Contacts of the helix formed by residues 263 - 271 (chain B) in PDB entry 1FO4
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 GLU 263 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262B THR* 1.3 81.7 + - - +
264B ILE* 1.3 67.8 + - + +
265B GLY 3.1 0.7 - - - -
266B ILE* 2.9 20.7 + - - +
267B GLU* 2.5 45.2 + - - +
354B THR* 3.2 39.6 - - + +
356B SER* 5.9 0.2 - - - -
394B ARG* 3.1 17.8 + - - -
4006B FAD 2.9 35.3 + - - +
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Residues in contact with ILE 264 (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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256B LYS* 3.9 22.0 - - + -
257B LEU 4.5 0.2 - - - +
258B VAL* 3.7 24.9 - - + -
261B ASN* 3.3 12.1 - - - +
263B GLU* 1.3 72.0 - - - +
265B GLY* 1.3 58.1 + - - +
267B GLU* 3.2 13.3 + - - +
268B MET* 2.9 56.0 + - + +
275B PHE* 4.0 17.5 - - + -
278B ILE* 5.3 1.6 - - + -
4006B FAD 2.8 52.1 + - - +
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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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74B LEU* 4.7 10.4 - - - +
261B ASN* 2.9 34.7 + - - -
264B ILE* 1.3 80.0 - - - +
266B ILE* 1.3 59.2 + - - +
268B MET* 4.1 7.5 - - - +
269B LYS* 3.1 30.3 + - - +
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Residues in contact with ILE 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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45B GLU* 3.9 30.7 - - + +
74B LEU* 4.2 13.0 - - + -
261B ASN 4.5 0.2 + - - -
262B THR 3.6 20.2 - - - +
263B GLU* 2.9 14.3 + - - +
265B GLY* 1.3 75.9 - - - +
267B GLU* 1.3 61.7 + - + +
270B PHE* 2.6 66.9 + - + -
271B LYS* 3.4 12.5 + - - -
4006B FAD 4.2 5.8 - - + -
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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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256B LYS* 4.8 3.6 - - - -
263B GLU* 2.5 47.6 + - - +
264B ILE* 3.6 18.1 - - - +
266B ILE* 1.3 77.8 - - + +
268B MET* 1.3 56.5 + - - +
271B LYS* 2.8 47.2 + - + +
273B GLN* 3.1 25.8 + - + +
275B PHE* 3.5 24.0 - - + -
354B THR* 5.4 0.3 - - - +
394B ARG* 4.3 5.4 + - - +
4006B FAD 5.1 2.6 + - - -
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Residues in contact with MET 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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22B PRO 5.9 3.1 - - - +
23B GLU* 5.3 18.8 - - + +
76B PRO* 6.3 0.2 - - + -
234B VAL* 5.7 4.7 - - - -
261B ASN* 3.9 13.9 - - - +
264B ILE* 2.9 40.2 + - + +
265B GLY* 4.1 6.5 - - - +
267B GLU* 1.3 78.4 - - - +
269B LYS* 1.3 59.3 + - - +
272B ASN* 4.3 7.8 + - - -
273B GLN 3.5 24.7 + - - +
274B LEU* 5.5 1.8 - - - -
275B PHE* 4.0 26.2 - - + -
278B ILE* 4.9 15.5 - - + -
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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
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44B GLY* 4.6 8.7 - - - +
74B LEU* 6.4 0.4 - - + -
265B GLY 3.1 18.5 + - - +
268B MET* 1.3 77.8 - - - +
270B PHE* 1.3 94.0 + - + +
272B ASN* 5.0 1.6 - - - +
676B GLU* 6.0 0.4 + - - -
679B GLU* 3.4 37.8 + - - +
828B ASP* 3.7 21.9 + - - -
830B ASN* 5.6 0.7 + - - -
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Residues in contact with PHE 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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43B CYS 4.0 10.5 - - - -
44B GLY 3.5 22.7 - - - -
45B GLU* 4.0 25.1 - - + -
266B ILE* 2.6 48.5 + - + +
269B LYS* 1.3 104.1 - - + +
271B LYS* 1.3 71.0 + - + +
272B ASN* 3.5 9.9 + - - -
828B ASP* 6.2 1.6 - - + -
829B ARG* 6.5 0.4 - - + -
830B ASN* 3.6 37.9 - - + +
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Residues in contact with LYS 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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266B ILE* 4.1 10.5 - - + +
267B GLU* 2.8 40.1 + - + +
270B PHE* 1.3 86.7 + - - +
272B ASN* 1.3 69.7 + - - +
273B GLN* 2.8 36.7 + - + +
394B ARG* 5.9 5.2 - - - +
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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