Contacts of the helix formed by residues 188 - 196 (chain N) in PDB entry 1L0V
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 LYS 188 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180N ASN* 3.1 33.8 - - + +
185N ASP* 3.7 9.5 + - - +
186N HIS* 3.1 40.3 + - - +
187N GLY* 1.3 75.8 - - - +
189N LYS* 1.3 89.1 + - + +
191N ARG* 2.8 32.8 + - - +
192N MET* 3.4 18.8 + - + +
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Residues in contact with LYS 189 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186N HIS* 4.0 12.6 - - - +
187N GLY* 4.5 3.1 - - - -
188N LYS* 1.3 107.5 - - + +
190N GLU* 1.3 60.2 + - + +
191N ARG 2.9 11.0 + - - -
192N MET* 3.6 19.7 + - - +
193N ALA* 4.2 6.9 + - - +
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Residues in contact with GLU 190 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115N ALA 5.1 2.4 - - - +
116N ILE 4.6 2.3 - - - +
117N LYS* 2.8 47.8 + - + +
121N ILE* 4.4 24.7 - - + -
187N GLY* 3.1 14.4 + - - +
189N LYS* 1.3 77.7 - - + +
191N ARG* 1.3 62.5 + - + +
193N ALA* 5.2 3.3 - - - +
194N GLN* 5.7 2.9 + - - +
4P ASN* 4.9 11.6 - - - +
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Residues in contact with ARG 191 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116N ILE* 2.9 37.4 + - + +
117N LYS* 2.8 21.6 + - + +
118N PRO* 4.7 1.0 - - - +
119N TYR 2.8 29.1 + - - +
121N ILE* 4.0 10.4 - - - +
176N ALA* 4.1 12.8 - - - +
179N TYR* 3.6 16.8 - - - +
180N ASN* 3.2 30.6 + - - +
185N ASP* 2.9 28.9 + - - -
187N GLY 3.3 15.5 + - - +
188N LYS 2.8 7.7 + - - +
189N LYS 2.9 0.2 - - - -
190N GLU* 1.3 83.6 - - + +
192N MET* 1.3 68.0 + - - +
193N ALA 3.2 2.0 - - - -
194N GLN* 3.0 12.0 + - - +
195N LEU* 2.9 23.8 + - + +
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Residues in contact with MET 192 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180N ASN* 5.0 8.5 - - - +
188N LYS* 3.7 25.1 - - + +
189N LYS* 3.6 9.8 + - - +
191N ARG* 1.3 77.5 - - - +
193N ALA* 1.3 56.6 + - - +
195N LEU* 2.7 21.3 + - - -
196N ASN* 2.5 42.6 + - - +
230N GLU* 3.6 47.6 - - + +
231N SER* 4.6 1.3 - - - +
234N ASP* 3.5 32.8 - - + +
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Residues in contact with ALA 193 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189N LYS 4.2 7.3 + - - +
190N GLU 5.6 2.2 - - - +
191N ARG 3.2 2.1 - - - -
192N MET* 1.3 78.4 - - - +
194N GLN* 1.3 62.7 + - + +
196N ASN* 3.6 12.4 + - - +
197N SER* 3.8 11.4 + - - -
4P ASN* 3.7 45.6 - - + +
5P PRO 4.0 10.9 - - - +
7P ARG* 5.5 0.2 - - - -
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Residues in contact with GLN 194 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115N ALA* 4.0 29.0 - - - +
116N ILE* 4.3 17.5 - - + -
168N ILE* 4.4 17.6 - - + +
190N GLU 5.8 2.7 - - - +
191N ARG* 3.0 11.8 + - - +
193N ALA* 1.3 79.7 - - + +
195N LEU* 1.3 67.2 + - + +
197N SER* 3.3 22.1 + - - -
199N ASN* 4.7 1.6 - - - +
200N GLY* 3.6 9.5 + - - -
0P MET 3.6 22.0 + - - -
1P ILE* 4.3 12.9 - - + +
2P ASN* 4.5 5.3 + - - +
3P PRO 5.6 1.1 - - - +
4P ASN* 5.4 2.7 - - - +
5P PRO* 4.1 24.6 - - + +
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Residues in contact with LEU 195 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116N ILE* 4.7 3.8 - - + -
168N ILE* 3.7 25.8 - - + -
173N ILE* 3.9 26.0 - - + +
176N ALA* 4.4 18.8 - - + -
177N HIS* 5.3 1.8 - - + +
180N ASN* 4.2 22.7 - - - +
191N ARG* 2.9 15.0 + - + +
192N MET* 2.7 27.5 + - - +
194N GLN* 1.3 70.0 - - - +
196N ASN* 1.3 61.5 + - - +
197N SER 3.0 10.3 + - - +
200N GLY* 3.5 1.2 - - - -
201N VAL* 3.1 41.6 + - + +
227N GLY* 5.4 7.2 - - - +
231N SER* 5.6 1.3 - - - -
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Residues in contact with ASN 196 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192N MET* 2.5 30.7 + - - +
193N ALA* 3.9 9.0 - - - +
195N LEU* 1.3 72.6 - - - +
197N SER* 1.3 58.0 + - - +
202N TRP* 4.2 10.8 - - - +
231N SER* 3.0 33.5 + - - +
234N ASP* 2.4 34.0 + - - +
235N PHE 5.9 0.2 - - - -
7P ARG* 3.2 31.6 - - + +
8P SER* 2.8 26.2 + - - -
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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