Contacts of the helix formed by residues 270 - 280 (chain f) in PDB entry 5T0J
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 ILE 270 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267f LEU* 5.6 2.9 - - + -
268f THR 4.3 3.1 - - - +
269f GLN* 1.3 81.4 - - - +
271f ASP* 1.3 89.7 + - - +
272f LYS 3.5 0.9 - - - -
274f LEU* 3.2 50.4 + - + +
275f TYR* 4.3 6.6 - - + -
293f ASN* 5.6 0.9 - - - +
296f VAL* 4.3 3.8 - - + -
297f ARG* 3.7 52.0 - - + +
300f CYS* 5.5 4.0 - - - -
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Residues in contact with ASP 271 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269f GLN* 3.4 5.0 - - - +
270f ILE* 1.3 96.5 - - - +
272f LYS* 1.3 68.2 + - - +
275f TYR* 3.2 47.4 + - + +
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Residues in contact with LYS 272 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269f GLN* 3.1 31.0 - - + +
271f ASP* 1.3 82.1 - - - +
273f TYR* 1.3 63.3 + - - +
276f SER* 3.2 20.6 + - - -
623f HIS* 5.3 13.3 - - - -
626f ARG* 3.1 40.5 - - - +
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Residues in contact with TYR 273 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269f GLN* 4.2 15.1 - - + +
270f ILE 4.2 0.2 + - - -
272f LYS* 1.3 77.3 - - - +
274f LEU* 1.3 80.5 + - + +
276f SER* 2.4 25.1 + - - -
277f SER* 3.1 17.1 + - - -
622f TYR* 3.2 26.0 - + + +
626f ARG* 3.3 38.8 - - - +
629f MET* 3.9 13.0 - - - -
646f ASP* 3.4 27.2 + - - +
647f VAL* 4.6 3.0 - - + +
650f ILE* 3.8 27.8 - - + +
654f LYS* 5.1 9.4 - - + -
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Residues in contact with LEU 274 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269f GLN 4.9 4.3 - - - +
270f ILE* 3.2 42.4 + - + +
272f LYS 3.5 0.4 - - - -
273f TYR* 1.3 93.3 - - + +
275f TYR* 1.3 62.9 + - + +
277f SER* 3.0 10.7 + - - -
278f GLU* 2.9 23.6 + - - +
292f VAL* 3.8 28.0 - - + -
293f ASN* 4.9 11.2 - - + +
296f VAL* 4.2 21.1 - - + -
650f ILE* 5.3 0.9 - - + -
654f LYS* 6.3 2.2 - - + -
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Residues in contact with TYR 275 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270f ILE* 4.3 9.0 - - + -
271f ASP* 3.2 54.0 + - + +
274f LEU* 1.3 81.8 - - + +
276f SER* 1.3 61.1 + - - +
278f GLU* 3.2 32.3 + - - +
279f ASP* 3.1 27.7 + - - +
302f PRO* 6.0 2.3 - - - +
303f ALA* 6.1 0.5 - - - +
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Residues in contact with SER 276 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272f LYS* 3.2 15.7 + - - -
273f TYR* 2.4 38.8 + - - -
275f TYR* 1.3 77.6 - - - +
277f SER* 1.3 58.6 + - - +
279f ASP* 3.4 21.9 + - - +
280f TYR* 3.4 10.2 + - - +
626f ARG* 4.9 5.8 + - - -
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Residues in contact with SER 277 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273f TYR* 3.1 17.2 + - - -
274f LEU* 3.0 14.6 + - - -
276f SER* 1.3 79.0 + - - +
278f GLU* 1.3 61.2 + - - +
279f ASP 3.3 0.2 - - - -
280f TYR* 3.0 16.0 + - - +
281f ILE 2.9 33.0 + - - +
289f CYS* 6.1 0.7 - - - -
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Residues in contact with GLU 278 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274f LEU 2.9 11.4 + - - +
275f TYR* 3.2 43.2 + - + +
277f SER* 1.3 76.5 - - - +
279f ASP* 1.3 63.8 + - - +
281f ILE* 2.9 33.2 + - + +
306f LEU* 3.8 27.2 - - + +
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Residues in contact with ASP 279 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275f TYR 3.1 14.5 + - - +
276f SER* 3.5 14.1 - - - +
277f SER 3.3 0.2 - - - -
278f GLU* 1.3 78.4 - - - +
280f TYR* 1.3 58.4 + - - +
281f ILE* 3.2 2.4 + - - +
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Residues in contact with TYR 280 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276f SER 3.4 6.9 + - - +
277f SER* 3.0 19.8 + - - +
279f ASP* 1.3 75.3 - - - +
281f ILE* 1.3 81.6 + - - +
282f LYS 3.5 3.4 + - - +
283f SER* 3.9 30.4 + - - -
284f GLY 5.0 2.4 + - - -
638f LEU* 4.8 11.8 - - - +
643f SER* 4.1 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