Contacts of the helix formed by residues 279 - 287 (chain B) in PDB entry 5T8Y
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 SER 279 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277B ALA 4.0 2.0 + - - -
278B ILE* 1.3 79.0 - - - +
280B ASN* 1.3 61.5 + - - +
281B ARG* 3.7 7.7 + - - +
282B GLU* 3.2 24.9 + - - +
283B PHE* 3.0 28.8 + - - +
297B LYS* 4.6 1.6 - - - -
29X A 4.6 7.0 - - - -
30X G 3.5 23.1 - - - -
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Residues in contact with ASN 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B SER* 1.3 72.4 - - - +
281B ARG* 1.3 61.0 + - - +
283B PHE* 3.3 7.4 + - - +
284B LYS* 2.9 55.0 + - - +
297B LYS* 2.7 29.6 + - - +
30X G 2.6 51.2 + - - +
31X A 3.1 19.0 + - - +
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Residues in contact with ARG 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B SER* 3.3 7.9 + - - +
280B ASN* 1.3 79.1 - - - +
282B GLU* 1.3 60.2 + - - +
284B LYS* 3.5 10.3 + - - +
285B GLU* 3.2 47.3 + - + +
29X A 2.9 50.7 + - - +
30X G 4.4 1.6 + - - -
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Residues in contact with GLU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B PRO 5.6 0.7 - - - +
278B ILE* 3.4 30.3 - - + +
279B SER* 3.2 17.6 + - - +
281B ARG* 1.3 79.2 - - - +
283B PHE* 1.3 60.2 + - - +
285B GLU* 3.5 13.2 + - - +
286B LYS* 3.0 47.7 + - + +
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Residues in contact with PHE 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B LEU* 5.9 2.2 - - + -
278B ILE* 3.8 16.1 - - + +
279B SER 3.0 18.4 + - - +
280B ASN* 3.6 9.0 - - - +
281B ARG 3.2 0.2 - - - -
282B GLU* 1.3 77.0 - - - +
284B LYS* 1.3 67.0 + - + +
287B PHE* 3.0 53.7 + + + +
288B GLY* 3.3 4.4 + - - -
293B SER* 3.8 28.0 - - - -
296B GLY* 3.3 26.5 - - - -
297B LYS* 3.4 39.9 - - + -
300B ILE* 4.0 17.5 - - + -
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Residues in contact with LYS 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B ASN* 2.9 38.3 + - - +
281B ARG* 3.9 8.7 - - - +
283B PHE* 1.3 83.6 - - + +
285B GLU* 1.3 59.2 + - + +
288B GLY* 3.2 26.2 + - - +
289B HIS* 5.7 1.9 + - - -
30X G 5.7 3.2 + - - -
31X A 6.0 1.8 - - - +
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Residues in contact with GLU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B ARG* 3.2 38.4 + - + +
282B GLU* 3.8 14.6 - - - +
283B PHE 3.2 0.2 - - - -
284B LYS* 1.3 80.2 - - + +
286B LYS* 1.3 65.8 + - + +
287B PHE 3.6 0.2 + - - -
288B GLY* 4.2 1.7 + - - -
289B HIS* 5.3 5.2 + - - -
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Residues in contact with LYS 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B GLU* 4.9 10.7 + - - +
267B ILE* 3.2 46.9 - - + +
278B ILE* 4.7 2.7 - - + -
282B GLU* 3.0 41.3 + - + +
285B GLU* 1.3 79.0 - - + +
287B PHE* 1.3 83.1 + - + +
289B HIS 5.3 0.5 + - - -
290B VAL* 5.2 0.3 - - - +
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Residues in contact with PHE 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B PHE* 4.1 24.9 - + + -
266B GLU 5.2 0.4 - - - -
267B ILE* 3.3 46.9 - - + -
270B PRO* 4.3 6.7 - - + -
275B LEU* 3.6 32.5 - - + -
278B ILE* 4.1 11.4 - - + -
283B PHE* 3.0 44.1 + + + +
286B LYS* 1.3 96.4 - - + +
288B GLY* 1.3 58.9 + - - +
289B HIS 3.1 4.7 + - - -
290B VAL* 3.2 21.6 - - + +
293B SER* 2.7 26.7 + - - -
300B ILE* 5.8 0.7 - - + -
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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