Contacts of the helix formed by residues 190 - 198 (chain Y) in PDB entry 3N5N
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 THR 190 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188Y PRO 3.5 0.2 - - - -
189Y ARG* 1.3 87.9 - - + +
191Y ALA* 1.3 55.7 + - - +
192Y GLU* 3.8 10.0 - - - +
193Y THR* 3.1 24.1 + - - +
194Y LEU* 2.7 40.6 + - - +
210Y ALA* 4.2 0.2 - - - -
216Y GLN* 3.2 19.3 - - - +
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Residues in contact with ALA 191 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190Y THR* 1.3 72.0 - - - +
192Y GLU* 1.3 64.8 + - - +
194Y LEU* 3.2 1.2 + - - -
195Y GLN* 3.0 20.9 + - - +
206Y ALA* 3.3 24.8 - - + +
207Y GLY* 4.5 1.8 - - - -
210Y ALA* 3.5 16.4 - - + +
216Y GLN* 2.7 24.9 + - - +
218Y THR* 4.0 15.7 - - + +
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Residues in contact with GLU 192 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190Y THR* 3.3 11.6 + - - +
191Y ALA* 1.3 78.4 - - - +
193Y THR* 1.3 65.2 + - - +
195Y GLN* 3.3 8.4 + - - +
196Y GLN* 2.8 38.9 + - - +
216Y GLN* 5.0 1.2 - - - +
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Residues in contact with THR 193 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188Y PRO* 2.4 50.9 - - + -
189Y ARG 3.7 3.1 - - - +
190Y THR* 3.1 20.0 + - - +
192Y GLU* 1.3 84.5 + - - +
194Y LEU* 1.3 60.2 + - - +
196Y GLN* 3.2 12.4 + - - +
197Y LEU* 3.0 46.0 + - + +
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Residues in contact with LEU 194 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187Y MET* 4.0 10.3 - - + -
188Y PRO* 2.8 54.1 - - + +
190Y THR 2.7 24.8 + - - +
191Y ALA 3.7 4.3 - - - +
193Y THR* 1.3 73.7 - - - +
195Y GLN* 1.3 60.1 + - - +
198Y LEU* 3.4 40.3 + - + +
201Y VAL* 3.4 10.3 - - + +
206Y ALA* 3.9 17.9 - - + +
209Y ILE* 3.6 33.9 - - + -
210Y ALA* 4.0 4.0 - - + +
214Y PHE* 4.0 6.7 - - + -
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Residues in contact with GLN 195 (chain Y).
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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191Y ALA 3.0 16.9 + - - +
192Y GLU* 3.7 8.0 - - - +
194Y LEU* 1.3 78.6 - - - +
196Y GLN* 1.3 64.2 + - - +
198Y LEU 4.2 6.6 - - - +
201Y VAL 3.8 17.7 - - - +
202Y GLY* 4.0 3.4 - - - -
203Y ARG* 3.4 46.1 - - - +
206Y ALA* 3.8 9.5 - - + +
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Residues in contact with GLN 196 (chain Y).
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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178Y LYS* 5.5 0.2 + - - -
192Y GLU* 2.8 26.0 + - + +
193Y THR* 3.7 15.8 + - - +
195Y GLN* 1.3 80.1 - - - +
197Y LEU* 1.3 71.1 + - + +
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Residues in contact with LEU 197 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178Y LYS* 2.9 43.0 + - - +
183Y LEU* 4.3 24.2 - - + -
188Y PRO* 3.8 24.2 - - + -
193Y THR* 3.0 30.0 + - - +
196Y GLN* 1.3 95.2 - - + +
198Y LEU* 1.3 64.8 + - + +
199Y PRO* 3.7 2.3 - - - +
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Residues in contact with LEU 198 (chain Y).
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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117Y TRP* 3.8 26.0 - - + -
175Y GLY 4.3 9.0 - - - +
178Y LYS* 5.0 4.9 - - + -
179Y VAL* 3.5 26.2 - - + -
183Y LEU* 5.1 1.3 - - + -
187Y MET* 3.9 13.2 - - + -
188Y PRO* 4.4 13.5 - - + -
194Y LEU* 3.4 41.1 + - + +
195Y GLN 4.2 7.4 - - - +
197Y LEU* 1.3 81.4 - - + +
199Y PRO* 1.3 72.6 - - + +
200Y GLY 3.6 0.2 + - - -
201Y VAL* 3.3 29.2 + - + +
209Y ILE* 5.4 1.8 - - + -
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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