Contacts of the helix formed by residues 182 - 188 (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 THR 182 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178R GLY 3.1 25.6 - - - +
179R LEU* 3.4 13.9 - - - +
181R ARG* 1.3 92.1 - - - +
183R LEU* 1.3 65.5 + - - +
185R GLN* 3.1 13.8 - - - +
186R LEU* 2.9 25.9 - - - +
207R PRO* 2.9 35.5 + - - +
210R SER* 5.0 1.1 - - - -
211R LEU* 3.5 28.6 - - + +
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Residues in contact with LEU 183 (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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179R LEU* 3.1 40.3 + - + +
180R LYS* 5.5 0.2 - - - -
182R THR* 1.3 77.8 - - + +
184R PRO* 1.3 62.1 - - + +
185R GLN 2.6 15.9 + - - -
186R LEU* 2.8 17.8 + - + +
187R GLU* 2.9 11.7 + - - +
211R LEU* 4.1 14.1 - - + -
277R ALA* 4.1 18.1 - - + +
280R LEU* 3.7 31.6 - - + -
281R LYS* 4.0 34.5 - - + +
284R THR* 3.5 11.9 - - + +
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Residues in contact with PRO 184 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180R LYS 3.9 12.3 - - - +
181R ARG* 3.0 29.2 - - - +
183R LEU* 1.3 93.5 - - + +
185R GLN* 1.3 65.2 + - - +
187R GLU* 3.6 13.7 - - + -
188R GLN* 3.3 27.9 + - + +
281R LYS* 5.1 11.6 - - - +
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Residues in contact with GLN 185 (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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181R ARG* 3.1 27.4 + - - +
182R THR* 3.1 15.3 - - - +
183R LEU 2.6 5.3 + - - -
184R PRO* 1.3 79.1 + - - +
186R LEU* 1.3 64.9 + - + +
188R GLN* 2.7 29.4 - - - +
189R MET* 4.1 4.1 - - - +
207R PRO* 4.5 13.0 - - + -
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Residues in contact with LEU 186 (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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182R THR* 2.9 32.1 - - - +
183R LEU* 2.8 10.7 + - + +
185R GLN* 1.3 74.4 - - + +
187R GLU* 1.3 68.3 + - - +
188R GLN 3.2 0.5 + - - -
189R MET* 3.3 44.3 - - + +
207R PRO* 4.1 16.6 - - + -
208R LEU* 3.2 36.3 - - + -
211R LEU* 4.9 10.5 - - + -
244R PHE* 5.4 0.9 - - + -
273R ILE* 4.1 25.1 - - + +
274R HIS* 3.4 10.3 + - - -
277R ALA* 4.6 11.0 - - + -
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Residues in contact with GLU 187 (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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183R LEU 2.9 12.8 + - - +
184R PRO* 3.4 19.1 - - + +
186R LEU* 1.3 76.4 - - - +
188R GLN* 1.3 78.2 + - - +
189R MET 3.4 0.2 + - - -
274R HIS* 3.0 36.1 + - - +
277R ALA* 4.8 9.8 - - + +
278R LYS* 5.1 9.7 + - - +
281R LYS* 3.0 31.6 - - - +
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Residues in contact with GLN 188 (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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184R PRO* 3.3 16.8 + - + +
185R GLN* 2.7 16.7 + - - +
186R LEU 3.1 0.2 - - - -
187R GLU* 1.3 103.2 + - + +
189R MET* 1.3 58.9 + - - +
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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