Contacts of the helix formed by residues 190 - 201 (chain A) in PDB entry 3SAJ
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 ARG 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ASP* 3.9 25.8 + - - +
134A ASP* 4.5 12.7 + - - -
160A LEU* 3.9 27.0 - - - +
186A CYS* 4.3 0.9 - - - -
187A GLU* 3.5 30.8 + - + +
188A SER 2.9 0.6 - - - -
189A GLU* 1.3 81.0 - - + +
191A LEU* 1.3 63.3 + - - +
192A ASN 3.3 2.7 - - - -
193A ALA* 3.4 12.1 + - + +
194A ILE* 3.2 43.5 + - + +
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Residues in contact with LEU 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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184A VAL* 4.2 11.2 - - + +
186A CYS* 3.6 24.7 - - - +
187A GLU 3.1 7.7 + - - +
188A SER* 3.1 14.8 + - - +
190A ARG* 1.3 79.0 - - - +
192A ASN* 1.3 64.3 + - - +
194A ILE* 3.5 0.7 + - - +
195A LEU* 3.0 28.8 + - + +
212A LEU* 3.4 46.9 - - + -
214A ASN* 5.3 4.5 - - + +
215A LEU 5.3 2.5 - - - +
216A GLY* 3.5 17.0 - - - +
220A ILE* 3.4 27.6 - - + -
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Residues in contact with ASN 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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188A SER 4.6 0.2 + - - -
189A GLU 5.6 2.7 - - - +
190A ARG 3.3 0.8 - - - -
191A LEU* 1.3 81.0 - - - +
193A ALA* 1.3 59.0 + - - +
195A LEU* 3.8 3.1 - - - +
196A GLY* 3.0 24.8 + - - -
220A ILE* 3.0 43.1 - - + +
221A ASP* 3.1 36.5 + - - +
224A LYS* 5.0 4.9 - - - +
225A PHE* 3.7 7.6 - - - -
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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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189A GLU 5.6 0.9 + - - +
190A ARG* 3.4 15.3 + - + +
191A LEU 3.3 0.6 - - - -
192A ASN* 1.3 78.6 - - - +
194A ILE* 1.3 62.3 + - + +
196A GLY* 3.4 1.4 + - - -
197A GLN* 3.0 28.1 + - - +
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Residues in contact with ILE 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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130A ILE* 4.6 9.0 - - + -
132A ASP* 5.4 1.8 - - + -
159A ILE* 4.2 29.4 - - + -
184A VAL* 3.8 26.2 - - + -
186A CYS* 3.9 20.2 - - + -
190A ARG* 3.2 47.7 + - + +
191A LEU 4.1 1.8 - - - +
193A ALA* 1.3 75.8 - - + +
195A LEU* 1.3 68.0 + - - +
197A GLN* 3.1 10.2 + - - +
198A ILE* 2.9 37.0 + - + +
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Residues in contact with LEU 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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184A VAL* 5.4 2.5 - - + -
191A LEU* 3.0 26.2 + - + +
192A ASN 3.8 2.5 - - - +
194A ILE* 1.3 77.7 - - - +
196A GLY* 1.3 63.8 + - - +
198A ILE* 3.4 8.8 - - + +
199A VAL* 3.0 43.1 + - + +
210A TYR* 4.5 28.0 - - + -
212A LEU* 5.2 13.2 - - + -
220A ILE* 4.6 8.7 - - + -
225A PHE* 2.9 46.2 - - + -
232A VAL* 5.0 14.4 - - + -
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Residues in contact with GLY 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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192A ASN 3.0 16.0 + - - -
193A ALA* 3.7 3.8 - - - -
195A LEU* 1.3 76.6 - - - +
197A GLN* 1.3 61.2 + - - +
199A VAL* 3.7 3.0 + - - +
200A LYS* 3.3 37.1 + - - +
224A LYS* 5.3 3.4 - - - -
225A PHE* 3.8 14.5 - - - -
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Residues in contact with GLN 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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159A ILE* 4.1 10.7 - - - +
162A THR 5.3 2.1 + - - +
163A THR* 6.2 1.4 - - - +
164A GLU* 4.9 18.0 + - + +
167A TYR* 4.1 24.1 + - - -
193A ALA 3.0 15.4 + - - +
194A ILE* 3.5 13.2 - - - +
196A GLY* 1.3 77.3 - - - +
198A ILE* 1.3 64.8 + - + +
200A LYS* 3.3 20.6 + - - +
201A LEU* 3.4 23.6 + - + +
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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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130A ILE* 4.0 15.3 - - + -
167A TYR* 3.9 35.9 - - + -
182A VAL* 4.7 0.7 - - + -
184A VAL* 3.9 28.3 - - + -
194A ILE* 2.9 35.0 + - + +
195A LEU* 3.4 14.4 - - + +
197A GLN* 1.3 79.8 - - + +
199A VAL* 1.3 63.5 + - + +
201A LEU* 3.5 16.3 + - + +
202A GLU* 3.7 8.7 + - - +
208A TYR* 5.8 0.9 - - - -
210A TYR* 3.7 27.9 + - + +
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Residues in contact with VAL 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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195A LEU* 3.0 30.0 + - + +
196A GLY* 4.1 4.0 - - - +
198A ILE* 1.3 75.5 - - - +
200A LYS* 1.3 66.6 + - + +
201A LEU 3.2 0.4 - - - -
202A GLU* 3.3 44.2 - - - +
210A TYR* 3.5 20.9 - - + +
225A PHE* 4.5 17.3 - - + -
228A SER* 5.5 6.5 - - - +
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Residues in contact with LYS 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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196A GLY* 3.3 25.5 + - - +
197A GLN* 3.4 12.6 - - - +
198A ILE 3.3 0.2 - - - -
199A VAL* 1.3 80.1 - - + +
201A LEU* 1.3 61.1 + - + +
202A GLU 3.1 8.6 + - - +
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Residues in contact with LEU 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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164A GLU* 4.0 26.2 - - + +
167A TYR* 3.3 52.2 - - + -
168A ARG* 4.3 23.7 - - + +
171A PHE* 4.7 6.1 - - - -
197A GLN* 3.4 21.9 + - + +
198A ILE* 3.9 13.0 - - - +
199A VAL 3.2 0.8 - - - -
200A LYS* 1.3 77.8 - - + +
202A GLU* 1.3 62.8 + - - +
203A LYS* 3.7 17.3 + - - +
208A TYR* 4.8 1.2 + - - -
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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