Contacts of the helix formed by residues 223 - 232 (chain B) in PDB entry 2IZZ
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 HIS 223 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ASP* 3.6 24.9 - - - -
199A ARG* 3.9 3.4 + - - -
217B LEU* 4.4 0.2 - - - -
221B GLU 4.1 0.4 + - - -
222B GLN* 1.3 75.4 - - - +
224B PRO* 1.3 70.4 - - + +
225B GLY* 3.0 28.5 + - - +
226B GLN* 2.9 21.0 + - + +
227B LEU* 3.2 10.4 + - - +
223C HIS* 4.2 19.4 + - + -
225C GLY* 3.3 25.6 + - - -
226C GLN* 3.5 33.0 - - + +
228C LYS* 5.9 0.2 - - - -
229C ASP* 2.8 29.6 + - - -
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Residues in contact with PRO 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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182A PHE* 3.5 30.5 - - + +
185A LEU 5.2 0.4 - - - -
186A ASP* 4.1 10.1 - - + +
199A ARG* 3.7 23.3 - - - +
203A VAL* 5.2 7.9 - - + -
217B LEU* 3.8 38.1 - - + -
222B GLN 3.8 0.6 - - - +
223B HIS* 1.3 95.1 - - + +
225B GLY* 1.3 55.2 + - - +
227B LEU* 3.4 4.7 + - + +
228B LYS* 3.0 29.3 + - - +
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Residues in contact with GLY 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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186A ASP* 5.2 4.8 + - - -
223B HIS* 3.0 19.3 + - - -
224B PRO* 1.3 78.0 - - - +
226B GLN* 1.3 55.8 + - - +
228B LYS* 3.4 12.1 - - - +
229B ASP* 3.0 33.8 + - - +
251B ARG* 6.4 0.4 - - - -
223C HIS* 3.3 19.1 - - - -
186D ASP* 5.9 0.7 - - - -
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Residues in contact with GLN 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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10A GLN* 5.5 0.2 - - - +
222B GLN* 3.4 36.6 - - + +
223B HIS* 2.9 19.0 + - + +
225B GLY* 1.3 69.5 - - - -
227B LEU* 1.3 65.4 + - - +
229B ASP* 3.2 12.3 + - - +
230B ASN* 2.9 46.4 + - - +
223C HIS* 3.5 26.7 - - + +
199D ARG* 5.9 2.1 - - - +
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Residues in contact with LEU 227 (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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182A PHE* 3.5 41.2 - - + -
216B MET* 4.2 21.8 - - + +
217B LEU* 3.8 34.3 - - + +
220B SER* 4.0 16.2 - - - +
222B GLN* 3.7 27.6 - - + +
223B HIS 3.2 9.7 + - - +
224B PRO 3.8 5.2 - - - +
226B GLN* 1.3 76.2 - - - +
228B LYS* 1.3 63.7 + - - +
230B ASN* 3.2 22.6 + - + +
231B VAL* 3.4 16.3 + - - +
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Residues in contact with LYS 228 (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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179A ALA* 4.1 17.2 - - + +
182A PHE* 3.5 17.3 - - + -
183A THR* 4.0 13.0 - - - +
224B PRO 3.0 14.9 + - - +
225B GLY* 3.4 13.5 - - - +
227B LEU* 1.3 76.1 - - - +
229B ASP* 1.3 77.1 + - - +
231B VAL* 3.1 12.8 + - - +
232B SER* 3.0 33.2 + - - -
239B ILE* 4.7 0.2 - - - +
242B LEU* 3.7 24.9 - - + +
251B ARG* 4.6 13.2 - - - +
223C HIS* 6.1 0.2 - - - -
186D ASP* 5.3 6.3 - - - -
190D ASP* 3.6 18.5 + - - +
199D ARG* 3.1 26.6 - - - +
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Residues in contact with ASP 229 (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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225B GLY 3.0 18.5 + - - +
226B GLN* 3.2 19.7 + - - +
228B LYS* 1.3 87.0 + - - +
230B ASN* 1.3 62.5 + - - +
232B SER* 3.2 19.1 + - - +
223C HIS* 2.9 28.8 + - - -
186D ASP* 4.9 0.3 - - - +
199D ARG* 2.9 60.1 + - + +
203D VAL* 5.8 0.2 - - - +
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Residues in contact with ASN 230 (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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10A GLN* 3.2 51.8 + - + +
124A THR* 4.6 8.2 - - + +
350A NAD 3.3 19.1 + - - -
216B MET* 6.1 1.0 - - - +
222B GLN* 4.3 14.3 + - - +
226B GLN* 2.9 37.1 + - - +
227B LEU* 3.5 20.0 - - - +
228B LYS 3.2 1.2 - - - -
229B ASP* 1.3 75.8 - - - +
231B VAL* 1.3 61.3 + - - +
232B SER 5.1 0.6 - - - -
233B SER 5.2 0.2 + - - -
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Residues in contact with VAL 231 (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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124A THR* 3.7 23.8 - - + +
175A GLY 3.8 14.8 - - - +
176A SER 4.3 0.4 - - - +
178A PRO* 4.3 3.4 - - + -
179A ALA* 3.8 19.5 - - + +
182A PHE* 4.1 13.7 - - + -
350A NAD 3.5 20.5 + - - +
1273A EDO 2.9 26.4 + - - -
227B LEU 3.5 14.4 - - - +
228B LYS 3.1 7.5 + - - +
230B ASN* 1.3 76.9 - - - +
232B SER* 1.3 57.7 + - - +
233B SER 3.2 4.6 + - - -
238B THR* 3.7 25.9 + - + +
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Residues in contact with SER 232 (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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228B LYS* 3.0 34.6 + - - -
229B ASP 3.2 15.5 + - - +
230B ASN 3.3 0.9 - - - -
231B VAL* 1.3 73.5 - - - +
233B SER* 1.3 66.6 + - - +
234B PRO* 3.5 4.5 - - - +
238B THR* 3.7 11.4 - - - +
239B ILE* 4.4 16.4 - - - +
242B LEU* 3.4 15.1 - - - +
193D VAL* 3.6 9.6 - - - +
199D ARG* 4.1 10.0 + - - +
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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