Contacts of the helix formed by residues 188 - 199 (chain D) in PDB entry 1I43
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 ASP 188 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184D ILE* 3.5 23.0 - - - +
185D ASP* 2.9 30.8 + - + +
186D PRO 4.9 0.9 - - - -
187D ALA* 1.3 72.5 - - - +
189D VAL* 1.3 61.4 + - - +
190D GLY* 3.3 5.0 + - - -
191D ALA* 2.8 41.3 + - + +
192D LEU 3.6 2.4 + - - -
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Residues in contact with VAL 189 (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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186D PRO 5.4 1.8 - - - +
187D ALA 2.7 20.3 + - - +
188D ASP* 1.3 71.8 - - - +
190D GLY* 1.3 61.3 + - - +
192D LEU* 3.2 11.1 + - + +
193D GLU* 2.9 28.7 + - - +
218D ASP* 6.0 2.2 - - + -
221D LEU* 4.1 28.3 - - + -
222D VAL* 5.5 8.5 - - + -
225D LEU* 3.5 28.3 - - + -
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Residues in contact with GLY 190 (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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188D ASP* 3.3 4.6 + - - -
189D VAL* 1.3 80.8 - - - +
191D ALA* 1.3 52.0 + - - +
193D GLU* 3.0 12.3 + - - +
194D LEU* 2.7 36.7 + - - +
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Residues in contact with ALA 191 (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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184D ILE* 3.6 25.2 - - + +
188D ASP* 2.8 34.9 + - - +
190D GLY* 1.3 74.0 - - - +
192D LEU* 1.3 52.5 + - - +
194D LEU* 3.2 10.2 + - - +
195D ALA* 2.8 36.6 + - - +
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Residues in contact with LEU 192 (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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157D VAL* 3.8 28.3 - - + -
184D ILE* 3.7 15.3 - - + +
188D ASP 3.6 2.5 + - - +
189D VAL* 3.2 12.4 + - + +
191D ALA* 1.3 78.4 - - - +
193D GLU* 1.3 51.9 + - - +
195D ALA* 3.2 4.5 + - - +
196D LEU* 2.7 62.7 + - + +
204D PHE* 3.8 21.1 - - + -
222D VAL* 3.7 40.6 - - + +
225D LEU* 4.3 17.0 - - + -
226D CYS* 4.6 2.2 - - - -
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Residues in contact with GLU 193 (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 VAL* 2.9 16.0 + - - +
190D GLY* 3.4 12.9 - - - +
192D LEU* 1.3 76.2 - - - +
194D LEU* 1.3 62.4 + - - +
196D LEU* 3.4 9.1 - - + +
197D ASN* 3.1 39.1 + - - +
225D LEU* 4.6 25.9 - - + +
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Residues in contact with LEU 194 (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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190D GLY 2.7 19.5 + - - +
191D ALA* 3.4 9.2 - - - +
193D GLU* 1.3 71.5 - - - +
195D ALA* 1.3 59.9 + - - +
197D ASN* 2.8 20.6 + - + +
198D GLN* 2.8 55.1 + - + +
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Residues in contact with ALA 195 (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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155D HIS* 5.5 0.4 - - - +
157D VAL* 4.5 13.2 - - + -
182D THR* 3.9 31.0 - - + +
184D ILE* 5.1 0.2 - - + -
191D ALA 2.8 20.4 + - - +
192D LEU* 3.7 5.6 - - - +
194D LEU* 1.3 73.3 - - - +
196D LEU* 1.3 62.8 + - - +
197D ASN 3.2 1.0 + - - -
198D GLN* 4.1 12.8 + - - +
199D LYS* 3.2 29.1 + - + +
201D VAL* 3.7 7.4 - - + +
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Residues in contact with LEU 196 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192D LEU* 2.7 56.7 + - + +
193D GLU* 3.4 12.3 - - + +
194D LEU 3.1 0.2 - - - -
195D ALA* 1.3 74.2 - - - +
197D ASN* 1.3 59.9 + - - +
199D LYS 3.6 8.3 - - - +
200D LYS* 5.4 0.3 - - - -
201D VAL* 3.8 28.0 + - + +
225D LEU* 4.1 9.4 - - + +
226D CYS* 4.1 17.9 - - - +
229D LYS* 3.6 43.6 - - + +
231D ALA* 4.0 13.0 - - + -
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Residues in contact with ASN 197 (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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193D GLU* 3.1 29.1 + - - +
194D LEU* 2.8 12.8 + - + +
196D LEU* 1.3 82.7 - - - +
198D GLN* 1.3 67.9 + - + +
199D LYS 4.0 1.8 - - - +
229D LYS* 3.4 31.4 + - - +
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Residues in contact with GLN 198 (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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194D LEU* 2.8 53.2 - - + +
195D ALA* 3.6 5.2 + - - +
197D ASN* 1.3 79.2 - - + +
199D LYS* 1.3 90.8 + - + +
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Residues in contact with LYS 199 (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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155D HIS* 3.9 32.5 - - + +
182D THR* 3.2 30.0 + - - +
195D ALA* 3.2 22.9 + - - +
196D LEU 3.6 9.9 - - - +
197D ASN 4.0 1.8 - - - +
198D GLN* 1.3 109.6 + - + +
200D LYS* 1.3 61.8 + - - +
201D VAL 3.4 4.3 + - - -
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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