Contacts of the helix formed by residues 266 - 278 (chain B) in PDB entry 5F3K
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 266 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B THR* 4.4 1.3 - - - -
149B ALA* 5.0 5.6 - - - -
262B LYS 4.9 1.1 - - - -
263B GLU* 3.1 19.2 + - - +
265B SER* 1.3 80.0 + - - +
267B GLU* 1.3 65.5 + - - +
268B ALA* 3.4 15.2 + - - +
269B ARG* 3.1 10.5 + - - +
270B VAL* 3.1 23.4 + - - +
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Residues in contact with GLU 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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147B THR* 3.8 23.2 + - - +
265B SER 3.9 0.8 + - - -
266B SER* 1.3 71.1 + - - +
268B ALA* 1.3 57.9 + - - +
270B VAL* 3.3 1.1 + - - +
271B ARG* 2.8 53.6 + - - +
287B LEU* 4.1 13.7 - - + +
288B ASN* 2.9 28.1 + - - +
290B ARG* 3.3 33.5 + - - -
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Residues in contact with ALA 268 (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 SER* 3.2 9.3 + - - +
267B GLU* 1.3 80.5 - - - +
269B ARG* 1.3 54.0 + - + +
271B ARG* 3.4 34.3 + - - +
272B ASP* 2.7 26.1 - - - +
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Residues in contact with ARG 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B SER 5.8 1.6 + - - -
110B GLU* 2.9 24.0 + - - +
263B GLU* 3.4 49.4 + - + +
264B PHE* 3.8 24.2 - - + -
266B SER* 3.1 8.4 + - - +
268B ALA* 1.3 76.9 - - - +
270B VAL* 1.3 65.3 + - - +
271B ARG 3.2 0.6 + - - -
272B ASP* 3.7 14.4 + - - +
273B VAL* 3.5 40.4 + - - +
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE* 4.4 8.3 - - + -
145B LEU* 4.7 1.8 - - + -
147B THR* 3.7 10.3 - - + -
154B ILE* 3.8 17.7 - - + -
264B PHE* 3.2 36.8 - - + +
266B SER 3.1 14.7 + - - +
267B GLU 4.0 2.0 - - - +
269B ARG* 1.3 74.7 - - - +
271B ARG* 1.3 59.9 + - - +
273B VAL* 3.3 7.8 + - - +
274B VAL* 2.8 48.3 + - + +
287B LEU* 4.0 21.8 - - + -
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Residues in contact with ARG 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 GLU* 2.8 47.3 + - - +
268B ALA* 3.6 30.2 + - - +
269B ARG 3.2 0.4 - - - -
270B VAL* 1.3 76.8 - - - +
272B ASP* 1.3 58.0 + - - +
275B THR* 2.7 43.7 + - - +
287B LEU* 3.8 13.0 - - + -
292B MET* 3.4 24.2 - - + +
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Residues in contact with ASP 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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268B ALA 2.7 25.3 - - - +
269B ARG* 3.8 11.6 + - - +
270B VAL 3.3 0.2 - - - -
271B ARG* 1.3 78.1 + - - +
273B VAL* 1.3 68.8 + - + +
275B THR* 3.9 4.8 - - - -
276B LYS* 3.2 23.0 + - - +
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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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110B GLU* 3.9 26.7 - - + +
113B ILE* 4.0 36.3 - - + -
114B ARG* 4.2 24.1 + - + +
264B PHE* 5.1 0.9 - - + -
269B ARG* 3.5 36.1 - - - +
270B VAL* 3.3 7.6 + - - +
272B ASP* 1.3 77.2 - - - +
274B VAL* 1.3 59.1 + - - +
276B LYS* 3.4 6.5 + - - +
277B TYR* 3.0 26.6 + - + +
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Residues in contact with VAL 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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113B ILE* 3.6 25.6 - - + -
117B ILE* 4.0 8.7 - - + +
145B LEU* 3.9 11.7 - - + -
270B VAL* 2.8 39.1 + - + +
271B ARG 3.9 1.1 - - - +
273B VAL* 1.3 75.1 - - + +
275B THR* 1.3 59.5 + - - +
277B TYR 4.4 0.4 - - - +
278B SER* 2.8 33.6 + - - -
285B LEU* 3.4 30.7 - - + -
287B LEU* 4.7 5.4 - - + -
292B MET* 3.9 17.5 - - + -
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Residues in contact with THR 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 ARG* 2.7 28.4 + - - +
272B ASP* 3.9 5.8 - - - -
274B VAL* 1.3 77.9 - - - +
276B LYS* 1.3 65.7 + - - +
278B SER* 3.2 16.1 + - - -
279B ASN* 3.4 12.9 + - - +
292B MET* 3.2 31.0 + - - +
293B ASN* 5.8 0.2 - - - -
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Residues in contact with LYS 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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114B ARG* 3.5 37.5 - - - +
272B ASP 3.2 11.4 + - - +
273B VAL* 3.6 8.1 - - - +
275B THR* 1.3 80.2 - - - +
277B TYR* 1.3 85.1 + - - +
279B ASN* 3.1 28.7 + - - +
280B PHE* 3.8 17.9 - - + -
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Residues in contact with TYR 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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114B ARG* 3.4 62.7 + - + -
117B ILE* 3.6 33.0 - - + -
118B SER* 3.7 21.5 + - - -
273B VAL* 3.0 18.1 + - + +
274B VAL 4.3 1.3 - - - +
276B LYS* 1.3 82.3 - - - +
278B SER* 1.3 56.4 + - - +
279B ASN 3.0 7.0 - - - -
280B PHE* 3.0 45.7 + + + +
281B VAL* 4.3 6.8 + - + +
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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
----------------------------------------------------------
117B ILE* 5.2 0.2 - - - +
274B VAL 2.8 26.4 + - - -
275B THR 3.2 9.9 + - - -
277B TYR* 1.3 69.4 - - - +
279B ASN* 1.3 62.6 + - - +
280B PHE 3.1 2.3 + - - -
281B VAL* 3.6 15.8 + - - +
285B LEU* 4.0 27.6 - - - +
292B MET 3.5 10.0 + - - -
293B ASN* 3.0 47.8 + - - +
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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