Contacts of the helix formed by residues 179 - 186 (chain D) 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 179 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141D PHE* 4.7 2.5 - - - -
166D LEU 3.7 18.2 + - - +
167D THR* 3.9 12.5 - - - +
171D PHE 4.8 1.6 - - - -
172D ARG* 3.6 27.1 + - - +
178D LYS* 1.3 78.9 - - - +
180D CYS* 1.3 74.7 + - - +
181D LEU* 3.2 7.4 + - + +
182D PRO* 3.4 20.7 - - + +
183D LYS* 3.5 11.8 + - - +
212D PHE* 2.9 45.1 - - + +
215D SER* 4.3 4.1 + - - -
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Residues in contact with CYS 180 (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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140D LEU* 4.1 20.2 - - + -
141D PHE* 4.3 10.2 - - + -
144D VAL* 3.8 18.1 - - + +
166D LEU* 3.7 34.1 + - - +
171D PHE 4.8 0.6 + - - -
179D THR* 1.3 79.9 - - - +
181D LEU* 1.3 57.7 + - - -
183D LYS* 3.4 11.0 - - - +
184D ALA* 3.0 26.0 + - - +
199D LEU* 3.8 18.2 - - - -
212D PHE* 3.8 16.4 - - - -
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Residues in contact with LEU 181 (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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179D THR* 3.2 2.4 - - + +
180D CYS* 1.3 76.3 - - - +
182D PRO* 1.3 69.5 - - + +
184D ALA* 3.1 5.3 + - + +
185D LEU* 2.9 49.1 + - + +
196D ILE* 3.9 37.5 - - + +
199D LEU* 4.5 6.7 - - + -
200D LEU* 4.6 4.7 - - + -
212D PHE* 3.7 34.3 - - + +
213D ILE* 4.3 14.4 - - + -
227D ALA* 3.8 10.8 - - + -
243D LEU* 3.8 27.8 - - + -
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Residues in contact with PRO 182 (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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178D LYS* 3.9 27.1 - - + -
179D THR* 3.4 22.9 - - - +
181D LEU* 1.3 96.3 - - + +
183D LYS* 1.3 57.0 + - - +
185D LEU* 3.3 1.4 + - + +
186D LEU* 2.9 38.0 + - - +
212D PHE 5.5 2.5 - - - +
215D SER 5.3 6.1 - - - +
217D PHE* 4.4 12.3 - - + -
227D ALA* 4.7 11.7 - - + -
230D ILE* 3.6 26.5 - - + -
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Residues in contact with LYS 183 (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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141D PHE* 3.6 33.9 - - + -
144D VAL* 3.8 12.7 - - + +
145D SER* 3.4 25.2 + - - +
173D GLU* 2.5 38.2 + - + +
178D LYS* 4.7 10.3 - - + +
179D THR 3.5 6.0 + - - +
180D CYS* 3.4 16.1 + - - +
181D LEU 3.3 0.6 - - - -
182D PRO* 1.3 78.6 - - - +
184D ALA* 1.3 59.8 + - - +
186D LEU* 3.7 5.8 + - + -
187D ASN* 3.2 35.7 + - - +
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Residues in contact with ALA 184 (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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144D VAL* 4.3 7.8 - - + +
180D CYS 3.0 14.2 + - - +
181D LEU* 3.1 11.4 + - - +
183D LYS* 1.3 75.4 - - - +
185D LEU* 1.3 62.5 + - - +
186D LEU 3.3 0.2 - - - -
187D ASN 3.2 11.3 + - - +
188D LEU* 3.9 0.7 + - - +
193D ASN* 3.2 31.3 + - - +
195D THR* 3.9 15.9 - - - +
196D ILE* 3.8 23.6 - - + -
199D LEU* 4.6 2.9 - - + -
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Residues in contact with LEU 185 (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 LEU* 2.9 53.0 + - + +
182D PRO* 3.9 4.0 - - + +
184D ALA* 1.3 76.5 - - - +
186D LEU* 1.3 58.7 + - - +
187D ASN 3.2 0.2 - - - -
188D LEU* 3.4 19.3 - - + +
196D ILE* 3.3 23.3 - - + -
227D ALA* 4.3 20.6 - - + +
230D ILE* 3.6 29.2 - - + +
231D ALA* 4.5 8.1 - - + +
234D ARG* 3.3 14.9 + - - +
236D CYS* 5.7 2.0 - - - -
239D TYR* 3.9 28.0 - - + -
243D LEU* 4.8 5.2 - - + -
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Residues in contact with LEU 186 (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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178D LYS* 3.4 38.4 - - + +
182D PRO 2.9 24.2 + - - +
183D LYS* 4.1 6.5 - - + +
184D ALA 3.3 0.2 - - - -
185D LEU* 1.3 75.4 - - - +
187D ASN* 1.3 67.6 + - - +
217D PHE* 5.1 2.9 - - + -
230D ILE* 4.0 27.4 - - + -
234D ARG* 3.4 40.8 + - - +
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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