Contacts of the helix formed by residues 190 - 203 (chain A) in PDB entry 1LTQ
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 ASN 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A GLY 3.8 13.7 + - - -
169A THR* 3.0 29.1 + - - +
170A LEU 2.9 12.3 + - - +
171A ALA 4.5 1.1 - - - +
172A LYS* 4.5 24.6 - - + +
188A VAL 3.8 0.2 + - - -
189A ILE* 1.3 70.6 - - - +
191A PRO* 1.3 74.4 - - - +
192A MSE 3.5 4.0 + - - +
193A VAL* 3.0 18.8 + - - +
194A VAL* 2.9 21.4 + - - +
296A VAL* 4.5 6.5 + - - +
297A ALA* 5.7 3.0 - - - +
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Residues in contact with PRO 191 (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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189A ILE* 2.9 28.2 - - + +
190A ASN* 1.3 88.7 - - - +
192A MSE 1.3 66.9 + - + +
194A VAL* 3.2 4.1 + - + +
195A GLU* 2.8 33.2 + - - +
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Residues in contact with MSE 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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190A ASN* 3.5 3.7 + - - +
191A PRO* 1.3 86.2 - - + +
193A VAL* 1.3 61.5 + - + +
195A GLU* 3.5 28.6 + - - +
196A LEU* 3.0 25.8 + - - +
199A MSE 5.8 0.3 - - - +
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Residues in contact with VAL 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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164A PHE* 3.8 18.6 - - + -
169A THR* 3.3 48.9 - - + +
170A LEU* 4.0 4.7 - - + -
190A ASN* 3.0 18.8 + - - +
192A MSE 1.3 76.6 - - + +
194A VAL* 1.3 68.8 + - - +
196A LEU* 3.0 17.4 + - + +
197A SER* 3.2 10.6 + - - -
276A ILE* 4.2 4.5 - - + -
296A VAL* 4.0 24.7 - - + -
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Residues in contact with VAL 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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170A LEU* 3.4 32.8 - - + +
189A ILE* 3.7 20.0 - - + -
190A ASN 2.9 19.7 + - - +
191A PRO* 3.7 6.3 - - + +
193A VAL* 1.3 74.3 - - - +
195A GLU* 1.3 63.8 + - - +
197A SER* 2.6 26.0 + - - -
198A LYS* 3.4 17.6 + - - +
236A ALA* 3.4 38.1 - - + +
238A VAL* 4.6 3.4 - - + -
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Residues in contact with GLU 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 PRO 2.8 18.5 + - - +
192A MSE 3.5 32.7 - - - +
194A VAL* 1.3 77.6 - - - +
196A LEU* 1.3 62.6 + - - +
198A LYS* 3.1 13.2 + - + +
199A MSE 3.0 41.0 + - + +
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Residues in contact with LEU 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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164A PHE* 3.9 12.1 - - + -
192A MSE 3.0 15.3 + - - +
193A VAL* 3.0 13.9 + - + +
195A GLU* 1.3 75.9 - - - +
197A SER* 1.3 62.3 + - - +
199A MSE 3.0 27.3 + - + +
200A TYR* 2.9 56.4 + - + +
276A ILE* 3.9 31.2 - - + -
294A TRP* 4.5 12.1 - - + -
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Residues in contact with SER 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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164A PHE* 3.4 37.1 - - - -
170A LEU* 4.5 2.2 - - - -
193A VAL 3.2 3.7 + - - -
194A VAL* 2.6 21.9 + - - -
196A LEU* 1.3 79.4 - - - +
198A LYS* 1.3 63.7 + - - +
200A TYR* 3.6 1.6 + - - +
201A ALA* 3.2 21.1 + - - +
207A ILE* 3.7 10.8 - - - +
238A VAL* 3.8 33.6 - - - +
239A PRO* 4.9 1.9 - - - +
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Residues in contact with LYS 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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194A VAL* 3.9 20.6 - - + +
195A GLU* 3.1 13.3 + - + +
197A SER* 1.3 82.6 + - - +
199A MSE 1.3 67.5 + - - +
201A ALA* 3.2 8.2 + - - +
202A LEU* 3.0 28.3 + - + +
236A ALA 3.1 27.6 + - - -
237A GLY* 3.5 18.2 - - - +
238A VAL* 4.6 0.7 - - - +
239A PRO* 4.4 13.0 - - + -
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Residues in contact with MSE 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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192A MSE 5.8 0.4 - - - +
195A GLU* 3.0 41.0 + - + +
196A LEU* 3.0 27.5 + - + +
198A LYS* 1.3 76.7 - - - +
200A TYR* 1.3 62.1 + - + +
202A LEU* 3.2 14.1 + - + +
203A MSE 3.1 34.0 + - + +
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Residues in contact with TYR 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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162A VAL* 3.9 19.1 - - + -
164A PHE* 4.2 8.7 - + + -
196A LEU* 2.9 54.0 + - + +
197A SER* 3.9 5.4 - - - +
199A MSE 1.3 73.6 - - + +
201A ALA* 1.3 66.5 + - - +
203A MSE 2.9 19.7 + - + +
204A GLY 3.1 0.3 + - - -
205A TYR* 3.1 56.1 + + + +
207A ILE* 5.0 4.0 - - + -
274A LEU* 3.6 19.5 - - + +
294A TRP* 3.2 28.9 - - - -
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Residues in contact with ALA 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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197A SER 3.2 7.7 + - - +
198A LYS* 3.2 9.3 + - - +
200A TYR* 1.3 76.0 - - - +
202A LEU* 1.3 57.3 + - + +
204A GLY* 2.6 27.5 + - - -
205A TYR 3.8 3.0 - - - +
207A ILE* 3.5 27.5 - - + +
239A PRO* 3.8 20.2 - - + -
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Residues in contact with LEU 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* 3.0 16.1 + - + +
199A MSE 3.2 14.3 + - - +
201A ALA* 1.3 76.1 - - - +
203A MSE 1.3 61.8 + - + +
204A GLY* 3.0 4.6 + - - -
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Residues in contact with MSE 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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199A MSE 3.1 26.9 + - + +
200A TYR* 2.9 17.7 + - + +
202A LEU* 1.3 79.2 - - + +
204A GLY* 1.3 58.9 + - - +
205A TYR* 3.5 21.6 + - + -
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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