Contacts of the helix formed by residues 265 - 275 (chain B) in PDB entry 5T0I
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 LYS 265 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B ASP* 4.0 20.6 + - - +
170B LEU* 3.6 31.2 - - + +
259B TYR* 6.2 0.9 - - + -
264B PRO* 1.3 88.1 - - + +
266B LEU* 1.3 63.5 + - + +
267B VAL 3.4 0.7 - - - -
268B ARG* 3.3 30.7 - - - +
269B GLU* 3.1 26.9 + - - +
225C GLY* 6.3 1.1 - - - -
227C GLY* 3.5 43.1 - - - +
228C ALA* 4.2 2.2 - - - +
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Residues in contact with LEU 266 (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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250B VAL* 5.0 12.8 - - + -
257B GLN* 5.2 9.0 - - + -
259B TYR* 3.2 48.5 - - + +
263B GLY* 3.9 7.4 + - - +
264B PRO 3.5 0.4 - - - -
265B LYS* 1.3 77.3 - - + +
267B VAL* 1.3 64.9 + - + +
268B ARG 3.1 1.1 - - - -
269B GLU* 3.2 33.0 + - - +
270B LEU* 3.2 29.0 + - + +
315B GLN* 5.0 3.6 - - - +
227C GLY 4.4 8.7 - - - +
229C ARG* 5.8 6.5 - - + -
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Residues in contact with VAL 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B GLY* 3.1 19.7 + - - +
264B PRO* 4.1 5.6 - - + +
265B LYS 3.4 0.2 - - - -
266B LEU* 1.3 75.7 - - + +
268B ARG* 1.3 57.7 + - - +
270B LEU* 3.4 5.9 + - + +
271B PHE* 2.9 30.5 + - + +
311B GLU* 5.9 1.8 - - - +
315B GLN* 3.3 42.2 - - + +
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Residues in contact with ARG 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A MET* 5.5 12.7 - - - +
170B LEU* 4.8 5.6 - - + -
264B PRO* 3.3 22.0 + - - +
265B LYS* 3.3 42.9 + - + +
266B LEU 3.1 0.8 - - - -
267B VAL* 1.3 75.6 - - + +
269B GLU* 1.3 60.2 + - - +
271B PHE* 3.8 5.3 - - - +
272B ARG* 2.9 38.3 + - - +
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Residues in contact with GLU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 3.3 26.6 - - + +
174B MET* 4.9 6.4 - - + +
248B LEU* 4.4 3.1 - - + +
250B VAL* 4.5 14.3 - - + +
265B LYS 3.1 13.4 + - - +
266B LEU* 3.2 38.8 + - - +
268B ARG* 1.3 77.7 - - - +
270B LEU* 1.3 63.9 + - + +
272B ARG* 3.6 28.6 + - - +
273B VAL* 3.3 16.5 - - - +
227C GLY 4.6 0.9 - - - +
229C ARG* 2.9 40.2 + - - +
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Residues in contact with LEU 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B LEU* 3.6 24.2 - - + -
250B VAL* 4.3 11.2 - - + -
266B LEU* 3.2 14.0 + - + +
267B VAL* 3.8 8.1 - - + +
268B ARG 3.2 0.2 - - - -
269B GLU* 1.3 78.2 - - + +
271B PHE* 1.3 61.7 + - - +
273B VAL* 3.3 16.7 - - - +
274B ALA* 3.6 11.8 + - - +
282B VAL* 3.6 29.7 - - + +
284B ILE* 6.3 3.4 - - + -
315B GLN* 3.4 29.2 - - - +
325B VAL* 5.1 17.4 - - + +
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Residues in contact with PHE 271 (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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267B VAL* 2.9 21.5 + - + +
268B ARG* 3.2 6.5 + - - +
270B LEU* 1.3 77.9 - - - +
272B ARG* 1.3 67.1 + - - +
274B ALA* 3.3 7.7 + - + +
275B GLU* 3.2 37.7 + - + +
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Residues in contact with ARG 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 3.1 24.7 + - - +
171B VAL* 3.3 57.1 + - + +
173B VAL* 3.5 7.7 - - - +
174B MET* 3.3 38.9 - - - +
268B ARG* 2.9 20.4 + - - +
269B GLU* 3.6 26.9 - - - +
271B PHE* 1.3 80.0 - - + +
273B VAL* 1.3 66.2 + - - +
275B GLU* 3.5 18.7 + - - +
276B GLU* 3.3 22.4 - - - +
229C ARG* 4.5 0.2 - - - +
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Residues in contact with VAL 273 (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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174B MET* 4.4 21.5 - - - -
246B THR* 4.7 18.8 - - + +
247B PHE 4.9 2.2 - - - +
248B LEU* 3.7 29.4 - - + -
269B GLU 3.3 19.3 - - - +
270B LEU 3.3 10.1 - - - +
272B ARG* 1.3 83.3 - - + +
274B ALA* 1.3 65.4 + - + +
275B GLU 3.2 0.6 + - - -
276B GLU* 3.7 20.4 + - + +
277B HIS* 4.2 8.6 + - + +
278B ALA 5.1 0.3 + - - -
279B PRO 5.5 0.5 - - - +
280B SER* 5.1 3.3 + - - +
282B VAL* 5.7 2.5 - - + -
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Residues in contact with ALA 274 (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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270B LEU 3.6 13.7 - - - +
271B PHE* 3.3 8.6 + - + +
272B ARG 3.3 0.4 - - - -
273B VAL* 1.3 78.8 - - + +
275B GLU* 1.3 59.5 + - - +
276B GLU 3.3 0.9 - - - -
278B ALA* 3.1 38.0 + - + +
279B PRO 4.9 0.2 - - - -
280B SER* 3.5 23.6 - - - +
324B ASP 5.3 1.8 - - - +
325B VAL* 5.1 7.6 - - + +
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Residues in contact with GLU 275 (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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271B PHE* 3.2 31.0 + - + +
272B ARG* 3.7 16.1 - - - +
273B VAL 3.2 1.0 - - - -
274B ALA* 1.3 78.0 - - - +
276B GLU* 1.3 69.3 + - - +
277B HIS 3.5 0.8 - - - -
278B ALA* 5.6 0.2 - - - -
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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