Contacts of the helix formed by residues 194 - 206 (chain A) 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 ASP 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A GLY 4.5 4.9 + - - +
149A PRO* 3.8 27.5 - - + +
192A ARG* 4.1 19.6 - - - +
193A ASN* 1.3 71.3 + - - +
195A THR* 1.3 60.4 + - - +
196A ILE 3.1 1.3 - - - -
197A PRO* 3.4 14.3 - - + +
198A ILE* 3.1 19.4 - - - +
239A TYR* 4.5 2.3 + - - -
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Residues in contact with THR 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ILE* 4.4 1.1 - - + +
144A VAL* 4.1 14.0 - - - +
147A GLY* 3.9 1.8 - - - -
148A SER 3.6 39.5 - - - +
149A PRO* 3.8 1.1 - - - +
152A LEU* 3.7 17.3 - - + -
184A ALA* 3.7 12.1 - - - +
193A ASN* 2.6 26.2 + - - +
194A ASP* 1.3 77.4 - - - +
196A ILE* 1.3 66.5 + - - +
197A PRO 3.4 0.2 - - - -
198A ILE* 3.2 9.5 + - - +
199A LEU* 2.8 32.0 + - - +
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Residues in contact with ILE 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A LEU* 4.1 20.2 - - + -
184A ALA* 3.5 23.6 - - + -
185A LEU* 3.6 34.8 - - + -
193A ASN* 2.9 31.6 + - + +
195A THR* 1.3 79.2 - - - +
197A PRO* 1.3 66.9 - - + +
199A LEU* 3.1 5.9 + - - +
200A LEU* 3.1 25.0 + - + +
239A TYR* 3.8 21.1 - - + -
242A LEU* 3.7 25.4 - - + -
243A LEU* 5.4 2.5 - - + -
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Residues in contact with PRO 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ASN 4.0 2.7 - - - +
194A ASP* 3.4 23.1 - - + +
196A ILE* 1.3 95.6 - - + +
198A ILE* 1.3 61.0 + - + +
200A LEU* 3.5 8.9 + - + +
201A ASP* 3.2 22.9 + - - +
238A HIS* 6.0 3.6 - - + -
239A TYR* 5.2 5.4 - - + +
242A LEU* 4.8 12.3 - - + -
246A LYS* 5.9 1.3 - - - -
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Residues in contact with ILE 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A PRO* 4.2 15.0 - - + +
152A LEU* 3.2 36.6 - - + +
194A ASP 3.1 25.6 - - - +
195A THR* 3.5 9.4 - - - +
197A PRO* 1.3 74.8 - - + +
199A LEU* 1.3 61.8 + - - +
201A ASP* 3.4 7.7 + - - +
202A ILE* 3.0 57.5 + - + +
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Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU* 4.5 2.2 - - + -
144A VAL* 4.1 8.5 - - + -
152A LEU* 3.7 22.2 - - + -
155A LEU* 4.3 14.6 - - + -
166A LEU* 3.9 13.0 - - + +
180A CYS* 3.9 39.3 - - - +
181A LEU* 4.8 3.6 - - + +
184A ALA* 4.5 5.4 - - + -
195A THR* 2.8 42.9 + - - +
196A ILE* 3.7 6.1 - - + +
198A ILE* 1.3 71.3 - - - +
200A LEU* 1.3 57.2 - - + +
202A ILE* 3.3 5.2 + - + +
203A ALA* 3.0 28.9 + - - +
212A PHE* 4.0 17.0 - - + -
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Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A LEU* 4.2 4.9 - - + -
196A ILE* 3.1 19.0 + - + +
197A PRO* 3.9 5.4 - - + +
199A LEU* 1.3 74.8 - - - +
201A ASP* 1.3 58.0 + - - +
203A ALA* 3.5 3.2 + - - -
204A GLU 3.0 21.1 + - - -
209A MET* 3.1 28.5 - - + +
212A PHE* 4.1 17.0 - - + -
213A ILE* 3.5 32.5 - - + -
242A LEU* 3.3 45.5 - - + -
243A LEU* 4.2 17.5 - - + -
246A LYS* 3.7 8.3 - - + -
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Residues in contact with ASP 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A LEU* 5.1 1.9 - - - +
197A PRO 3.2 14.9 + - - +
198A ILE* 3.8 8.0 - - - +
200A LEU* 1.3 76.6 - - - +
202A ILE* 1.3 64.6 + - - +
204A GLU* 3.2 16.3 + - - +
205A LYS* 2.6 64.6 + - - +
209A MET* 4.3 0.9 - - - +
246A LYS* 5.5 2.2 - - - +
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Residues in contact with ILE 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A LEU 4.7 1.1 - - - +
155A LEU* 3.7 33.4 - - + -
156A LEU* 4.1 30.2 - - + +
159A LEU* 3.4 32.3 - - + -
166A LEU* 4.0 9.0 - - + -
198A ILE* 3.0 49.1 + - + +
199A LEU* 3.6 7.6 - - + +
201A ASP* 1.3 81.0 - - - +
203A ALA* 1.3 60.4 + - - +
205A LYS* 3.2 4.0 + - - +
206A THR* 2.9 26.9 + - - +
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Residues in contact with ALA 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LEU* 4.5 4.9 - - + +
199A LEU 3.0 16.8 + - - +
200A LEU 3.6 5.8 - - - +
202A ILE* 1.3 77.7 - - - +
204A GLU* 1.3 55.8 + - - +
206A THR* 3.1 12.0 + - - -
208A ASN* 2.7 37.1 + - - +
209A MET* 3.8 9.2 - - + -
212A PHE* 3.6 38.4 - - + -
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Residues in contact with GLU 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A LEU 3.0 14.0 + - - +
201A ASP* 3.4 19.3 - - - +
202A ILE 3.1 0.4 - - - -
203A ALA* 1.3 76.7 - - - +
205A LYS* 1.3 63.3 + - + +
207A GLY* 3.1 18.2 + - - -
209A MET* 3.9 37.2 - - + +
246A LYS* 5.1 3.5 - - - -
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Residues in contact with LYS 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A LEU* 3.7 30.7 - - + -
160A LEU* 4.0 13.3 - - + +
201A ASP* 2.6 50.9 + - - +
202A ILE 3.2 4.9 + - - +
204A GLU* 1.3 81.3 + - + +
206A THR* 1.3 57.3 + - - +
207A GLY 3.4 2.1 + - - -
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Residues in contact with THR 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LEU* 3.9 10.1 - - + -
159A LEU* 4.1 24.5 - - + +
160A LEU* 3.4 28.9 - - + -
164A LYS 4.3 4.3 - - - +
165A ARG* 4.0 22.1 - - - +
166A LEU 5.3 0.9 + - - -
202A ILE* 2.9 20.0 + - - +
203A ALA* 3.1 13.0 + - - -
204A GLU 3.1 0.2 - - - -
205A LYS* 1.3 75.5 - - - +
207A GLY* 1.3 62.2 + - - +
208A ASN* 3.2 13.3 + - - +
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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