Contacts of the helix formed by residues 286 - 297 (chain C) in PDB entry 5TJ4
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 286 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354B ARG* 3.2 27.1 - - - +
282C ASN 3.2 30.4 + - - +
283C TYR* 3.1 9.4 + - - +
284C LEU 2.9 4.6 + - - -
285C LEU* 1.3 80.8 - - - +
287C ASP* 1.3 65.7 + - - +
288C GLU* 2.9 9.8 + - - +
289C GLY 3.1 14.7 + - - -
290C LEU* 3.0 22.1 + - - +
304C LEU* 3.5 10.9 - - - +
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Residues in contact with ASP 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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286C THR* 1.3 72.7 - - - +
288C GLU* 1.3 58.8 + - - +
291C GLU* 3.1 31.8 + - - +
304C LEU* 4.0 0.9 - - - +
306C SER* 3.0 35.9 + - - -
307C TYR* 3.3 36.7 + - + +
310C GLU* 4.4 9.3 - - - +
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Residues in contact with GLU 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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26C LYS* 5.6 12.6 - - + -
283C TYR 5.6 0.2 - - - +
286C THR* 3.0 8.4 + - - +
287C ASP* 1.3 79.7 - - - +
289C GLY* 1.3 61.5 + - - +
291C GLU* 3.6 4.8 + - - +
292C ALA* 3.3 20.6 + - - +
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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
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23C VAL* 3.5 19.9 - - - +
283C TYR 3.5 21.1 + - - -
284C LEU* 3.6 7.6 - - - -
286C THR* 3.0 8.1 + - - -
288C GLU* 1.3 77.3 - - - +
290C LEU* 1.3 64.2 + - - +
292C ALA* 3.1 14.7 + - - +
293C VAL* 3.2 10.7 + - - +
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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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108C ILE* 3.9 21.3 - - + +
284C LEU* 3.3 26.3 + - + +
285C LEU* 4.5 8.3 - - + -
286C THR 3.0 11.5 + - - +
289C GLY* 1.3 70.8 - - - +
291C GLU* 1.3 55.3 + - - +
293C VAL* 3.2 5.3 + - - +
294C ASN* 2.8 38.3 + - - +
299C LEU* 3.9 22.1 - - + +
302C VAL* 3.9 20.2 - - + -
304C LEU* 3.5 39.3 - - + +
307C TYR* 4.0 16.4 - - + -
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Residues in contact with GLU 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C ASP* 3.1 20.8 + - - +
288C GLU* 3.7 6.7 - - - +
290C LEU* 1.3 78.6 - - - +
292C ALA* 1.3 55.4 + - - +
294C ASN* 3.9 1.0 - - - +
295C LYS* 3.0 32.8 + - + +
307C TYR* 3.5 36.8 - - - +
310C GLU* 4.3 7.8 - - - +
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Residues in contact with ALA 292 (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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19C GLY* 3.7 24.3 - - - +
22C GLU* 4.8 9.0 - - + -
23C VAL* 3.9 8.5 - - + +
288C GLU 3.3 10.0 + - - +
289C GLY* 3.1 11.9 + - - +
291C GLU* 1.3 81.4 - - - +
293C VAL* 1.3 63.3 + - - +
295C LYS* 3.6 5.7 + - - +
296C ASP* 3.5 12.0 + - - +
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Residues in contact with VAL 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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11C ILE* 5.8 5.6 - - + -
15C LYS* 6.2 0.2 - - + -
16C GLY* 3.6 24.0 - - - +
19C GLY* 4.1 8.3 - - - -
20C LEU* 4.0 24.0 - - + -
23C VAL* 4.2 1.8 - - + -
284C LEU* 3.8 24.2 - - + -
289C GLY 3.6 12.3 - - - +
290C LEU* 3.2 5.5 + - - +
292C ALA* 1.3 75.9 - - - +
294C ASN* 1.3 62.4 + - - +
296C ASP* 3.0 15.1 + - - +
297C LYS 3.2 12.6 + - - +
299C LEU* 3.7 29.6 - - + -
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Residues in contact with ASN 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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290C LEU 2.8 21.6 + - - +
291C GLU 3.9 3.6 - - - +
293C VAL* 1.3 73.3 - - - +
295C LYS* 1.3 61.8 + - - +
297C LYS 4.1 5.6 - - - -
298C PRO* 3.3 32.3 - - - +
299C LEU* 3.1 35.0 + - + +
300C GLY 4.4 6.8 + - - +
307C TYR* 3.7 15.5 + - + +
311C LEU* 3.6 29.2 - - - +
317C ILE* 5.9 1.0 - - - +
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Residues in contact with LYS 295 (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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233C SER* 4.4 2.8 + - - -
291C GLU* 3.0 23.0 + - + +
292C ALA* 3.8 6.3 - - - +
294C ASN* 1.3 75.7 - - - +
296C ASP* 1.3 65.8 + - - +
298C PRO* 5.6 0.5 - - - +
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Residues in contact with ASP 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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15C LYS 4.8 0.2 - - - +
16C GLY* 3.2 14.9 - - - -
17C TYR 3.5 0.5 + - - -
18C ASN* 3.1 28.4 + - - +
19C GLY* 3.0 34.2 + - - +
233C SER* 2.6 28.3 + - - -
292C ALA 3.5 3.0 + - - +
293C VAL 3.0 11.0 + - - +
294C ASN 4.0 0.2 - - - -
295C LYS* 1.3 78.7 - - - +
297C LYS* 1.3 63.4 + - - +
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Residues in contact with LYS 297 (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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13C GLY 5.2 1.1 - - - +
14C ASP* 3.1 25.6 - - - +
15C LYS* 3.9 9.7 - - - +
16C GLY* 3.7 21.3 + - - +
17C TYR* 6.5 0.2 - - + -
230C TRP* 4.0 13.2 - - - +
233C SER* 3.8 11.7 - - - -
234C ASN* 4.6 13.7 - - - +
293C VAL 3.2 10.4 + - - +
294C ASN* 3.5 3.0 - - - -
296C ASP* 1.3 96.5 - - - +
298C PRO* 1.4 75.4 - - + +
299C LEU* 3.6 5.5 + - - +
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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
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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