Contacts of the helix formed by residues 171 - 181 (chain R) in PDB entry 1G4W
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 LEU 171 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172R LEU* 1.3 78.8 + - + +
173R ASP* 3.2 17.2 + - - +
174R ILE* 3.6 20.1 + - + +
175R ALA* 3.5 16.6 + - + +
217R ASN* 4.0 46.2 - - + +
218R LEU* 5.8 0.4 - - + -
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Residues in contact with LEU 172 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171R LEU* 1.3 93.3 - - + +
173R ASP* 1.3 65.3 + - - +
174R ILE 3.0 2.9 - - - -
175R ALA* 3.8 8.2 - - - +
176R LEU* 3.0 30.9 + - + +
218R LEU* 3.7 22.7 - - + -
287R LEU* 4.0 24.0 - - + -
290R ILE* 5.2 8.5 - - + -
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Residues in contact with ASP 173 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171R LEU 3.2 18.9 + - - +
172R LEU* 1.3 78.6 + - - +
174R ILE* 1.3 63.5 + - + +
176R LEU* 4.2 2.5 - - - +
177R LYS* 3.1 31.4 + - - +
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Residues in contact with ILE 174 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171R LEU* 3.6 20.4 + - + +
172R LEU 3.0 0.2 - - - -
173R ASP* 1.3 81.6 - - + +
175R ALA* 1.3 54.2 + - - +
176R LEU 2.7 9.4 + - - -
177R LYS* 4.9 1.3 - - - -
178R GLY* 2.6 35.4 + - - +
214R ASN* 3.0 10.7 + - - +
217R ASN* 5.5 6.7 - - - +
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Residues in contact with ALA 175 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171R LEU* 3.5 13.6 + - + +
172R LEU* 3.6 3.1 + - - -
174R ILE* 1.3 77.1 - - - +
176R LEU* 1.3 56.6 + - - +
179R LEU* 3.3 26.5 - - - +
214R ASN* 3.1 42.8 + - + +
217R ASN* 4.6 7.3 - - + +
218R LEU* 3.9 21.4 - - + +
287R LEU* 4.0 6.1 - - - +
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Residues in contact with LEU 176 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172R LEU* 3.0 18.5 + - + +
173R ASP* 4.2 4.0 - - - +
174R ILE 2.7 2.6 + - - -
175R ALA* 1.3 79.3 - - - +
177R LYS* 1.3 76.1 + - + +
178R GLY 3.3 0.4 - - - -
179R LEU* 3.1 5.9 + - - +
180R LYS* 2.8 38.3 + - + +
284R THR* 4.7 12.9 - - + +
287R LEU* 3.5 50.5 - - + +
288R GLU* 3.7 12.1 - - + +
290R ILE 5.6 1.8 - - - +
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Residues in contact with LYS 177 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173R ASP* 3.1 19.1 - - - +
174R ILE* 3.2 2.8 + - - +
176R LEU* 1.3 83.4 - - + +
178R GLY* 1.3 58.6 + - - +
179R LEU 2.9 10.5 + - - -
180R LYS* 3.0 39.2 + - - +
181R ARG* 3.3 18.9 + - - +
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Residues in contact with GLY 178 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174R ILE* 2.6 19.2 + - - +
177R LYS* 1.3 71.8 - - - +
179R LEU* 1.3 54.6 + - - +
181R ARG* 4.0 21.2 - - - +
182R THR* 3.1 20.5 - - - +
210R SER* 4.4 4.0 + - - -
214R ASN* 3.1 29.9 + - - +
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Residues in contact with LEU 179 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175R ALA 3.3 26.0 - - - +
176R LEU* 3.5 4.5 - - - +
177R LYS 2.9 0.4 - - - -
178R GLY* 1.3 76.5 - - - +
180R LYS* 1.3 60.9 + - - +
181R ARG 3.1 5.9 + - - -
182R THR* 3.4 7.0 - - - -
183R LEU* 3.1 33.8 + - + +
211R LEU* 4.0 14.4 - - + -
214R ASN* 4.3 6.5 - - + +
215R LEU* 3.8 30.1 - - + -
218R LEU* 4.9 2.5 - - + -
280R LEU* 4.4 6.7 - - + +
283R VAL* 4.7 14.6 - - + -
284R THR* 3.0 32.5 - - + +
287R LEU* 5.0 2.2 - - + -
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Residues in contact with LYS 180 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176R LEU* 2.8 24.3 + - + +
177R LYS* 3.0 33.3 + - - +
179R LEU* 1.3 78.1 - - - +
181R ARG* 1.3 56.3 + - - +
183R LEU* 5.5 0.7 - - - -
184R PRO* 3.9 13.8 - - - +
284R THR* 4.5 18.6 - - + +
288R GLU* 3.3 31.3 + - - +
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Residues in contact with ARG 181 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177R LYS 3.3 13.7 + - - +
178R GLY* 4.0 18.7 - - - -
180R LYS* 1.3 81.2 - - - +
182R THR* 1.3 76.7 + - - +
183R LEU 3.3 1.8 - - - -
184R PRO* 3.0 22.3 - - - +
185R GLN* 3.1 23.2 + - - +
207R PRO* 5.4 4.8 - - - +
210R SER* 3.4 25.6 + - - -
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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