Contacts of the helix formed by residues 286 - 297 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88G LYS* 6.0 3.4 - - - +
281G GLU 4.2 2.2 - - - +
282G ASN* 3.2 32.0 + - - +
283G TYR 3.1 9.4 + - - +
284G LEU 2.9 1.6 + - - -
285G LEU* 1.3 79.5 - - - +
287G ASP* 1.3 65.9 + - - +
288G GLU* 3.7 10.1 + - - +
289G GLY 3.1 14.7 + - - -
290G LEU* 2.4 36.0 + - - +
304G LEU* 3.5 5.4 - - - -
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Residues in contact with ASP 287 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286G THR* 1.3 71.4 - - - +
288G GLU* 1.3 66.2 + - + +
291G GLU* 3.1 26.2 + - - +
304G LEU* 4.0 1.2 - - - +
306G SER* 3.0 35.2 + - - -
307G TYR* 3.3 35.3 + - + +
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Residues in contact with GLU 288 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286G THR* 3.1 8.9 - - - +
287G ASP* 1.3 80.4 - - + +
289G GLY* 1.3 62.5 + - - +
291G GLU* 3.7 4.2 - - - +
292G ALA* 3.3 20.6 + - - +
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Residues in contact with GLY 289 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G VAL* 3.5 20.7 - - - +
283G TYR 3.5 21.0 + - - -
284G LEU* 3.6 7.0 - - - -
286G THR* 3.0 7.7 + - - -
288G GLU* 1.3 75.9 - - - +
290G LEU* 1.3 64.9 + - - +
292G ALA* 3.1 14.4 + - - +
293G VAL* 3.2 11.6 + - - +
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Residues in contact with LEU 290 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108G ILE* 4.5 11.2 - - + +
284G LEU* 2.6 29.2 - - + +
285G LEU* 3.5 16.6 - - + -
286G THR 2.4 49.1 + - - +
287G ASP* 4.6 0.2 - - - -
289G GLY* 1.3 72.9 - - - +
291G GLU* 1.3 54.2 + - - +
293G VAL* 3.2 8.7 + - - +
294G ASN* 2.8 38.4 + - - +
299G LEU* 4.2 10.2 - - + +
302G VAL* 4.3 17.5 - - + -
304G LEU* 3.7 27.1 - - + -
307G TYR* 4.1 17.5 - - + -
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Residues in contact with GLU 291 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287G ASP 3.1 21.3 + - - +
288G GLU* 3.7 5.8 - - - +
289G GLY 3.3 0.2 - - - -
290G LEU* 1.3 78.3 - - - +
292G ALA* 1.3 56.4 + - - +
294G ASN* 3.9 1.0 - - - +
295G LYS* 3.0 32.2 + - - +
307G TYR* 3.5 29.8 + - + +
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Residues in contact with ALA 292 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G GLY* 3.7 25.0 - - - +
22G GLU* 4.8 8.3 - - + -
23G VAL* 3.9 9.0 - - + +
288G GLU 3.3 10.0 + - - +
289G GLY* 3.1 11.7 + - - +
291G GLU* 1.3 80.8 - - - +
293G VAL* 1.3 62.5 + - - +
295G LYS* 3.6 5.4 + - - +
296G ASP* 3.5 12.1 + - - +
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Residues in contact with VAL 293 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G ILE* 5.8 5.4 - - + -
15G LYS* 6.2 0.2 - - + -
16G GLY* 3.6 24.0 - - - +
19G GLY* 4.1 7.4 - - - -
20G LEU* 4.0 24.5 - - + +
23G VAL* 4.2 1.3 - - + -
284G LEU* 3.8 22.9 - - + -
289G GLY 3.2 13.9 + - - +
290G LEU* 3.2 6.1 + - - +
292G ALA* 1.3 75.0 - - - +
294G ASN* 1.3 63.9 + - - +
296G ASP* 3.0 15.8 + - - +
297G LYS 3.2 12.5 + - - +
299G LEU* 3.7 28.7 - - + -
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Residues in contact with ASN 294 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290G LEU 2.8 21.6 + - - +
291G GLU 3.9 3.1 - - - +
293G VAL* 1.3 73.9 - - - +
295G LYS* 1.3 60.9 + - - +
297G LYS 3.5 5.3 + - - -
298G PRO* 3.3 32.7 - - - +
299G LEU* 3.1 35.4 + - + +
300G GLY 4.3 6.6 + - - +
302G VAL* 5.3 1.5 - - - +
307G TYR* 3.8 28.2 + - + +
311G LEU* 6.1 2.2 - - - +
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Residues in contact with LYS 295 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233G SER* 4.5 2.3 + - - -
291G GLU 3.0 18.9 + - - +
292G ALA* 3.7 6.5 - - - +
293G VAL 3.2 0.2 - - - -
294G ASN* 1.3 75.9 - - - +
296G ASP* 1.3 65.8 + - - +
298G PRO* 5.6 0.5 - - - +
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Residues in contact with ASP 296 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G GLY* 3.2 14.1 - - - -
17G TYR* 3.5 1.0 + - - -
18G ASN* 3.1 22.6 + - - +
19G GLY* 3.0 34.6 + - - +
233G SER* 2.7 28.4 + - - -
292G ALA 3.5 2.4 + - - +
293G VAL 3.0 10.1 + - - +
295G LYS* 1.3 79.0 - - - +
297G LYS* 1.3 64.1 + - - +
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Residues in contact with LYS 297 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G GLY 5.3 2.9 - - - -
14G ASP* 3.0 26.5 - - - +
15G LYS* 3.9 9.2 - - - +
16G GLY 3.8 20.3 + - - +
17G TYR* 6.5 0.7 - - - -
230G TRP* 4.0 11.7 - - - +
233G SER* 3.7 9.0 - - - +
234G ASN* 3.4 28.9 - - - +
293G VAL 3.2 10.2 + - - +
294G ASN* 3.5 2.8 - - - -
296G ASP* 1.3 98.1 - - - +
298G PRO* 1.3 75.8 - - + +
299G LEU* 3.5 5.4 + - - +
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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