Contacts of the helix formed by residues 245 - 257 (chain C) in PDB entry 1FIU
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 ALA 245 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9C ARG* 3.5 4.0 - - - +
13C HIS* 4.0 9.9 - - + +
47C ILE* 3.8 18.6 - - + +
51C LEU* 4.5 1.1 - - + -
243C HIS* 3.1 8.7 + - + -
244C PHE* 1.3 101.0 - - + +
246C LEU* 1.3 60.7 + - - +
248C GLU* 3.3 22.0 - - - +
249C LEU* 2.9 27.7 + - - +
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Residues in contact with LEU 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B TYR* 3.6 31.6 - - + +
243C HIS* 3.5 14.7 + - + -
245C ALA* 1.3 76.0 - - - +
247C TYR* 1.3 62.5 + - + +
249C LEU* 3.2 3.7 + - + +
250C GLU* 2.9 28.1 + - - +
265C PHE* 3.6 31.1 - - + -
269C VAL* 4.3 4.9 - - + -
274C LEU* 3.8 22.0 - - + -
275C LYS* 3.8 26.5 - - - +
276C ASP* 3.0 28.9 + - + +
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Residues in contact with TYR 247 (chain C).
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 3.8 18.4 - - - -
164B ILE* 3.7 9.0 - - + -
165B ALA 3.2 15.2 + - - -
166B THR* 3.9 20.9 + - + +
167B TYR* 4.9 2.9 - + - -
9C ARG* 3.5 33.4 - - - -
245C ALA 3.4 0.6 - - - -
246C LEU* 1.3 84.9 - - + +
248C GLU* 1.3 64.3 + - - +
250C GLU* 3.3 15.7 + - - +
251C GLN* 3.0 29.6 + - - +
276C ASP* 3.7 19.6 + - + +
278C SER* 3.2 18.5 + - - -
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Residues in contact with GLU 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ARG* 2.8 42.8 + - - -
47C ILE* 4.2 12.8 - - + -
50C LEU* 3.7 39.6 - - + +
51C LEU* 3.7 23.3 - - + +
245C ALA* 3.3 17.4 - - + +
247C TYR* 1.3 76.0 - - - +
249C LEU* 1.3 66.1 + - - +
251C GLN* 3.2 2.8 + - - +
252C ILE* 3.0 29.6 + - - +
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Residues in contact with LEU 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ILE* 3.6 17.7 - - + -
47C ILE* 4.0 9.7 - - + +
223C PRO 3.2 21.8 - - - +
225C PRO* 4.5 3.4 - - + -
228C ILE* 4.1 17.7 - - + -
243C HIS* 3.9 26.5 - - + +
245C ALA 2.9 17.2 + - - +
246C LEU* 3.2 6.5 + - + +
248C GLU* 1.3 74.9 - - - +
250C GLU* 1.3 62.7 + - - +
252C ILE* 3.0 9.9 - - - +
253C LEU* 3.0 42.5 + - + +
265C PHE* 3.8 26.7 - - + -
274C LEU* 5.1 0.9 - - + -
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Residues in contact with GLU 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B TYR* 5.1 8.1 + - - -
246C LEU 2.9 9.5 + - - +
247C TYR* 3.6 17.1 - - - +
249C LEU* 1.3 77.8 - - - +
251C GLN* 1.3 63.0 + - - +
253C LEU* 3.3 7.5 + - - +
254C GLN* 3.1 31.8 + - + +
262C LEU* 5.4 0.7 - - + -
265C PHE* 3.6 30.9 - - + -
266C TYR* 2.5 38.5 + - + +
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Residues in contact with GLN 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C LEU* 3.4 36.3 - - + +
247C TYR 3.0 17.9 + - - +
248C GLU* 3.2 5.8 + - - +
250C GLU* 1.3 77.4 - - - +
252C ILE* 1.3 63.1 + - - +
254C GLN* 3.2 10.9 + - + +
255C SER* 3.0 29.0 + - - +
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Residues in contact with ILE 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ILE* 2.8 57.2 - - + +
46C GLY* 3.4 31.9 - - - -
47C ILE* 3.1 17.0 - - + -
50C LEU* 3.6 12.8 - - + -
248C GLU 3.0 11.6 + - - +
249C LEU* 3.0 15.5 - - - +
251C GLN* 1.3 73.2 - - - +
253C LEU* 1.3 60.7 + - - +
255C SER* 3.2 6.5 + - - -
256C LEU* 2.9 42.1 + - + +
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Residues in contact with LEU 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ILE* 3.9 30.7 - - + -
225C PRO* 3.9 7.4 - - + -
249C LEU* 3.0 36.3 + - + +
250C GLU* 3.3 5.4 + - - +
252C ILE* 1.3 79.2 - - + +
254C GLN* 1.3 62.0 + - - +
256C LEU* 3.6 2.8 + - - -
257C ASN* 3.6 14.7 + - - -
258C TYR* 4.2 11.2 + - + +
261C ALA* 3.9 23.8 - - + +
262C LEU* 3.8 26.4 - - + +
265C PHE* 3.7 42.4 - - + -
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Residues in contact with GLN 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C GLU* 3.1 22.9 + - + +
251C GLN* 3.3 11.2 - - + +
253C LEU* 1.3 79.8 - - - +
255C SER* 1.3 61.0 + - - +
257C ASN* 4.0 5.2 + - - -
262C LEU* 3.2 24.2 - - + +
266C TYR* 3.2 30.4 + - - +
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Residues in contact with SER 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C GLN* 3.0 19.8 + - - +
252C ILE* 3.2 10.7 + - - -
254C GLN* 1.3 78.1 - - - +
256C LEU* 1.3 65.8 + - - +
257C ASN* 3.7 2.1 + - - +
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Residues in contact with LEU 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ASN* 4.0 37.0 - - + +
43C ILE* 4.1 9.6 - - + +
46C GLY* 6.2 0.2 - - - -
252C ILE* 2.9 24.7 + - + +
253C LEU 3.6 2.4 + - - +
254C GLN 3.4 0.2 - - - -
255C SER* 1.3 80.5 - - - +
257C ASN* 1.3 72.2 + - - +
258C TYR* 3.4 46.8 + - + +
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Residues in contact with ASN 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ARG* 5.2 0.9 + - - -
253C LEU 3.6 7.4 + - - -
254C GLN 4.0 4.2 + - - -
255C SER 3.5 4.6 - - - +
256C LEU* 1.3 80.7 - - - +
258C TYR* 1.3 63.7 + - - +
259C GLU* 3.3 32.9 + - - +
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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