Contacts of the helix formed by residues 219 - 226 (chain C) in PDB entry 4IXU
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 MET 219 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274B ARG* 3.3 41.7 - - - +
327B ARG* 3.9 16.6 - - + +
197C GLY* 3.4 34.8 - - - +
198C LEU 3.1 5.3 + - - +
199C ARG* 3.6 25.6 - - + -
218C SER* 1.3 74.0 - - - +
220C ARG* 1.3 56.9 + - - +
222C ILE* 3.2 12.2 + - + +
223C ASP* 2.9 35.2 + - - +
269C GLY 3.5 15.0 - - - +
270C GLY 3.5 15.0 - - - -
271C LEU* 3.7 13.7 - - + +
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Residues in contact with ARG 220 (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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278B TYR* 3.4 18.1 - - + -
281B GLU* 3.1 40.5 + - - +
282B GLU* 2.6 32.9 + - - -
285B ASN* 3.6 13.5 - - - +
326B THR* 6.5 0.4 - - - -
327B ARG* 3.6 27.8 - - + +
328B GLU* 4.0 22.3 + - + +
218C SER* 3.1 10.8 + - - +
219C MET* 1.3 78.5 - - - +
221C ASP* 1.3 63.2 + - - +
223C ASP* 3.2 4.1 + - - +
224C ARG* 3.1 51.5 + - - +
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Residues in contact with ASP 221 (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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328B GLU* 3.8 9.9 - - - +
216C TYR* 3.6 12.3 - - - +
217C PHE* 3.5 25.6 - - + -
218C SER* 2.9 35.1 + - - +
220C ARG* 1.3 77.6 + - - +
222C ILE* 1.3 58.0 + - - +
224C ARG* 3.3 14.0 + - - +
225C LEU* 2.8 39.7 + - + +
230C VAL* 4.5 1.8 - - - -
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Residues in contact with ILE 222 (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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274B ARG* 3.5 6.9 + - - +
196C ILE* 4.0 18.2 - - + -
197C GLY 4.3 3.8 - - - +
217C PHE 4.5 2.9 - - - +
218C SER 3.0 12.1 + - - +
219C MET* 3.2 21.5 + - - +
221C ASP* 1.3 73.6 - - - +
223C ASP* 1.3 61.5 + - - +
226C GLY* 2.8 27.4 + - - -
227C ILE* 4.1 21.5 - - + +
230C VAL* 4.0 21.1 - - + -
271C LEU* 3.6 28.0 - - + -
275C GLU* 3.4 28.5 - - - +
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Residues in contact with ASP 223 (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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226B GLY* 6.0 0.3 - - - -
227B ILE* 4.6 18.5 + - + +
228B GLN* 4.9 3.1 + - - +
274B ARG* 2.8 48.8 + - - +
275B GLU* 6.3 0.4 - - - -
278B TYR* 4.3 14.5 - - + +
327B ARG* 2.8 38.6 + - - -
219C MET 2.9 12.2 + - - +
220C ARG* 3.2 7.8 + - - +
222C ILE* 1.3 75.7 - - - +
224C ARG* 1.3 61.5 + - - +
226C GLY 4.7 0.7 + - - -
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Residues in contact with ARG 224 (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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228B GLN* 3.1 52.2 + - - +
232B GLU* 5.0 2.4 + - - +
278B TYR* 2.7 55.0 + - + +
282B GLU* 4.8 2.6 + - - -
220C ARG* 3.1 39.0 + - - +
221C ASP* 3.6 16.7 + - - +
223C ASP* 1.3 80.6 - - - +
225C LEU* 1.3 69.5 + - + +
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Residues in contact with LEU 225 (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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228B GLN* 5.7 0.9 - - - +
217C PHE* 4.0 32.5 - - + -
221C ASP* 2.8 25.5 + - + +
224C ARG* 1.3 82.3 - - + +
226C GLY* 1.3 69.5 + - - +
229C LYS* 3.6 36.0 + - + +
230C VAL* 4.1 7.0 - - + +
233C ARG* 3.7 43.1 - - - +
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Residues in contact with GLY 226 (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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223A ASP 6.1 0.7 - - - -
222C ILE* 2.8 19.9 + - - -
223C ASP 4.6 1.0 + - - -
224C ARG 3.5 1.2 - - - -
225C LEU* 1.3 83.2 - - - +
227C ILE* 1.3 65.0 + - - -
228C GLN 3.2 4.1 + - - -
229C LYS 3.3 0.6 + - - -
230C VAL* 3.1 21.2 + - - +
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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