Contacts of the helix formed by residues 190 - 203 (chain A) in PDB entry 2JAJ
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 SER 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A GLY 3.6 1.0 - - - -
189A SER* 1.3 82.6 - - - +
191A GLU* 1.3 65.1 + - - +
192A SER* 3.6 7.4 + - - -
193A ALA 3.1 14.6 + - - -
194A GLN* 3.1 20.0 + - - +
214A PRO 5.7 0.4 + - - -
216A ASP* 2.4 34.0 + - - -
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Residues in contact with GLU 191 (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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190A SER* 1.3 73.5 - - - +
192A SER* 1.3 62.5 + - - +
194A GLN* 3.9 3.9 - - - +
195A LYS* 2.9 64.0 + - + +
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Residues in contact with SER 192 (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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168A ALA* 4.6 13.6 - - - +
169A ASP* 4.8 4.3 + - - -
171A LEU* 4.2 26.4 - - - +
176A PHE* 5.0 4.7 - - - -
190A SER* 3.6 8.4 + - - -
191A GLU* 1.3 77.3 - - - +
193A ALA* 1.3 63.8 + - - +
195A LYS* 3.1 11.3 + - - +
196A ALA* 2.9 25.0 + - - +
216A ASP* 5.0 0.9 - - - -
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Residues in contact with ALA 193 (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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176A PHE* 3.6 37.7 - - + -
187A ILE* 3.7 6.5 - - + +
188A GLY 3.4 29.2 - - - +
190A SER* 3.1 16.0 + - - +
192A SER* 1.3 78.2 - - - +
194A GLN* 1.3 58.4 + - - +
196A ALA* 3.2 4.0 + - - +
197A LEU* 2.8 29.6 + - - +
216A ASP* 3.9 0.2 - - - +
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Residues in contact with GLN 194 (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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187A ILE* 4.1 10.7 - - - +
188A GLY 3.0 22.3 + - - +
189A SER* 3.8 14.8 - - - +
190A SER 3.1 17.4 + - - +
191A GLU* 4.1 3.6 - - - +
193A ALA* 1.3 76.8 - - - +
195A LYS* 1.3 61.5 + - - +
197A LEU* 3.5 17.7 + - - +
198A LYS* 3.2 53.3 + - - +
210A LYS* 4.4 10.3 + - - +
212A THR* 4.1 14.1 + - - +
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Residues in contact with LYS 195 (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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191A GLU* 2.9 60.1 + - + +
192A SER* 3.4 8.3 - - - +
194A GLN* 1.3 75.7 - - - +
196A ALA* 1.3 61.1 + - - +
198A LYS* 3.7 8.3 + - - +
199A ILE* 3.4 33.1 + - + +
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Residues in contact with ALA 196 (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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165A VAL* 4.1 20.8 - - + +
166A PRO 5.0 5.4 - - - +
173A LEU* 4.7 3.1 - - + -
176A PHE* 3.5 32.3 - - + -
192A SER 2.9 8.9 + - - +
193A ALA 3.2 8.0 + - - +
195A LYS* 1.3 75.9 - - - +
197A LEU* 1.3 65.0 + - - +
199A ILE* 3.3 5.3 + - - +
200A MET* 3.0 28.5 + - + +
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Residues in contact with LEU 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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185A ILE* 4.7 17.7 - - + -
187A ILE* 3.8 39.0 - - + -
193A ALA 2.8 19.7 + - - +
194A GLN* 3.8 21.1 - - - +
196A ALA* 1.3 72.5 - - - +
198A LYS* 1.3 54.5 + - + +
200A MET* 3.3 22.0 + - + +
201A GLN* 2.8 62.6 + - + +
210A LYS* 3.9 24.7 - - + +
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Residues in contact with LYS 198 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A GLN* 3.2 41.5 + - - +
195A LYS* 3.9 8.5 - - + +
197A LEU* 1.3 73.5 - - + +
199A ILE* 1.3 61.5 + - + +
201A GLN* 3.4 12.3 + - - +
202A GLN* 2.8 44.1 + - - +
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Residues in contact with ILE 199 (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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164A THR 4.6 0.7 - - - +
165A VAL* 4.0 20.6 - - + -
166A PRO* 4.5 21.3 - - + +
195A LYS* 3.4 20.6 + - + +
196A ALA* 3.3 8.4 + - - +
198A LYS* 1.3 76.7 - - + +
200A MET* 1.3 60.4 - - - +
202A GLN* 3.2 18.8 + - - +
203A MET* 3.1 41.0 + - + +
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Residues in contact with MET 200 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A LEU* 4.2 11.2 - - + -
138A PHE* 3.4 69.1 - - + -
165A VAL* 4.0 15.0 - - + -
173A LEU* 4.0 23.3 - - + -
176A PHE* 5.2 0.2 - - + -
177A CYS* 4.4 13.7 - - + -
185A ILE* 5.1 7.4 - - + -
187A ILE* 4.7 5.2 - - + -
196A ALA* 3.0 16.0 + - + +
197A LEU* 3.6 37.0 - - + +
198A LYS 3.3 0.2 - - - -
199A ILE* 1.3 74.3 - - - +
201A GLN* 1.3 63.4 + - + +
203A MET* 3.2 13.4 + - - -
204A SER* 3.4 4.9 + - - -
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Residues in contact with GLN 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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185A ILE* 5.9 1.8 - - + +
197A LEU* 2.8 57.1 + - + +
198A LYS* 3.7 10.8 - - - +
200A MET* 1.3 75.5 - - + +
202A GLN* 1.3 63.3 + - - +
204A SER* 3.1 19.7 - - - +
206A HIS 5.2 4.0 - - - +
208A TYR* 4.0 37.0 + - + +
210A LYS* 5.0 11.7 + - - +
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Residues in contact with GLN 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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198A LYS* 2.8 31.3 + - + +
199A ILE* 3.2 23.1 + - - +
201A GLN* 1.3 75.3 - - - +
203A MET* 1.3 57.9 - - + +
204A SER 3.3 0.6 - - - +
6B PRO* 3.3 24.4 - - - +
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Residues in contact with MET 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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136A GLU* 5.1 0.9 - - - +
138A PHE* 3.7 20.2 - - + -
163A SER* 3.5 30.2 + - - +
164A THR 3.4 29.2 - - - +
165A VAL* 4.5 2.5 - - + -
199A ILE* 3.1 24.2 + - + +
200A MET* 3.2 15.6 + - - +
202A GLN* 1.3 78.9 - - + +
204A SER* 1.3 57.8 + - - +
-4B GLY* 3.6 26.5 - - - -
-3B PRO* 4.9 7.8 - - + +
5B HIS* 3.8 10.0 + - - +
6B PRO* 3.8 15.5 - - - +
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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