Contacts of the helix formed by residues 195 - 209 (chain C) in PDB entry 3ZXR
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 TYR 195 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138C ILE* 3.9 54.1 + - + -
140C ASP* 4.8 0.9 + - - -
157C ALA* 4.1 5.9 - - - +
158C ILE* 3.8 10.9 + - + +
159C SER* 2.8 45.2 + - - -
193C ASP* 3.2 2.4 + - - -
194C GLN* 1.3 94.1 - - + +
196C VAL* 1.3 66.1 + - - +
197C ASP 3.4 1.8 - - - -
198C LEU* 3.2 14.8 + - + +
199C ARG* 2.9 40.6 + - - +
218C HIS* 4.0 13.2 - + - -
224C GLY* 3.4 22.8 + - - -
258C LYS* 4.3 18.4 - - + -
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Residues in contact with VAL 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B HIS* 4.0 12.1 - - + -
84B ARG* 3.4 51.8 - - + +
190C ALA* 4.2 13.2 - - + -
193C ASP* 3.3 37.9 - - + +
194C GLN 3.7 1.6 - - - -
195C TYR* 1.3 77.3 - - - +
197C ASP* 1.3 57.9 + - - +
199C ARG* 3.4 11.1 + - - +
200C ASP* 3.0 29.7 + - - +
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Residues in contact with ASP 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B PHE 4.9 3.6 - - - +
84B ARG* 3.8 16.7 - - - +
85B ALA* 3.7 31.8 + - - +
86B ALA 5.1 0.2 + - - -
255B GLN* 5.4 4.0 + - - -
195C TYR 3.4 0.4 - - - -
196C VAL* 1.3 79.2 - - - +
198C LEU* 1.3 63.0 + - - +
200C ASP* 3.3 10.4 + - - +
201C LYS* 3.0 32.9 + - - +
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Residues in contact with LEU 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ILE* 3.8 23.3 - - + -
195C TYR* 3.2 18.9 + - + +
197C ASP* 1.3 78.6 - - - +
199C ARG* 1.3 63.0 + - - +
201C LYS* 3.0 13.0 + - + +
202C MET* 3.0 34.2 + - + +
252C THR* 4.1 14.1 - - + +
253C ALA* 4.5 1.3 - - - -
256C ASN* 3.8 35.9 - - + +
258C LYS* 3.7 33.2 - - + -
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Residues in contact with ARG 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B HIS* 4.2 10.7 + - - -
36B THR* 5.5 2.8 + - - -
138C ILE* 4.3 17.0 - - + -
193C ASP* 2.6 43.8 + - - -
195C TYR* 2.9 33.2 + - - +
196C VAL* 3.9 11.9 - - - +
198C LEU* 1.3 71.7 - - - +
200C ASP* 1.3 52.5 + - - +
202C MET* 3.2 15.4 + - - +
203C LEU* 2.8 43.4 + - + +
216C GLY 4.6 3.2 + - - -
217C HIS* 3.5 23.5 - - - +
218C HIS* 3.5 24.7 - - - +
226C ALA* 3.7 24.5 - - + +
227C GLU 4.9 2.5 - - - -
228C ILE* 4.1 9.8 - - + +
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Residues in contact with ASP 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 3.4 15.3 + - + -
36B THR* 4.9 0.2 - - - -
84B ARG* 2.7 49.6 + - - +
86B ALA* 4.0 21.3 + - + +
88B THR* 4.4 0.2 + - - -
196C VAL* 3.0 16.9 + - - +
197C ASP* 3.4 15.1 - - - +
198C LEU 3.2 0.2 - - - -
199C ARG* 1.3 75.1 - - - +
201C LYS* 1.3 57.7 + - + +
203C LEU* 3.4 16.4 + - - +
204C THR* 2.9 33.8 + - - -
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Residues in contact with LYS 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C ASP* 3.0 23.6 + - - +
198C LEU* 3.0 13.4 + - - +
200C ASP* 1.3 73.5 - - + +
202C MET* 1.3 59.9 + - - +
204C THR* 3.3 6.0 + - - -
205C ASN* 2.9 37.1 + - - +
252C THR* 4.0 13.5 - - + -
256C ASN* 3.0 35.3 + - - +
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Residues in contact with MET 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C PHE* 3.9 24.2 - - + -
138C ILE* 4.0 22.4 - - + -
198C LEU* 3.0 19.2 + - + +
199C ARG* 3.3 22.2 - - - +
201C LYS* 1.3 75.6 - - - +
203C LEU* 1.3 62.3 + - - +
205C ASN* 3.3 2.4 + - - +
206C LEU* 3.0 30.9 + - - +
228C ILE* 3.7 12.3 - - + -
248C ILE* 4.4 1.0 - - - +
249C ILE* 3.7 39.7 - - + +
252C THR* 3.7 23.1 - - + +
253C ALA* 4.0 19.3 - - + +
260C VAL* 4.3 0.2 - - + -
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Residues in contact with LEU 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 3.4 35.0 - - + +
36B THR* 4.3 13.0 - - + +
38B PRO* 5.9 3.1 - - + -
199C ARG* 2.8 26.0 + - + +
200C ASP* 3.6 15.9 - - - +
202C MET* 1.3 73.2 - - - +
204C THR* 1.3 59.0 + - - +
206C LEU* 3.3 7.7 + - - +
207C ILE* 2.9 34.7 + - + +
213C LEU* 3.8 17.0 - - + +
215C LYS* 4.4 2.5 - - - +
216C GLY* 4.4 19.5 - - - +
228C ILE* 3.7 33.9 - - + -
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Residues in contact with THR 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLU* 4.3 11.8 + - - +
20B TYR* 2.6 26.3 + - - -
86B ALA* 5.2 2.3 - - - +
200C ASP 2.9 14.3 + - - -
201C LYS* 3.7 6.7 - - - -
203C LEU* 1.3 74.7 - - - +
205C ASN* 1.3 61.1 + - - +
207C ILE* 3.2 7.6 + - + +
208C ASN* 2.8 48.2 + - - +
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Residues in contact with ASN 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C PRO* 4.5 21.6 - - + +
83C PHE* 3.7 12.5 - - - -
201C LYS* 2.9 21.1 + - - +
202C MET 3.8 3.8 - - - +
204C THR* 1.3 79.8 - - - +
206C LEU* 1.3 60.6 + - - +
208C ASN* 3.5 9.5 + - - +
209C SER* 2.9 28.7 + - - -
248C ILE* 3.8 16.2 - - + -
252C THR* 2.9 29.9 + - - +
255C GLN* 5.8 0.2 + - - -
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Residues in contact with LEU 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C MET 3.0 21.9 + - - +
203C LEU* 3.6 5.8 - - - +
205C ASN* 1.3 73.2 - - - +
207C ILE* 1.3 65.5 + - - +
209C SER 3.0 10.7 + - - -
211C PHE* 3.1 53.5 + - + +
213C LEU* 3.8 17.5 - - + -
228C ILE* 3.6 31.2 - - + -
230C TYR* 5.5 0.4 - - + -
245C TYR* 3.9 28.7 - - + +
248C ILE* 3.8 23.8 - - + -
249C ILE* 4.1 8.3 - - + -
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Residues in contact with ILE 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLU 5.7 0.9 - - - +
20B TYR* 3.9 27.8 - - + +
38B PRO* 4.3 16.2 - - + -
40B SER* 5.7 2.0 - - - +
203C LEU 2.9 23.7 + - - +
204C THR* 3.6 6.1 - - + +
206C LEU* 1.3 70.8 - - - +
208C ASN* 1.3 68.6 + - - +
210C GLY* 2.9 22.3 + - - -
211C PHE 3.9 11.7 + - - +
213C LEU* 3.5 20.9 - - + +
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Residues in contact with ASN 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C ILE* 5.4 3.5 - - - +
82C PRO* 6.0 4.5 - - + -
204C THR* 2.8 41.2 + - - +
205C ASN* 4.0 10.2 + - - +
206C LEU 3.3 0.2 - - - -
207C ILE* 1.3 79.8 - - - +
209C SER* 1.3 58.2 + - - +
210C GLY 3.3 1.9 + - - -
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Residues in contact with SER 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C ARG* 3.3 31.4 + - - +
80C ILE 4.4 11.6 + - - +
82C PRO* 4.0 12.1 - - - +
205C ASN 2.9 13.9 + - - -
206C LEU 3.0 9.7 + - - -
208C ASN* 1.3 75.8 - - - +
210C GLY* 1.3 62.7 + - - +
211C PHE* 3.3 11.8 + - - -
244C LEU* 4.6 7.0 - - - -
248C ILE* 3.2 24.4 - - - +
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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