Contacts of the helix formed by residues 187 - 201 (chain R) in PDB entry 6QX2
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 ASN 187 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100R ARG* 3.4 5.3 - - - +
101R TYR* 3.7 2.0 - - - -
186R HIS* 1.3 72.2 - - - +
188R LEU* 1.3 60.3 + - - +
189R THR* 3.2 34.5 + - - -
190R GLU* 3.3 29.8 + - + +
191R LEU* 3.0 30.2 + - - +
215R GLY 5.0 2.2 + - - -
217R ASP* 3.0 33.5 + - + +
482R ASP* 2.9 23.8 + - - +
483R ASP 3.3 14.3 + - - -
484R ARG* 3.4 5.5 - - - +
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Residues in contact with LEU 188 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101R TYR* 2.9 29.5 + - + +
131R ILE* 4.1 15.9 - - + -
164R PHE* 3.9 24.0 - - + -
165R PRO* 4.0 15.3 - - + -
169R ALA* 4.6 6.5 - - + -
186R HIS 3.7 1.6 + - - -
187R ASN* 1.3 68.0 - - - +
189R THR* 1.3 60.0 + - - +
191R LEU* 3.2 8.2 + - + +
192R ILE* 2.9 49.5 + - + +
476R ILE* 4.6 9.6 - - + -
480R PHE* 3.8 36.3 - - + +
481R GLY* 4.1 6.5 - - - +
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Residues in contact with THR 189 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187R ASN* 3.2 10.8 + - - -
188R LEU* 1.3 78.7 - - - +
190R GLU* 1.3 63.4 + - + +
192R ILE* 3.3 1.6 + - - +
193R ASN* 3.1 42.7 + - - +
477R ARG* 3.9 22.3 + - + +
481R GLY* 3.1 24.1 - - - -
482R ASP 3.2 11.9 + - - -
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Residues in contact with GLU 190 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187R ASN* 3.3 25.3 + - + +
189R THR* 1.3 77.2 - - + +
191R LEU* 1.3 57.0 + - - +
193R ASN* 3.4 8.3 + - - +
194R GLY 2.9 24.1 + - - -
212R ASP* 3.2 23.6 - - - +
213R ILE* 3.6 16.7 - - + +
214R GLU* 3.1 30.6 + - - +
215R GLY 4.0 2.4 - - - +
484R ARG* 2.8 49.8 + - - +
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Residues in contact with LEU 191 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165R PRO* 3.7 24.7 - - + +
168R LEU* 3.7 28.7 - - + -
169R ALA* 3.4 41.5 - - + +
186R HIS* 3.8 17.9 - - + -
187R ASN 3.0 16.3 + - - +
188R LEU* 3.2 10.5 + - - +
190R GLU* 1.3 76.1 - - - +
192R ILE* 1.3 56.6 + - - +
194R GLY* 3.0 5.4 + - - -
195R VAL* 2.9 32.4 + - - +
213R ILE* 3.9 24.6 - - + +
352R LEU* 4.6 4.1 - - + +
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Residues in contact with ILE 192 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165R PRO* 4.2 7.9 - - + -
188R LEU* 2.9 36.6 + - + +
189R THR 3.9 2.9 - - - +
191R LEU* 1.3 73.4 - - - +
193R ASN* 1.3 60.2 + - - +
195R VAL* 3.1 9.0 + - - +
196R LEU* 2.9 41.9 + - + +
473R LEU* 3.6 50.7 - - + +
474R THR 4.6 0.2 - - - +
476R ILE* 3.9 14.1 - - + -
477R ARG* 3.7 41.1 - - + +
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Residues in contact with ASN 193 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189R THR* 3.1 33.6 + - - +
190R GLU* 3.6 9.4 - - - +
192R ILE* 1.3 74.6 - - - +
194R GLY* 1.3 55.8 - - - +
196R LEU* 3.4 8.6 + - - +
197R SER* 3.0 33.1 + - - -
212R ASP* 3.6 20.3 + - + +
477R ARG* 2.7 34.5 + - - +
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Residues in contact with GLY 194 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190R GLU 2.9 14.0 + - - -
191R LEU 3.0 5.6 + - - -
193R ASN* 1.3 75.0 - - - +
195R VAL* 1.3 55.6 + - - +
197R SER* 3.3 4.5 + - - -
198R LEU* 3.0 24.9 + - - +
209R LEU* 3.5 19.0 - - - +
212R ASP* 3.6 16.5 - - - +
213R ILE* 4.3 9.4 - - - -
352R LEU* 4.5 3.6 - - - -
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Residues in contact with VAL 195 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165R PRO* 4.8 4.9 - - + -
191R LEU 2.9 20.7 + - - +
192R ILE* 3.1 9.2 + - - +
194R GLY* 1.3 71.7 - - - +
196R LEU* 1.3 55.7 + - - +
198R LEU* 3.3 9.1 + - - +
199R SER* 2.8 32.7 + - - -
352R LEU* 3.7 26.2 - - + +
355R TYR* 4.2 22.0 - - + -
356R LEU* 3.9 28.7 - - + +
473R LEU* 3.7 26.7 - - + -
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Residues in contact with LEU 196 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192R ILE* 2.9 26.9 + - + +
193R ASN* 3.6 9.0 - - - +
194R GLY 3.3 0.2 - - - -
195R VAL* 1.3 72.7 - - - +
197R SER* 1.3 64.8 + - - +
199R SER* 2.8 22.1 + - - -
200R LYS* 3.2 24.7 + - - +
470R ARG* 3.7 46.7 - - + +
473R LEU* 4.6 10.8 - - + -
474R THR* 3.7 16.6 - - - +
477R ARG* 3.7 22.9 - - - +
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Residues in contact with SER 197 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193R ASN 3.0 8.4 + - - -
194R GLY 3.4 6.7 - - - -
196R LEU* 1.3 75.2 - - - +
198R LEU* 1.3 62.2 + - - +
200R LYS* 3.2 12.6 + - - +
201R ASN* 3.1 22.3 + - - +
204R ILE* 3.8 21.0 - - - +
209R LEU* 4.7 0.4 - - - -
212R ASP* 2.7 31.4 + - - -
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Residues in contact with LEU 198 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194R GLY 3.0 13.8 + - - +
195R VAL* 3.5 9.4 - - - +
197R SER* 1.3 74.1 - - - +
199R SER* 1.3 56.6 + - - +
200R LYS 3.1 0.2 - - - -
201R ASN 3.1 31.6 + - - +
202R PRO* 3.4 10.6 - - + +
204R ILE* 3.6 27.2 - - + +
209R LEU* 4.5 6.3 - - + -
349R LYS* 4.0 12.8 - - + -
352R LEU* 3.7 18.2 - - + +
353R VAL* 3.7 49.6 - - + +
356R LEU* 4.1 17.7 - - + +
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Residues in contact with SER 199 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195R VAL* 2.8 19.5 + - - -
196R LEU* 2.8 16.9 + - - -
198R LEU* 1.3 71.6 - - - +
200R LYS* 1.3 53.3 + - - +
202R PRO* 5.2 3.4 - - - +
356R LEU* 3.7 30.3 - - - -
466R LEU* 3.4 19.3 - - - +
470R ARG* 2.9 49.3 + - - +
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Residues in contact with LYS 200 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196R LEU* 3.2 26.5 + - - +
197R SER* 3.6 10.1 - - - +
198R LEU 3.1 0.8 - - - -
199R SER* 1.3 77.9 - - - +
201R ASN* 1.3 58.5 + - + +
202R PRO* 4.0 6.7 - - - +
470R ARG* 3.7 32.5 - - - +
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Residues in contact with ASN 201 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197R SER 3.1 10.3 + - - +
198R LEU* 3.1 10.6 + - - +
200R LYS* 1.3 81.2 - - + +
202R PRO* 1.3 66.7 - - - +
203R ASP* 3.0 21.8 + - - +
204R ILE* 3.1 41.7 + - + +
208R GLU* 3.8 9.7 + - - -
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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