Contacts of the helix formed by residues 269 - 280 (chain B) in PDB entry 4YQF
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 HIS 269 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198B TYR* 2.9 36.8 + + + +
199B PRO* 4.7 0.7 - - + -
212B VAL* 4.3 19.5 + - + +
213B ASN* 3.1 31.9 - - - -
216B PHE* 3.7 30.3 - + + +
264B LEU* 3.0 23.4 + - + +
268B THR* 1.3 101.2 + - - +
270B MET* 1.3 66.4 + - - +
271B GLN 3.2 2.7 - - - -
272B ASN* 2.9 22.4 + - - +
273B ILE* 2.9 15.9 + - + +
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Residues in contact with MET 270 (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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22B PHE* 3.6 33.9 - - + -
24B PHE* 3.5 28.0 - - + -
81B MET* 3.7 25.4 - - + -
265B LEU 3.2 21.9 + - - +
266B ILE* 3.3 23.1 - - - +
267B ARG 4.3 6.1 - - - +
268B THR 3.5 1.4 - - - -
269B HIS* 1.3 77.1 - - - +
271B GLN* 1.3 75.9 + - + +
273B ILE* 3.5 3.9 + - - -
274B LYS* 3.3 20.9 + - - +
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Residues in contact with GLN 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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22B PHE* 3.1 35.3 - - - -
267B ARG 5.3 0.6 + - - -
268B THR 5.0 3.2 + - - +
269B HIS 3.2 0.6 - - - -
270B MET* 1.3 90.7 - - + +
272B ASN* 1.3 58.3 + - - +
274B LYS* 3.2 6.5 + - - +
275B ASP* 2.9 45.1 + - - +
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Residues in contact with ASN 272 (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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198B TYR* 3.2 22.5 + - - +
199B PRO* 5.7 1.2 - - - +
213B ASN* 5.9 1.4 + - - -
268B THR 5.5 0.9 + - - +
269B HIS* 2.9 12.5 + - - +
271B GLN* 1.3 76.8 - - - +
273B ILE* 1.3 59.0 + - - +
275B ASP* 3.3 12.6 + - - +
276B ILE* 3.0 44.5 + - - +
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Residues in contact with ILE 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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24B PHE* 4.0 10.3 - - + -
134B HIS* 3.3 35.9 - - + +
135B CYS* 3.9 10.5 - - + -
163B ASN* 3.2 11.0 + - + +
198B TYR* 3.5 30.1 - - + -
265B LEU* 3.8 40.4 - - + +
269B HIS* 2.9 26.8 + - + +
270B MET 3.7 4.9 - - - +
272B ASN* 1.3 74.9 - - - +
274B LYS* 1.3 58.3 + - - +
277B THR* 2.4 33.3 + - - -
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Residues in contact with LYS 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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22B PHE* 3.2 40.7 - - + -
23B GLU* 3.2 30.9 + - - +
24B PHE* 3.9 9.9 - - + -
130B ASP* 3.6 17.6 + - - +
132B ARG* 5.4 1.1 - - - +
134B HIS* 3.4 31.0 - - + +
270B MET* 3.3 13.2 + - - +
271B GLN* 3.2 13.0 + - - +
273B ILE* 1.3 78.1 - - - +
275B ASP* 1.3 58.6 + - - +
277B THR* 3.0 8.5 + - - -
278B SER* 2.8 32.3 + - - -
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Residues in contact with ASP 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 GLN* 2.9 36.6 + - - +
272B ASN* 3.3 14.3 + - - +
274B LYS* 1.3 75.9 - - - +
276B ILE* 1.3 57.4 + - + +
278B SER* 3.4 5.0 + - - +
279B SER* 2.7 41.9 + - - +
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Residues in contact with ILE 276 (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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163B ASN* 3.3 24.7 - - - +
198B TYR* 4.3 9.4 - - + -
200B GLN* 4.1 11.0 - - - +
203B PHE* 4.0 31.9 - - + -
272B ASN* 3.0 35.8 + - - +
273B ILE* 3.9 4.0 - - - +
275B ASP* 1.3 75.7 - - + +
277B THR* 1.3 61.4 + - - +
279B SER* 3.9 5.2 - - - +
280B ILE* 2.9 46.9 + - + +
281B HIS* 3.4 5.7 + - - +
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Residues in contact with THR 277 (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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112B TYR* 3.8 20.4 - - + +
132B ARG* 4.5 8.1 - - + +
133B VAL 3.6 22.7 - - - +
134B HIS* 3.3 28.2 + - + +
163B ASN* 3.2 10.0 + - - -
273B ILE 2.4 22.0 + - - -
274B LYS 3.0 7.3 + - - -
276B ILE* 1.3 77.5 - - - +
278B SER* 1.3 58.2 + - - +
281B HIS* 3.6 10.6 + - + +
282B PHE* 2.9 31.2 + - - +
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Residues in contact with SER 278 (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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115B TYR* 5.6 0.5 + - - -
132B ARG* 4.0 29.8 + - - +
274B LYS 2.8 15.9 + - - -
275B ASP* 3.9 5.6 - - - -
277B THR* 1.3 79.2 - - - +
279B SER* 1.3 60.4 + - - +
282B PHE* 3.7 6.1 - - - +
283B GLU* 3.2 30.5 + - - +
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Residues in contact with SER 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ASP* 2.7 28.5 + - - +
276B ILE* 3.9 4.2 - - - +
278B SER* 1.3 75.8 - - - +
280B ILE* 1.3 76.0 + - - +
283B GLU* 3.4 22.1 - - - +
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Residues in contact with ILE 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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203B PHE* 3.6 44.6 - - + -
276B ILE* 2.9 25.4 + - + +
279B SER* 1.3 93.8 - - - +
281B HIS* 1.3 79.1 + - + +
282B PHE 3.5 0.2 - - - -
283B GLU* 3.9 0.9 - - - +
284B ALA* 3.0 33.7 + - + +
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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