Contacts of the helix formed by residues 279 - 287 (chain A) in PDB entry 1T5A
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 ARG 279 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A ARG 3.4 21.1 - - - +
247A LYS* 3.6 24.2 - - - +
275A GLU* 2.8 45.6 + - + +
276A GLY 3.5 4.5 - - - -
278A ARG* 1.3 79.7 - - + +
280A PHE* 1.3 62.2 + - - +
281A ASP 3.4 2.2 - - - -
282A GLU* 3.2 42.1 + - + +
283A ILE* 3.1 22.0 + - + +
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Residues in contact with PHE 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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271A ILE* 4.0 11.7 - - + -
276A GLY 3.1 9.1 + - - +
277A VAL* 3.3 16.8 - - - +
278A ARG 3.1 3.8 + - - -
279A ARG* 1.3 76.3 - - - +
281A ASP* 1.3 59.4 + - - +
283A ILE* 2.8 6.1 + - + +
284A LEU* 2.7 60.8 + - + -
290A ILE* 3.7 41.1 - - + -
312A MET* 4.4 4.9 - - + -
313A MET* 3.2 39.9 - - + -
316A ARG* 3.8 37.5 - - + +
317A CYS* 3.8 10.1 - - - -
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Residues in contact with ASP 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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278A ARG 4.9 2.3 + - - +
279A ARG 3.4 0.8 - - - -
280A PHE* 1.3 82.0 - - - +
282A GLU* 1.3 63.0 + - - +
284A LEU* 3.5 6.3 + - - +
285A GLU* 3.1 24.3 + - - +
316A ARG* 3.2 39.9 + - - +
319A ARG* 5.3 4.0 + - - -
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Residues in contact with GLU 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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247A LYS* 3.3 12.3 - - - +
248A ALA* 2.6 49.0 + - + +
249A SER 4.4 0.9 + - - -
279A ARG* 3.2 42.6 + - + +
280A PHE 3.1 0.2 - - - -
281A ASP* 1.3 80.2 - - - +
283A ILE* 1.3 59.2 + - - +
285A GLU* 3.5 7.7 - - - +
286A ALA* 3.4 14.4 + - - +
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Residues in contact with ILE 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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245A ILE* 3.7 16.2 - - + +
246A ARG 3.5 19.7 - - - +
247A LYS 4.0 18.4 - - - +
248A ALA* 4.7 2.0 - - - +
251A VAL* 4.0 6.5 - - + -
269A SER* 3.6 33.7 - - - +
271A ILE* 3.6 15.9 - - + -
276A GLY 3.5 24.5 - - - +
279A ARG 3.2 9.4 - - - +
280A PHE* 2.8 7.1 + - - +
282A GLU* 1.3 72.8 - - - +
284A LEU* 1.3 62.9 + - - +
285A GLU 3.1 2.2 - - - -
286A ALA* 3.1 4.2 + - - +
287A SER* 2.6 31.0 + - - +
290A ILE* 4.1 7.9 - - + -
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Residues in contact with LEU 284 (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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280A PHE* 2.7 47.8 + - + +
281A ASP* 3.9 7.4 - - - +
283A ILE* 1.3 73.6 - - - +
285A GLU* 1.3 58.4 - - - +
287A SER* 3.4 6.6 + - - +
289A GLY* 5.1 2.9 - - - +
290A ILE* 3.8 25.7 - - + +
316A ARG* 3.7 26.2 - - + +
317A CYS* 4.0 4.7 - - - -
320A ALA* 4.0 11.9 - - + -
322A LYS* 2.8 52.6 + - + -
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Residues in contact with GLU 285 (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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252A HIS* 5.3 3.3 + - - -
281A ASP 3.1 18.1 + - - +
282A GLU* 3.5 8.6 - - - +
283A ILE 3.1 0.4 - - - -
284A LEU* 1.3 77.1 - - - +
286A ALA* 1.3 66.5 + - - +
287A SER 3.2 0.2 - - - -
322A LYS* 2.8 22.5 + - - +
706A GOL 2.8 27.0 + - - -
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Residues in contact with ALA 286 (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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248A ALA* 4.3 7.6 - - + -
251A VAL* 3.3 17.8 - - + +
252A HIS* 3.6 31.9 - - + +
255A ARG* 3.0 26.3 + - - -
282A GLU 3.4 8.9 + - - +
283A ILE 3.1 7.6 + - - +
285A GLU* 1.3 86.8 + - - +
287A SER* 1.3 58.1 + - - +
706A GOL 4.6 7.1 - - - -
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Residues in contact with SER 287 (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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251A VAL* 3.6 7.1 - - - +
255A ARG* 4.7 1.1 - - - +
267A ILE 3.6 8.7 - - - -
269A SER* 2.8 24.6 + - - -
283A ILE* 2.6 23.7 + - - +
284A LEU* 3.4 6.5 + - - -
285A GLU 3.2 1.0 - - - -
286A ALA* 1.3 79.9 - - - +
288A ASP* 1.3 63.5 + - - +
289A GLY 3.4 20.4 - - - -
290A ILE* 4.7 0.7 - - - -
322A LYS* 2.7 30.8 + - - -
706A GOL 3.3 6.8 - - - -
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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