Contacts of the helix formed by residues 219 - 226 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A ARG* 3.4 42.2 - - - +
327A ARG* 3.9 17.0 - - - +
197B GLY* 3.4 34.7 - - - +
198B LEU 3.0 8.5 + - - +
199B ARG* 3.6 27.1 - - + -
218B SER* 1.3 74.4 - - - +
220B ARG* 1.3 58.1 + - - +
222B ILE* 3.2 12.0 + - + +
223B ASP* 2.8 34.4 + - - +
269B GLY 3.4 13.5 - - - +
270B GLY 3.6 13.9 - - - -
271B LEU* 3.7 14.4 - - + +
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Residues in contact with ARG 220 (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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278A TYR* 3.4 18.3 - - + -
281A GLU* 3.1 40.2 + - - +
282A GLU* 2.6 32.5 + - - -
285A ASN* 3.5 12.8 - - - +
326A THR* 6.5 0.9 - - - -
327A ARG* 3.6 31.9 - - + +
328A GLU* 4.4 14.1 - - - +
218B SER* 3.1 10.2 + - - +
219B MET* 1.3 76.0 - - - +
221B ASP* 1.3 68.0 + - - +
223B ASP* 3.2 3.6 + - - +
224B ARG* 3.1 51.6 + - - +
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Residues in contact with ASP 221 (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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328A GLU* 4.3 5.9 - - - +
216B TYR* 3.5 12.6 - - - +
217B PHE* 3.4 25.5 - - + -
218B SER* 2.9 34.8 + - - +
220B ARG* 1.3 77.9 + - - +
222B ILE* 1.3 59.5 + - - +
224B ARG* 3.3 13.6 + - - +
225B LEU* 2.8 40.6 + - + +
230B VAL* 4.6 1.1 - - - -
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Residues in contact with ILE 222 (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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274A ARG* 3.5 7.3 + - - +
196B ILE* 3.9 18.8 - - + -
197B GLY 4.2 3.8 - - - +
217B PHE 4.5 3.4 - - - +
218B SER 3.0 13.9 + - - +
219B MET* 3.5 18.4 - - - +
221B ASP* 1.3 75.8 - - - +
223B ASP* 1.3 60.3 + - - +
226B GLY* 2.8 28.3 + - - -
227B ILE* 4.2 20.6 - - + +
230B VAL* 4.0 21.3 - - + -
271B LEU* 3.7 27.4 - - + -
275B GLU* 3.4 28.3 - - - +
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Residues in contact with ASP 223 (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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227A ILE* 4.7 18.6 + - + +
228A GLN* 5.1 2.8 + - - +
274A ARG* 2.7 50.1 + - - +
275A GLU* 5.4 0.9 - - - -
278A TYR* 4.4 12.5 - - + +
327A ARG* 2.9 38.1 + - - -
219B MET 2.8 11.9 + - - +
220B ARG* 3.4 7.9 - - - +
222B ILE* 1.3 77.0 - - - +
224B ARG* 1.3 60.3 + - - +
226B GLY* 4.6 1.0 + - - -
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Residues in contact with ARG 224 (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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228A GLN* 3.1 53.9 + - - +
232A GLU* 5.0 1.8 + - - -
278A TYR* 2.8 51.0 + - + +
282A GLU* 4.8 2.2 + - - -
220B ARG* 3.1 42.5 + - - +
221B ASP* 3.7 12.6 + - - +
223B ASP* 1.3 79.3 - - - +
225B LEU* 1.3 69.4 + - + +
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Residues in contact with LEU 225 (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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228A GLN* 5.8 0.4 - - - +
217B PHE* 4.0 28.9 - - + -
221B ASP* 2.8 26.3 + - + +
224B ARG* 1.3 82.2 - - + +
226B GLY* 1.3 69.5 + - - +
229B LYS* 3.7 37.1 + - + +
230B VAL* 4.1 5.8 - - + +
233B ARG* 3.7 45.3 - - - +
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Residues in contact with GLY 226 (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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222B ILE* 2.8 19.7 + - - -
223B ASP 4.5 0.8 + - - -
224B ARG 3.5 1.2 - - - -
225B LEU* 1.3 83.7 - - - +
227B ILE* 1.3 65.9 + - - -
228B GLN 3.2 3.7 + - - -
229B LYS 3.4 0.5 + - - -
230B VAL* 3.2 21.3 + - - +
275B GLU* 6.0 0.2 - - - -
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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