Contacts of the helix formed by residues 272 - 283 (chain A) in PDB entry 1T0K
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A GLY* 3.5 22.1 + - - +
6A LYS* 2.6 47.9 + - - +
7A LEU* 3.6 8.8 - - + +
58A ASP* 4.0 10.9 + - - +
270A SER* 3.1 6.9 + - - -
271A PRO* 1.3 92.8 - - - +
273A LYS* 1.3 62.5 + - - +
274A GLU* 3.3 3.6 - - - +
275A LEU* 3.3 17.3 + - + +
276A ALA* 3.2 16.8 + - - +
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Residues in contact with LYS 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ALA* 3.6 25.8 - - + +
78A GLU 5.8 1.0 - - - +
266A ILE* 4.0 21.3 - - + +
267A ASN 3.7 10.1 - - - +
268A ALA* 3.6 25.4 + - - +
270A SER* 3.2 21.8 - - - +
271A PRO 3.3 3.8 + - - +
272A ASN* 1.3 75.8 - - - +
274A GLU* 1.4 64.6 + - + +
276A ALA* 3.1 13.2 + - - +
277A LYS* 3.2 12.5 + - - +
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Residues in contact with GLU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A ASN* 3.3 1.7 - - - +
273A LYS* 1.4 79.0 - - + +
275A LEU* 1.3 63.4 + - + +
277A LYS* 3.5 20.1 + - - +
278A GLU* 3.6 11.1 + - - +
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Residues in contact with LEU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLY* 3.9 21.8 - - - +
6A LYS 4.5 1.8 - - - +
7A LEU* 3.5 20.4 - - + +
27A PHE* 3.8 3.2 - - + -
33A ILE* 3.4 49.6 - - + -
272A ASN* 3.3 18.0 + - + +
273A LYS 3.3 0.4 - - - -
274A GLU* 1.3 79.1 - - + +
276A ALA* 1.4 65.1 + - - +
278A GLU* 3.3 19.4 + - - +
279A PHE* 3.0 19.1 + - - +
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Residues in contact with ALA 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 3.4 24.8 - - + +
58A ASP* 5.3 0.4 - - + +
59A ILE* 3.9 13.7 - - + -
266A ILE* 3.7 28.0 - - + -
272A ASN 3.2 8.3 + - - +
273A LYS 3.1 11.5 + - - +
275A LEU* 1.4 76.8 - - - +
277A LYS* 1.4 52.9 - - - +
279A PHE* 3.3 1.9 + - - +
280A LEU* 2.9 40.9 + - + +
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Residues in contact with LYS 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A THR* 3.1 42.4 + - + +
81A PRO* 4.3 1.6 - - - -
82A ASP* 5.2 2.2 - - - +
106A TYR* 3.4 11.9 - - - +
266A ILE* 4.3 7.9 - - + +
273A LYS 3.2 7.5 + - - +
274A GLU* 3.6 17.6 + - - +
275A LEU 3.3 0.2 - - - -
276A ALA* 1.4 78.5 - - - +
278A GLU* 1.4 56.5 + - - +
280A LEU* 5.0 1.6 - - - -
281A GLU* 2.8 74.2 + - - +
282A ASN* 5.9 1.6 - - - +
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Residues in contact with GLU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PHE* 4.0 15.7 - - + -
31A THR* 4.3 18.7 - - - +
33A ILE* 6.1 0.2 - - - -
274A GLU 3.6 8.2 + - - +
275A LEU* 3.3 21.7 + - - +
277A LYS* 1.4 78.8 - - - +
279A PHE* 1.3 58.2 + - - +
282A ASN* 2.9 48.1 + - + +
283A TYR* 3.5 21.6 + - + -
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Residues in contact with PHE 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 3.9 10.5 - - + -
9A ILE* 3.1 31.9 - - + -
20A LEU* 4.0 24.9 - - + -
23A VAL* 3.7 24.2 - - + -
24A GLY* 4.0 9.6 - - - -
27A PHE* 3.5 34.9 - + + -
35A VAL* 3.8 15.5 - - + -
59A ILE* 3.7 19.1 - - + -
61A PHE* 5.5 0.7 - + - -
275A LEU 3.0 12.2 + - - +
276A ALA 3.5 5.8 - - - +
278A GLU* 1.3 75.8 - - - +
280A LEU* 1.3 76.5 + - + +
283A TYR* 2.9 31.6 + - + +
284A LEU* 3.2 11.0 + - + -
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Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ILE* 3.7 35.2 - - + -
61A PHE* 3.9 15.3 - - + -
106A TYR* 4.7 20.4 - - + -
108A ILE* 5.0 1.1 - - + -
264A ALA* 3.4 35.9 - - + +
266A ILE* 4.3 15.3 - - + -
276A ALA* 2.9 30.7 + - + +
277A LYS* 4.4 2.0 - - - +
279A PHE* 1.3 78.5 - - + +
281A GLU* 1.4 55.9 + - - +
284A LEU* 3.8 15.4 - - + +
285A LEU* 3.0 36.7 + - - +
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Residues in contact with GLU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PRO* 3.3 18.8 - - - +
82A ASP* 5.0 5.5 - - - +
85A PHE* 3.4 39.9 - - + +
106A TYR* 2.6 42.6 + - + +
277A LYS* 2.8 55.7 + - - +
280A LEU* 1.4 74.5 - - - +
282A ASN* 1.3 73.4 + - - +
283A TYR 3.6 0.4 - - - -
285A LEU 3.7 13.3 - - - +
286A THR* 4.2 2.3 - - - +
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Residues in contact with ASN 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LYS* 4.7 5.9 + - - -
85A PHE* 5.5 2.6 - - - -
277A LYS* 5.0 1.6 - - - +
278A GLU* 2.9 38.4 + - + +
281A GLU* 1.3 89.6 + - - +
283A TYR* 1.3 74.9 + - + +
286A THR* 4.3 14.9 + - - +
288A GLU* 4.8 1.9 - - - +
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Residues in contact with TYR 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A VAL* 3.5 19.0 - - + +
26A LYS* 4.0 43.2 + - + +
27A PHE* 3.7 51.8 - + + -
30A ASP* 3.7 24.3 + - + +
31A THR* 5.1 2.1 - - - +
278A GLU* 3.5 27.9 + - + -
279A PHE* 2.9 14.7 + - + +
281A GLU 3.6 0.2 - - - -
282A ASN* 1.3 93.1 - - + +
284A LEU* 1.3 59.3 - - - +
286A THR* 3.5 8.4 + - - -
288A GLU* 5.2 0.3 - - - +
289A GLY* 3.5 18.0 + - - -
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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