Contacts of the helix formed by residues 214 - 228 (chain D) in PDB entry 1IB1
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 SER 214 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163D THR* 2.6 31.3 + - - -
165D PRO* 3.9 20.4 - - - -
168D LEU* 3.5 18.0 - - - +
211D TYR* 4.3 2.8 - - - +
212D LYS* 3.5 2.2 + - - -
213D ASP* 1.3 78.4 + - - +
215D THR* 1.3 64.2 + - - +
216D LEU 3.2 3.1 - - - -
217D ILE* 3.1 17.7 + - - +
218D MET* 3.2 17.4 + - - +
88H GLY 4.0 8.1 - - - -
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Residues in contact with THR 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D LYS* 3.3 21.7 + - - +
213D ASP 3.4 3.8 + - - -
214D SER* 1.3 72.6 - - - +
216D LEU* 1.3 57.9 + - - +
218D MET* 3.1 14.3 + - + +
219D GLN* 2.9 30.5 + - + +
41H THR* 4.8 1.3 - - - +
43H GLU* 3.5 48.9 + - + +
44H ASP* 3.3 22.5 + - - +
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Residues in contact with LEU 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D ASP 5.0 0.4 + - - -
214D SER 3.2 0.6 - - - -
215D THR* 1.3 79.3 - - - +
217D ILE* 1.3 56.8 + - - +
219D GLN* 3.0 11.0 + - + +
220D LEU* 2.8 51.8 + - + +
33H PRO* 4.7 2.5 - - + -
36H GLU* 3.5 24.9 - - - +
38H ARG* 3.5 42.6 - - - +
44H ASP* 4.4 2.3 + - - +
85H PHE* 3.8 25.1 - - + -
88H GLY* 3.7 24.0 + - - +
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Residues in contact with ILE 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D PRO* 3.4 37.5 - - + +
168D LEU* 3.7 36.8 - - + +
169D GLY* 3.8 5.6 - - - +
172D LEU* 4.5 12.1 - - + +
214D SER* 3.1 12.2 + - - +
216D LEU* 1.3 75.4 - - - +
218D MET* 1.3 56.0 + - - +
220D LEU* 3.6 11.8 - - + +
221D LEU* 3.1 28.4 + - + +
32H LEU* 4.2 8.7 - - + -
87H GLU 3.9 7.0 - - - +
88H GLY* 3.6 36.3 - - - +
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Residues in contact with MET 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D THR* 5.4 1.6 - - - -
168D LEU* 3.9 19.7 - - + -
196D PHE* 3.5 32.7 - - + +
199D ALA* 3.5 31.6 - - + -
200D ILE* 3.6 31.2 - - + +
203D LEU* 4.3 14.6 - - + -
214D SER* 3.2 17.7 + - - +
215D THR* 3.3 11.9 - - + +
216D LEU 3.0 0.6 - - - -
217D ILE* 1.3 76.2 - - - +
219D GLN* 1.3 66.0 + - - +
220D LEU 3.1 0.4 - - - -
221D LEU* 3.1 8.9 + - + +
222D ARG 2.9 19.4 + - - -
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Residues in contact with GLN 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D THR* 2.9 18.4 + - + +
216D LEU* 3.0 13.4 + - + +
218D MET* 1.3 73.9 - - - +
220D LEU* 1.3 61.1 + - + +
222D ARG* 2.9 39.2 - - - +
223D ASP* 2.8 62.2 + - - +
41H THR* 5.8 4.7 - - + +
43H GLU* 5.4 18.6 + - + +
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Residues in contact with LEU 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D LEU* 3.7 27.4 - - + -
216D LEU* 2.8 38.9 + - + +
217D ILE* 3.6 12.3 - - + +
219D GLN* 1.3 81.4 - - + +
221D LEU* 1.3 59.7 + - - +
223D ASP* 3.4 5.6 + - - +
224D ASN* 3.1 27.7 + - - -
30H HIS* 3.7 34.4 - - + +
31H TPO 4.2 4.9 - - - +
33H PRO* 3.8 27.8 - - + -
38H ARG* 5.2 6.5 - - - +
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Residues in contact with LEU 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D LEU* 4.3 31.2 - - + +
171D ALA* 4.4 1.6 - - + -
172D LEU* 3.8 39.3 - - + +
175D SER* 4.6 0.2 - - - +
192D ALA* 3.8 32.8 - - + +
195D ALA* 4.4 14.4 - - + -
196D PHE* 4.4 17.3 - - + +
217D ILE 3.1 21.2 + - - +
218D MET* 3.1 13.8 + - + +
220D LEU* 1.3 74.7 - - - +
222D ARG* 1.3 63.5 + - - +
224D ASN* 3.4 5.1 + - + +
225D LEU* 3.1 26.8 + - - +
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Residues in contact with ARG 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D PHE* 3.7 39.4 - - + -
200D ILE* 6.1 0.2 - - - +
218D MET 2.9 9.8 + - - +
219D GLN* 2.9 49.5 - - - +
221D LEU* 1.3 73.2 - - - +
223D ASP* 1.3 66.3 + - - +
225D LEU* 3.0 13.7 + - + +
226D THR* 2.8 35.6 + - - +
43H GLU* 6.1 2.0 - - - +
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Residues in contact with ASP 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D GLN* 2.8 41.5 + - - +
220D LEU* 3.6 8.0 - - - +
222D ARG* 1.3 78.0 - - - +
224D ASN* 1.3 57.7 - - - +
226D THR* 3.3 9.5 + - - -
227D LEU* 2.8 28.5 + - - +
30H HIS* 3.7 25.5 + - + +
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Residues in contact with ASN 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D LEU* 3.2 17.8 + - + +
175D SER* 5.1 0.2 + - - -
176D VAL* 3.7 12.9 - - - +
192D ALA* 5.7 1.8 - - + -
220D LEU 3.1 9.8 + - - +
221D LEU* 3.5 9.6 - - - +
223D ASP* 1.3 74.8 - - - +
225D LEU* 1.3 60.9 + - + +
227D LEU* 3.2 8.0 + - - +
228D TRP* 2.8 58.0 + - + -
29H ARG* 3.7 5.2 - - - -
30H HIS* 2.9 56.5 + - - +
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Residues in contact with LEU 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D CYS* 3.9 33.2 - - + +
192D ALA* 3.9 23.1 - - + +
193D LYS* 3.9 32.1 - - + +
196D PHE* 4.9 7.9 - - + -
221D LEU 3.1 17.8 + - - +
222D ARG* 3.0 16.0 + - + +
224D ASN* 1.3 75.8 - - - +
226D THR* 1.3 63.3 + - - +
228D TRP* 2.9 26.1 + - + -
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Residues in contact with THR 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222D ARG* 2.8 23.1 + - - +
223D ASP* 3.4 13.1 + - - -
225D LEU* 1.3 72.7 - - - +
227D LEU* 1.3 62.1 + - - +
228D TRP 4.3 2.8 - - - -
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Residues in contact with LEU 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D ASP 2.8 13.4 + - - +
224D ASN* 3.2 12.8 - - - +
226D THR* 1.3 80.1 - - - +
228D TRP* 1.3 82.9 + - + +
27H GLN* 3.6 43.5 - - + +
28H ARG 4.4 2.2 - - - +
29H ARG* 3.8 27.6 - - + +
30H HIS* 6.2 0.7 - - + -
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Residues in contact with TRP 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D SER* 4.1 16.8 - - - -
176D VAL* 3.9 13.7 - - + -
179D TYR* 3.5 63.4 - + + -
188D ALA* 4.2 18.2 - - + -
189D CYS* 3.8 34.1 - - - -
192D ALA* 4.7 5.2 - - + -
224D ASN* 2.8 55.9 + - + +
225D LEU* 2.9 17.2 + - + +
226D THR 4.3 2.7 - - - -
227D LEU* 1.3 102.1 - - + +
29H ARG* 4.0 15.4 - - + +
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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