Contacts of the helix formed by residues 272 - 283 (chain D) 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 ASN 272 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D GLU 2.9 20.0 + - - -
4D GLU* 3.6 5.5 - - - +
5D GLY* 3.1 22.4 + - - -
6D LYS 2.7 28.8 + - - +
7D LEU* 3.7 16.2 - - + -
58D ASP* 3.3 12.7 + - - -
270D SER* 2.9 10.3 + - - +
271D PRO* 1.3 82.4 - - - +
273D LYS* 1.3 58.1 + - - +
274D GLU 3.3 2.7 - - - -
275D LEU* 3.1 15.7 + - + +
276D ALA* 2.9 28.7 + - - +
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Residues in contact with LYS 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D ALA* 3.8 20.0 - - + -
266D ILE* 3.9 29.3 - - + +
267D ASN 3.8 8.5 - - - +
268D ALA* 2.9 27.3 + - - +
270D SER* 3.3 21.3 + - - +
271D PRO 3.3 4.8 + - - +
272D ASN* 1.3 76.1 - - - +
274D GLU* 1.3 57.8 + - - +
276D ALA* 3.4 2.8 + - - +
277D LYS* 2.9 29.2 + - - +
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Residues in contact with GLU 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D PRO 5.1 1.0 + - - -
272D ASN 3.3 0.6 - - - -
273D LYS* 1.3 73.4 - - - +
275D LEU* 1.3 61.8 + - + +
277D LYS* 3.5 10.8 + - - +
278D GLU* 3.1 27.7 + - - +
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Residues in contact with LEU 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D GLY* 4.1 25.1 - - - -
6D LYS 4.7 0.4 - - - +
7D LEU* 4.1 15.0 - - + -
27D PHE* 3.9 11.6 - - + -
31D THR* 4.9 2.0 - - - +
33D ILE* 3.3 43.3 - - + -
272D ASN* 3.1 23.2 + - + +
274D GLU* 1.3 75.7 - - + +
276D ALA* 1.3 60.0 + - - +
278D GLU* 3.2 8.0 + - + +
279D PHE* 2.8 29.5 + - - +
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Residues in contact with ALA 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D LEU* 3.9 16.3 - - + +
58D ASP* 5.2 2.2 - - + +
59D ILE* 3.7 25.4 - - + -
266D ILE* 3.8 24.0 - - + -
272D ASN 2.9 15.1 + - - +
273D LYS 3.6 7.4 - - - +
275D LEU* 1.3 72.8 - - - +
277D LYS* 1.3 57.3 + - - +
279D PHE* 3.2 0.5 + - - +
280D LEU* 2.9 35.7 + - - +
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Residues in contact with LYS 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D THR* 2.8 36.7 + - - +
81D PRO* 4.7 0.7 - - - -
82D ALA* 5.2 2.3 - - - +
106D TYR* 3.3 20.0 - - + +
266D ILE* 4.1 8.7 - - + +
273D LYS 2.9 17.8 + - - +
274D GLU* 3.5 11.2 - - + +
275D LEU 3.3 0.2 - - - -
276D ALA* 1.3 76.0 - - - +
278D GLU* 1.3 57.5 + - - +
280D LEU* 4.0 2.1 - - - +
281D GLU* 2.9 61.9 + - - +
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Residues in contact with GLU 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D PHE* 4.5 10.3 - - + -
274D GLU 3.1 11.3 + - - +
275D LEU* 3.2 11.2 + - + +
277D LYS* 1.3 79.4 - - - +
279D PHE* 1.3 58.1 + - - +
281D GLU* 4.9 0.2 - - - -
282D ASN* 3.0 48.1 + - - +
283D TYR* 3.7 5.5 + - + -
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Residues in contact with PHE 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D LEU* 3.8 13.9 - - + -
9D ILE* 3.3 29.8 - - + -
20D LEU* 4.1 18.2 - - + -
23D VAL* 3.8 38.6 - - + -
24D GLY* 4.2 9.0 - - - -
27D PHE* 3.7 36.0 - + + -
35D VAL* 4.6 4.0 - - + -
59D ILE* 3.8 18.4 - - + -
61D PHE* 5.4 0.2 - + - -
275D LEU 2.8 16.5 + - - +
276D ALA 3.2 3.3 + - - +
278D GLU* 1.3 77.0 - - - +
280D LEU* 1.3 72.0 + - + +
283D TYR* 3.2 8.6 + - + +
284D LEU* 2.9 27.5 + - + -
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Residues in contact with LEU 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D ILE* 4.0 18.6 - - + -
61D PHE* 4.0 5.6 - - + -
106D TYR* 3.6 39.3 - - + -
108D ILE* 5.2 2.0 - - + -
264D ALA* 3.8 28.5 - - + +
266D ILE* 4.2 14.1 - - + -
276D ALA 2.9 23.9 + - - +
277D LYS 4.1 1.6 - - - +
279D PHE* 1.3 83.4 - - + +
281D GLU* 1.3 60.1 + - - +
284D LEU* 3.9 22.9 - - + -
285D LEU* 2.9 39.6 + - + +
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Residues in contact with GLU 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D PRO* 3.6 10.8 - - - +
82D ALA* 4.6 5.7 + - - +
85D PHE* 3.6 46.9 - - + +
88D LYS* 5.3 3.8 + - - -
106D TYR* 2.8 35.4 + - + -
277D LYS* 2.9 45.9 + - - +
278D GLU* 4.9 0.2 - - - -
280D LEU* 1.3 79.9 - - - +
282D ASN* 1.3 72.6 + - - +
285D LEU 3.5 17.8 - - - +
286D THR* 4.2 1.4 - - - +
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Residues in contact with ASN 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D PHE* 5.8 0.9 - - - -
88D LYS* 5.7 2.9 + - - -
278D GLU* 3.0 31.7 + - - +
281D GLU* 1.3 89.4 - - - +
283D TYR* 1.3 76.1 + - + +
286D THR* 3.2 18.9 - - - +
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Residues in contact with TYR 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D VAL* 3.8 11.3 - - + +
26D LYS* 3.7 14.1 - - + -
27D PHE* 3.5 52.7 - + + -
30D ASP* 3.1 32.2 + - + +
31D THR* 4.8 3.7 + - - -
278D GLU* 3.9 7.4 - - + -
279D PHE* 3.2 22.0 + - + +
282D ASN* 1.3 98.2 - - + +
284D LEU* 1.3 62.1 + - - +
286D THR* 3.1 17.4 + - - -
289D GLY* 3.5 11.4 - - - -
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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