Contacts of the helix formed by residues 260 - 269 (chain B) in PDB entry 4QOZ
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 260 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B LEU* 3.8 27.8 - - + -
229B THR 3.1 19.1 + - - +
230B ASP* 4.0 13.2 - - + +
258B ILE* 3.3 3.6 + - - -
259B ASN* 1.3 70.0 - - - +
261B ARG* 1.3 63.2 + - - +
263B SER* 3.7 6.3 - - - -
264B TYR* 2.9 28.4 + - - +
280B MET* 3.3 11.5 - - + +
302B ILE* 4.1 13.5 - - + +
305B ILE* 3.9 23.8 - - + -
306B ALA* 3.9 31.2 - - + +
309B MET* 4.0 14.4 - - - -
316B LEU* 4.5 7.2 - - + -
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Residues in contact with ARG 261 (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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24A C 3.0 33.0 + - - +
25A C 2.8 58.4 + - - -
230B ASP* 2.6 47.1 + - - +
231B GLY* 3.8 9.8 - - - +
259B ASN* 2.9 12.3 + - - +
260B ILE* 1.3 76.2 - - - +
262B LYS* 1.3 58.9 + - - +
264B TYR* 3.4 2.1 + - - +
265B GLY* 2.9 27.4 + - - -
275B THR* 3.5 41.1 + - + +
276B LYS* 4.5 7.9 - - - +
277B LEU 4.7 0.8 - - - +
280B MET* 3.5 6.7 - - + +
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Residues in contact with LYS 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A C 3.3 34.6 + - - +
21A C 3.0 36.8 + - - -
23A C 6.2 1.6 - - - +
259B ASN* 3.4 18.8 + - - +
261B ARG* 1.3 78.7 - - - +
263B SER* 1.3 63.2 + - - +
265B GLY* 3.3 2.1 + - - -
266B ASN* 3.0 33.2 + - - +
319B ASN* 4.1 21.6 + - + +
320B GLU* 2.9 33.8 + - - +
329B SER* 4.5 3.2 + - - +
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Residues in contact with SER 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B ILE* 3.9 10.9 - - - +
259B ASN 3.2 14.3 + - - -
260B ILE* 3.8 9.2 - - - -
261B ARG 3.2 0.2 - - - -
262B LYS* 1.3 77.2 - - - +
264B TYR* 1.3 57.0 + - - +
266B ASN* 3.3 7.8 + - - +
267B PHE* 2.9 31.2 + - - +
309B MET* 3.7 4.0 - - - -
314B CYS* 4.9 3.8 - - - -
316B LEU* 3.8 26.0 - - - +
317B ARG 4.8 2.1 + - - -
319B ASN* 3.2 15.1 + - - +
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Residues in contact with TYR 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B VAL* 4.7 1.4 - - - +
260B ILE 2.9 10.5 + - - +
261B ARG 3.7 0.9 - - - +
263B SER* 1.3 73.5 - - - +
265B GLY* 1.3 64.3 + - - +
267B PHE* 4.6 0.2 - - - -
268B TYR* 3.0 54.1 + + - +
269B LYS 4.1 0.2 + - - -
270B VAL* 4.0 29.1 + - + -
275B THR* 5.0 4.0 - - + -
280B MET* 2.8 79.5 + - + -
283B LYS* 3.4 19.1 - - + +
284B LEU* 3.7 17.5 - - + +
305B ILE* 4.0 13.9 - - + -
309B MET* 3.6 14.3 - - - +
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Residues in contact with GLY 265 (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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261B ARG 2.9 16.3 + - - -
262B LYS* 3.7 1.8 - - - -
264B TYR* 1.3 78.6 - - - +
266B ASN* 1.3 63.1 + - - +
269B LYS* 3.1 26.2 + - - +
270B VAL 3.7 10.7 + - - -
275B THR* 5.2 6.0 + - - -
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Residues in contact with ASN 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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18A A 5.7 0.3 + - - -
19A G 3.5 46.8 + - - +
20A C 2.8 32.9 + - - -
104B LYS* 5.1 0.2 + - - -
262B LYS* 3.0 27.6 + - - +
263B SER* 3.8 6.5 - - - +
265B GLY* 1.3 78.2 - - - +
267B PHE* 1.3 56.6 + - - +
269B LYS* 3.1 30.3 + - - -
319B ASN* 5.9 0.6 - - - +
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Residues in contact with PHE 267 (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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18A A 5.3 3.1 - - - -
19A G 5.7 0.2 - - - -
104B LYS* 3.3 55.8 - - + +
108B ASN* 5.5 1.1 - - + -
263B SER 2.9 17.2 + - - +
264B TYR 4.1 0.2 - - - +
265B GLY 3.3 0.2 - - - -
266B ASN* 1.3 77.3 - - + +
268B TYR* 1.3 103.8 + + - +
269B LYS* 3.6 6.0 + - - +
309B MET* 4.1 10.8 - - + -
312B ASP* 3.3 32.8 - - + -
313B GLY 4.1 3.4 - - - -
314B CYS* 3.5 44.0 - - + -
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Residues in contact with TYR 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ASP* 3.5 24.4 - - - +
101B VAL* 3.8 37.2 - - + -
104B LYS* 4.0 10.8 - - + -
264B TYR* 3.0 52.1 + + + +
267B PHE* 1.3 100.6 - + - +
269B LYS* 1.3 70.1 + - - +
270B VAL* 3.3 12.0 + - + +
284B LEU* 3.8 17.8 - - + +
308B ARG* 4.0 1.7 + - - +
309B MET* 3.7 28.9 - - + +
312B ASP* 2.6 30.3 + - - +
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Residues in contact with LYS 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A A 3.8 14.8 + - - -
19A G 5.8 0.9 - - - -
100B ASP* 5.2 5.9 - - - +
104B LYS* 3.7 18.0 - - - +
265B GLY 3.1 14.8 + - - +
266B ASN* 3.1 24.5 + - - +
267B PHE 3.3 12.3 + - - -
268B TYR* 1.3 80.4 - - - +
270B VAL* 1.3 64.7 + - - +
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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