Contacts of the helix formed by residues 195 - 206 (chain C) in PDB entry 3JXI
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 THR 195 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143C ILE* 4.1 11.7 - - + +
144C VAL* 3.9 14.3 - - - +
147C GLY 4.0 0.9 - - - -
148C SER 3.4 39.3 - - - +
149C PRO* 3.9 1.5 - - - +
152C LEU* 4.0 19.7 - - + -
184C ALA* 3.8 11.6 - - - +
193C ASN* 2.6 24.2 + - - +
194C ASP* 1.3 77.7 - - - +
196C ILE* 1.3 59.1 + - - +
197C PRO 3.6 0.2 - - - -
198C ILE* 3.4 7.1 + - - +
199C LEU* 2.9 31.2 + - - +
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Residues in contact with ILE 196 (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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181C LEU* 4.2 15.7 - - + -
184C ALA* 3.5 28.3 - - + -
185C LEU* 3.1 39.9 - - + +
193C ASN* 3.0 24.0 + - + +
195C THR* 1.3 74.6 - - - +
197C PRO* 1.3 73.0 - - + +
199C LEU* 3.1 9.3 + - - +
200C LEU* 3.0 27.4 + - + +
239C TYR* 3.9 28.7 - - + -
242C LEU* 4.2 10.1 - - + -
243C LEU* 5.5 2.7 - - + -
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Residues in contact with PRO 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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193C ASN 4.1 2.2 - - - +
194C ASP* 3.7 21.1 - - + +
196C ILE* 1.3 99.6 - - + +
198C ILE* 1.3 59.4 + - + +
200C LEU* 3.5 11.4 + - + +
201C ASP* 2.9 29.6 + - - +
239C TYR* 4.8 7.0 - - + +
242C LEU* 4.5 11.7 - - + -
246C LYS* 5.0 3.4 + - - +
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Residues in contact with ILE 198 (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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149C PRO* 3.7 28.9 - - + -
152C LEU* 3.8 22.2 - - + -
194C ASP 3.4 21.1 - - - +
195C THR* 3.5 7.9 - - - +
196C ILE 3.2 0.6 - - - -
197C PRO* 1.3 75.8 - - + +
199C LEU* 1.3 56.3 - - - +
201C ASP* 3.6 6.7 - - + +
202C ILE* 2.8 55.6 + - + +
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Residues in contact with LEU 199 (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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140C LEU* 4.7 0.9 - - + -
144C VAL* 4.0 21.5 - - + -
152C LEU* 4.4 19.5 - - + -
155C LEU* 4.6 6.7 - - + -
166C LEU* 3.9 12.2 - - + +
180C CYS* 3.6 46.9 - - - +
181C LEU* 4.4 6.3 - - + -
184C ALA* 4.4 4.9 - - + -
195C THR* 2.9 32.2 + - - +
196C ILE* 3.5 10.3 - - + +
198C ILE* 1.3 76.5 - - - +
200C LEU* 1.3 56.6 + - + +
202C ILE* 3.3 6.9 + - - +
203C ALA* 2.9 28.8 + - - +
212C PHE* 4.2 13.7 - - + -
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Residues in contact with LEU 200 (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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181C LEU* 3.9 23.6 - - + -
196C ILE* 3.0 24.1 + - + +
197C PRO* 3.8 5.4 - - + +
199C LEU* 1.3 72.7 - - - +
201C ASP* 1.3 55.0 - - - +
203C ALA* 3.2 6.7 + - - +
204C GLU 2.8 24.1 + - - -
209C MET* 2.8 31.2 - - + +
212C PHE* 4.1 8.3 - - + -
213C ILE* 3.8 29.2 - - + -
242C LEU* 3.7 36.6 - - + +
243C LEU* 4.2 10.5 - - + -
246C LYS* 4.0 14.4 - - + +
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Residues in contact with ASP 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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156C LEU* 5.7 0.3 - - - +
197C PRO 2.9 18.8 + - - +
198C ILE* 3.6 8.9 - - - +
200C LEU* 1.3 74.9 - - - +
202C ILE* 1.3 67.3 + - - +
204C GLU* 3.3 17.1 - - - +
205C LYS* 3.0 56.1 + - - +
209C MET* 3.9 3.3 - - - +
246C LYS* 4.5 4.9 + - - +
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Residues in contact with ILE 202 (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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152C LEU* 4.7 3.6 - - + +
155C LEU* 3.5 37.2 - - + -
156C LEU* 4.0 33.0 - - + +
159C LEU* 3.6 30.5 - - + -
166C LEU* 4.1 7.0 - - + -
198C ILE* 2.8 42.0 + - + +
199C LEU* 3.6 5.8 - - - +
201C ASP* 1.3 75.3 - - - +
203C ALA* 1.3 57.6 + - - +
205C LYS* 3.2 4.9 + - - +
206C THR* 3.0 26.6 + - - -
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Residues in contact with ALA 203 (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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166C LEU* 4.8 5.2 - - + -
199C LEU 2.9 17.2 + - - +
200C LEU* 3.2 6.3 + - - +
202C ILE* 1.3 75.3 - - - +
204C GLU* 1.3 62.2 + - - +
206C THR* 3.4 9.7 + - - -
207C GLY 3.2 4.7 + - - -
208C ASN* 2.9 32.2 + - - +
209C MET* 3.8 13.7 - - - +
212C PHE* 3.6 32.3 - - + -
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Residues in contact with GLU 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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200C LEU 2.8 16.1 + - - +
201C ASP* 3.3 23.7 - - - +
203C ALA* 1.3 73.6 - - - +
205C LYS* 1.3 60.8 + - + +
206C THR 3.1 0.2 - - - -
207C GLY* 3.0 21.1 + - - -
209C MET* 3.5 36.3 - - + +
246C LYS* 4.1 10.8 + - - -
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Residues in contact with LYS 205 (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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156C LEU* 3.4 43.5 - - + +
160C LEU* 4.2 10.9 - - + +
201C ASP* 3.0 45.4 + - - +
202C ILE* 3.7 0.4 - - - +
204C GLU* 1.3 77.3 - - + +
206C THR* 1.3 58.9 + - - +
207C GLY* 3.4 0.6 + - - -
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Residues in contact with THR 206 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C LEU* 4.7 2.6 - - - +
159C LEU* 4.3 8.9 - - + +
160C LEU* 3.8 19.9 - - - +
164C LYS 3.6 16.1 + - - -
165C ARG* 2.7 55.0 + - + +
166C LEU* 5.0 1.8 - - + +
202C ILE* 3.0 15.7 + - - +
203C ALA* 3.5 8.5 - - - +
204C GLU 3.1 0.6 - - - -
205C LYS* 1.3 77.6 - - - +
207C GLY* 1.3 51.4 + - - +
208C ASN* 3.4 24.2 - - + +
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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