Contacts of the helix formed by residues 187 - 198 (chain D) in PDB entry 4RZR
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 GLY 187 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181D ALA* 5.5 0.7 - - - -
186D ILE* 1.3 76.1 - - - +
188D ASN* 1.3 67.8 + - - -
189D ILE 3.2 2.6 + - - -
190D THR 3.4 0.5 + - - -
191D ALA* 3.0 22.7 + - - +
404D NA 4.2 4.5 - - - -
12F T 2.8 33.1 + - - -
13F C 3.8 12.1 + - - -
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Residues in contact with ASN 188 (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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181D ALA* 5.1 8.0 - - - +
187D GLY* 1.3 70.5 - - - -
189D ILE* 1.3 65.7 + - + +
191D ALA* 3.2 7.7 + - - +
192D GLU* 3.0 28.8 + - + +
12F T 4.6 1.0 + - - -
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Residues in contact with ILE 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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187D GLY 3.2 0.2 - - - -
188D ASN* 1.3 80.4 - - + +
190D THR* 1.3 62.8 + - - +
192D GLU* 3.2 13.2 + - - +
193D LYS* 3.2 25.3 + - - +
11F G 3.4 50.9 - - + +
12F T 3.6 19.5 + - - +
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Residues in contact with THR 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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186D ILE* 4.1 28.0 - - + -
187D GLY 4.1 2.9 - - - -
189D ILE* 1.3 76.8 - - - +
191D ALA* 1.3 62.2 + - - +
193D LYS* 3.3 10.5 + - + +
194D LEU* 3.0 28.0 + - + +
217D ILE* 3.6 29.4 - - + -
221D LYS* 4.4 11.7 - - + -
11F G 3.3 11.3 + - - -
12F T 2.6 29.7 + - - -
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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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180D ILE* 4.8 5.6 - - + +
181D ALA* 3.7 29.6 - - + +
186D ILE* 3.7 10.6 - - + +
187D GLY 3.0 18.6 + - - +
188D ASN* 3.2 7.6 + - - +
190D THR* 1.3 75.5 - - - +
192D GLU* 1.3 57.1 + - + +
194D LEU* 3.5 7.3 + - - +
195D LYS* 2.9 33.3 + - + +
199D ILE 4.8 0.7 - - - +
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Residues in contact with GLU 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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188D ASN* 3.0 16.0 + - + +
189D ILE* 3.2 9.8 + - - +
191D ALA* 1.3 74.2 - - + +
193D LYS* 1.3 67.4 + - + +
195D LYS* 3.1 37.8 + - - +
196D LYS* 3.2 22.0 + - - +
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Residues in contact with LYS 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 ILE* 3.2 22.2 + - - +
190D THR* 3.3 14.1 + - - +
192D GLU* 1.3 78.1 - - + +
194D LEU* 1.3 61.8 + - - +
196D LYS* 3.5 20.2 + - - +
197D LEU* 3.6 13.3 + - - +
216D MET* 3.7 54.1 + - + +
217D ILE* 4.7 7.0 - - + +
10F A 4.5 0.2 + - - -
11F G 2.7 43.3 + - - -
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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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180D ILE* 4.3 25.8 - - + -
186D ILE* 4.6 4.3 - - + -
190D THR* 3.0 33.4 + - + +
191D ALA* 3.6 4.9 - - - +
193D LYS* 1.3 75.6 - - - +
195D LYS* 1.3 64.7 + - - +
197D LEU* 3.1 21.1 + - + +
198D GLY 3.2 0.2 + - - -
199D ILE* 3.0 41.4 + - + +
213D LEU* 3.3 33.7 - - + -
217D ILE* 4.3 11.9 - - + -
225D LEU* 3.8 23.1 - - + -
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Residues in contact with LYS 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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180D ILE* 6.4 0.4 - - + -
191D ALA* 2.9 21.8 + - + +
192D GLU* 3.3 35.0 - - - +
194D LEU* 1.3 75.1 - - - +
196D LYS* 1.3 59.7 + - + +
198D GLY* 3.0 18.2 + - - +
199D ILE 3.7 7.8 + - - +
200D ASN* 3.2 30.1 + - - +
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Residues in contact with LYS 196 (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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94A GLU* 3.8 29.7 + - - +
192D GLU* 3.2 16.5 + - + +
193D LYS* 3.6 12.3 - - - +
194D LEU 3.2 0.4 - - - -
195D LYS* 1.3 77.6 - - + +
197D LEU* 1.3 63.3 + - + +
198D GLY* 3.4 0.9 + - - -
216D MET* 6.3 1.1 - - - -
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Residues in contact with LEU 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 LYS 3.7 11.4 - - - +
194D LEU* 3.1 24.7 + - + +
196D LYS* 1.3 78.2 - - + +
198D GLY* 1.3 60.0 + - - +
199D ILE* 4.4 4.9 - - + +
208D ILE* 3.6 33.4 - - + +
212D LYS* 4.0 28.7 - - + +
213D LEU* 4.2 9.0 - - + -
216D MET* 3.9 36.3 - - + -
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Residues in contact with GLY 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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195D LYS 3.0 14.8 + - - -
196D LYS 3.2 1.4 - - - -
197D LEU* 1.3 79.0 - - - +
199D ILE* 1.3 62.3 + - - +
200D ASN* 3.8 11.1 + - - +
204D ASP* 3.7 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