Contacts of the helix formed by residues 179 - 186 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B PHE* 4.3 4.9 - - - -
166B LEU 4.0 15.9 - - - +
167B THR* 4.5 4.5 - - - -
171B PHE 4.0 7.2 - - - -
172B ARG* 4.2 10.5 - - + +
177B GLY 3.3 1.0 + - - -
178B LYS* 1.3 81.8 - - - +
180B CYS* 1.3 64.6 + - - +
181B LEU* 3.1 15.4 + - - +
182B PRO* 3.2 20.7 - - + +
183B LYS* 3.8 6.6 + - - +
212B PHE* 3.4 27.2 + - + -
215B SER* 3.5 36.1 + - - +
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Residues in contact with CYS 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B LEU* 4.0 32.5 - - + -
141B PHE* 4.0 15.3 - - + -
144B VAL* 3.7 15.1 - - + +
166B LEU* 4.4 7.8 + - - -
171B PHE* 4.2 2.4 + - - -
179B THR* 1.3 73.9 - - - +
181B LEU* 1.3 58.2 + - - +
183B LYS* 3.5 7.9 - - - +
184B ALA* 2.9 27.0 + - - +
199B LEU* 3.7 30.5 - - - +
212B PHE* 3.8 17.7 - - - -
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Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B THR* 3.1 4.4 + - - +
180B CYS* 1.3 74.8 - - - +
182B PRO* 1.3 71.0 - - + +
183B LYS 3.1 0.9 - - - -
184B ALA* 3.0 14.7 + - - +
185B LEU* 3.1 25.5 + - + +
196B ILE* 4.1 34.1 - - + +
199B LEU* 4.6 4.5 - - + -
200B LEU* 4.4 9.2 - - + -
212B PHE* 3.6 31.6 - - + +
213B ILE* 3.9 24.7 - - - -
227B ALA* 3.4 27.8 - - + -
243B LEU* 4.1 14.6 - - + -
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Residues in contact with PRO 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B LYS* 3.7 24.0 - - + -
179B THR* 3.2 23.3 - - - +
181B LEU* 1.3 93.2 - - + +
183B LYS* 1.3 55.3 + - - +
185B LEU* 3.3 7.0 + - + +
186B LEU* 3.1 36.4 + - - +
215B SER 5.3 4.5 - - - +
217B PHE* 3.9 23.3 - - + -
227B ALA* 4.8 9.4 - - + +
230B ILE* 3.5 24.0 - - + +
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Residues in contact with LYS 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B PHE* 4.2 27.9 - - + +
144B VAL* 3.5 18.9 - - + +
145B SER* 2.9 25.0 - - - +
173B GLU* 5.8 3.0 + - - -
178B LYS* 5.1 9.3 - - + +
179B THR 3.8 5.6 + - - +
180B CYS* 3.5 15.2 + - - +
181B LEU 3.1 0.6 - - - -
182B PRO* 1.3 78.7 - - - +
184B ALA* 1.3 63.4 + - - +
186B LEU* 3.7 6.8 + - + -
187B ASN* 2.7 42.8 + - - +
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Residues in contact with ALA 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B VAL* 4.0 5.6 - - + +
180B CYS 2.9 16.3 + - - +
181B LEU 3.0 7.4 + - - +
183B LYS* 1.3 75.2 - - - +
185B LEU* 1.3 57.0 + - - +
187B ASN 3.0 19.8 + - - +
188B LEU* 3.7 0.7 - - - +
193B ASN* 3.1 26.3 + - - +
195B THR* 3.6 17.7 - - - +
196B ILE* 3.5 28.3 - - + -
199B LEU* 4.4 5.8 - - + -
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Residues in contact with LEU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B LEU* 3.1 29.2 + - + +
182B PRO* 3.8 3.1 - - + +
184B ALA* 1.3 76.5 - - - +
186B LEU* 1.3 58.1 + - - +
187B ASN 3.3 0.7 - - - -
188B LEU* 3.4 27.0 - - + +
196B ILE* 3.5 25.1 - - + -
227B ALA* 3.7 42.4 - - + +
230B ILE* 3.8 15.7 - - + -
231B ALA* 4.4 11.0 - - + +
234B ARG* 4.1 12.9 - - + +
236B CYS* 5.2 2.7 - - - -
239B TYR* 4.0 27.6 - - + -
243B LEU* 4.3 5.2 - - + -
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Residues in contact with LEU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B LYS* 3.3 35.7 - - - +
182B PRO 3.1 19.4 + - - +
183B LYS* 4.1 7.6 - - + +
184B ALA 3.2 0.4 - - - -
185B LEU* 1.3 76.5 - - - +
187B ASN* 1.3 68.0 + - - +
188B LEU* 3.9 1.7 + - - -
230B ILE* 3.6 30.1 - - + -
233B GLU* 5.9 0.2 - - - +
234B ARG* 3.8 42.1 + - - +
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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