281C ILE* 1.3 76.3 - - - +
283C ASN* 1.3 64.1 + - - +
285C LYS* 3.0 21.1 + - + +
286C ALA* 3.1 10.7 + - - +
296C PRO* 5.4 6.0 - - + +
310C ASP* 3.0 37.7 + - + +
311C GLY* 5.9 1.2 - - - -
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Residues in contact with ASN 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C GLU* 5.1 2.6 + - - -
279C ASP* 2.7 28.8 + - - +
280C THR* 3.1 22.3 + - - +
282C GLU* 1.3 78.8 - - - +
284C VAL* 1.3 62.9 + - - +
286C ALA* 3.2 20.9 + - - +
287C LYS* 3.3 25.1 + - - +
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Residues in contact with VAL 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C ILE* 5.0 5.4 - - + -
273C LEU* 4.1 24.5 - - + -
275C VAL* 3.8 28.0 - - + -
279C ASP* 4.3 6.1 - - - +
280C THR 3.0 19.0 + - - +
281C ILE* 3.1 11.6 + - - +
283C ASN* 1.3 73.0 - - - +
285C LYS* 1.3 66.3 + - - +
287C LYS* 3.1 12.0 + - - +
288C ILE* 3.0 27.8 + - + +
301C LEU* 4.2 10.5 - - + -
314C LEU* 4.4 15.3 - - + -
325C LEU* 5.1 4.0 - - + -
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Residues in contact with LYS 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C ILE* 2.9 26.6 + - - +
282C GLU* 3.2 11.0 - - - +
284C VAL* 1.3 76.6 - - - +
286C ALA* 1.3 52.0 + - - +
288C ILE* 3.2 1.6 + - - -
289C GLN* 2.8 31.2 + - - +
296C PRO* 2.9 36.2 + - + +
297C ASP* 5.1 1.2 - - - +
299C GLN* 2.9 58.3 + - + +
300C ARG* 4.6 5.1 - - - +
301C LEU* 4.2 13.9 - - + +
308C LEU 5.5 2.8 + - - -
310C ASP* 2.7 37.3 + - - +
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Residues in contact with ALA 286 (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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282C GLU 3.1 7.8 + - - +
283C ASN* 3.3 20.0 - - - +
284C VAL 3.2 0.2 - - - -
285C LYS* 1.3 76.7 - - - +
287C LYS* 1.3 59.7 + - + +
289C GLN* 2.8 33.0 + - - +
290C ASP* 3.0 14.3 + - - +
296C PRO* 4.7 4.4 - - + +
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Residues in contact with LYS 287 (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 LEU* 4.1 15.3 - - + -
274C GLU 2.8 28.8 + - - +
275C VAL* 3.5 4.4 - - + +
276C GLU* 3.4 15.1 + - - -
279C ASP* 2.7 27.8 + - - -
283C ASN* 3.3 25.3 + - - +
284C VAL* 3.1 15.2 + - - +
286C ALA* 1.3 79.2 - - + +
288C ILE* 1.3 56.6 + - - +
290C ASP* 3.4 6.4 + - - +
291C LYS* 3.0 36.2 + - + +
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Residues in contact with ILE 288 (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 VAL* 4.4 8.1 - - + -
271C ILE* 6.4 0.7 - - + -
273C LEU* 3.7 30.5 - - + -
284C VAL* 3.0 19.2 + - + +
285C LYS 3.5 0.7 - - - +
287C LYS* 1.3 74.5 - - - +
289C GLN* 1.3 56.1 + - - +
291C LYS* 4.2 7.2 - - + -
292C GLU* 2.7 45.6 + - + +
294C ILE* 6.0 0.7 - - + -
299C GLN* 3.2 33.2 - - + +
301C LEU* 3.9 28.7 - - + -
327C LEU* 4.1 23.1 - - + -
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Residues in contact with GLN 289 (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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285C LYS 2.8 13.6 + - - +
286C ALA* 2.8 16.9 + - - +
288C ILE* 1.3 77.0 - - - +
290C ASP* 1.3 58.5 + - - +
293C GLY* 2.8 37.6 + - - +
294C ILE 3.6 17.7 - - - +
295C PRO* 3.8 8.0 - - + +
296C PRO* 3.3 25.3 - - + +
299C GLN* 3.2 6.7 - - - +
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Residues in contact with ASP 290 (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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286C ALA 3.0 10.7 + - - +
287C LYS* 3.7 8.9 - - - +
289C GLN* 1.3 77.9 - - - +
291C LYS* 1.3 75.0 + - - +
292C GLU 4.2 2.6 - - - +
293C GLY* 4.9 0.2 - - - -
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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
----------------------------------------------------------
263C VAL* 6.0 0.2 - - + -
271C ILE* 3.7 40.4 - - + -
272C THR 4.4 11.0 + - - -
273C LEU* 3.8 31.5 - - + +
274C GLU 5.6 1.4 - - - +
287C LYS* 3.0 15.6 + - - +
288C ILE* 3.7 6.1 - - + +
290C ASP* 1.3 90.0 + - - +
292C GLU* 1.3 67.1 + - + +
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Residues in contact with GLU 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C VAL* 6.5 0.2 - - + -
265C THR* 4.3 8.4 - - + +
269C LYS* 2.7 40.3 + - - -
271C ILE* 3.4 18.5 - - + +
288C ILE* 2.7 32.0 + - + +
289C GLN 3.7 0.4 - - - -
290C ASP 4.2 2.3 - - - +
291C LYS* 1.3 80.5 - - + +
293C GLY* 1.3 59.4 + - - +
294C ILE* 3.7 20.4 - - + +
327C LEU* 4.9 10.3 - - + -
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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