Contacts of the helix formed by residues 283 - 293 (chain C) in PDB entry 3JXI
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 GLN 283 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C ILE* 2.9 31.1 + - - +
233C GLU* 4.8 0.6 - - - +
235C ARG* 3.1 46.5 - - - +
278C ALA 2.9 12.9 + - - +
281C THR* 2.7 33.9 + - - +
282C ASN* 1.3 80.3 - - - +
284C PRO* 1.4 59.2 - - - +
285C HIS 3.3 2.2 - - - -
286C ILE* 2.9 40.3 + - + +
287C VAL* 3.0 12.8 + - - +
331C MET* 3.5 2.3 - - - +
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Residues in contact with PRO 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C ASN* 3.3 16.4 - - - +
283C GLN* 1.4 87.2 - - - +
285C HIS* 1.3 65.9 + - + +
287C VAL* 3.3 8.2 + - + +
288C HIS* 2.8 45.5 + - + +
331C MET* 3.7 15.0 - - + -
334C LEU* 4.2 16.3 - - + +
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Residues in contact with HIS 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C LYS* 3.7 24.0 + - + -
283C GLN 3.3 1.2 + - - -
284C PRO* 1.3 87.5 - - + +
286C ILE* 1.3 59.0 + - + +
288C HIS* 3.6 15.6 + + - +
289C TYR* 3.0 25.6 + - - +
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Residues in contact with ILE 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C ILE* 4.4 11.9 - - + -
235C ARG 4.9 0.2 - - - -
236C CYS 4.6 2.2 - - - +
237C LYS* 4.0 34.8 - - + +
240C VAL* 3.9 32.3 - - + -
278C ALA* 3.6 19.5 - - + -
283C GLN* 2.9 39.6 + - + +
285C HIS* 1.3 74.6 - - + +
287C VAL* 1.3 59.6 + - - +
288C HIS 3.3 0.2 - - - -
289C TYR* 3.9 5.1 - - - +
290C LEU* 3.0 41.9 + - + +
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Residues in contact with VAL 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C LEU* 3.9 17.8 - - + +
278C ALA* 3.9 5.4 - - + -
279C ALA* 3.7 35.9 - - + +
283C GLN 3.0 14.7 + - - +
284C PRO* 3.5 9.6 - - + +
286C ILE* 1.3 74.2 - - - +
288C HIS* 1.3 56.9 + - + +
290C LEU 3.5 0.3 + - - -
291C THR* 2.7 40.2 + - + +
331C MET* 4.1 8.7 - - - -
334C LEU* 4.0 15.7 - - + -
335C LEU* 3.6 27.1 - - + -
338C LYS* 5.3 4.9 - - + -
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Residues in contact with HIS 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C PRO* 2.8 36.9 + - + +
285C HIS* 3.7 17.0 - + - +
287C VAL* 1.3 74.8 - - - +
289C TYR* 1.3 56.9 + - - +
291C THR* 3.9 1.1 - - - -
292C GLU* 2.7 68.2 + - - +
334C LEU* 3.6 34.5 - - + +
338C LYS* 4.2 12.3 - - + +
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Residues in contact with TYR 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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237C LYS* 3.1 32.5 - - + +
240C VAL* 4.2 15.3 - - + -
241C GLU* 3.3 53.3 + - + +
244C VAL* 3.8 24.4 - - + +
245C GLU* 3.9 11.3 - - - +
285C HIS 3.0 10.8 + - - +
286C ILE* 3.9 6.1 - - - +
287C VAL 3.4 0.4 - - - -
288C HIS* 1.3 76.9 - - - +
290C LEU* 1.3 55.4 + - + +
292C GLU* 4.8 1.3 - - - -
293C ASN* 2.6 73.0 + - + +
295C HIS* 4.2 3.8 - + - -
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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
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228C LEU* 5.0 7.6 - - + -
232C ILE* 4.3 6.1 - - + -
240C VAL* 4.3 10.3 - - + -
244C VAL* 4.0 27.1 - - + -
250C VAL* 4.5 13.9 - - + -
274C PRO* 3.9 10.5 - - + +
275C LEU* 3.9 37.2 - - + +
278C ALA* 4.3 0.9 - - + -
286C ILE* 3.0 36.5 + - + +
288C HIS 3.3 0.2 - - - -
289C TYR* 1.3 78.8 - - + +
291C THR* 1.3 55.7 + - - +
293C ASN* 3.6 3.1 + - - +
297C GLN* 2.9 10.9 - - - -
298C ALA* 2.6 42.2 + - + -
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Residues in contact with THR 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C LEU* 3.9 21.3 - - + -
287C VAL* 2.7 27.3 + - + +
288C HIS* 3.3 4.9 + - - -
290C LEU* 1.3 79.1 - - - +
292C GLU* 1.3 58.5 + - - +
297C GLN* 2.9 25.7 + - - +
298C ALA 3.5 20.6 - - - +
300C LEU* 4.1 18.8 - - + -
335C LEU* 5.8 0.2 - - + -
338C LYS* 3.4 18.3 - - + +
342C LEU* 3.9 24.9 - - + +
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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
----------------------------------------------------------
288C HIS* 2.7 58.3 + - - +
289C TYR* 4.6 1.5 - - - +
291C THR* 1.3 78.6 - - - +
293C ASN* 1.3 68.5 + - - +
294C GLY* 4.7 0.2 - - - -
297C GLN* 3.6 5.2 - - - +
338C LYS* 2.8 34.0 + - - +
342C LEU* 6.1 0.2 - - + -
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Residues in contact with ASN 293 (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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244C VAL* 3.9 2.6 - - - +
289C TYR* 2.6 68.7 + - + +
290C LEU* 3.6 12.5 + - - +
292C GLU* 1.3 78.0 - - - +
294C GLY* 1.3 58.7 + - - +
295C HIS* 2.9 31.5 + - + +
296C LYS 2.8 32.5 + - - +
297C GLN* 2.8 33.8 - - - +
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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
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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