Contacts of the helix formed by residues 189 - 198 (chain C) in PDB entry 1IXR
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 189 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187C ARG* 4.7 3.8 - - - +
188C ILE* 1.3 77.8 - - - +
190C GLU* 1.3 60.4 + - - +
191C GLU* 2.4 34.1 + - - +
192C ALA* 3.2 5.6 - - + +
193C ALA* 2.8 36.5 + - - +
226C ILE 3.0 0.6 + - - -
227C THR* 3.0 44.1 - - + +
228C ARG 3.4 0.9 - - - +
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Residues in contact with GLU 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C ALA 4.4 11.6 - - - +
175C GLN* 5.3 4.3 - - - -
178C MET* 3.8 29.8 - - - +
187C ARG* 5.4 1.0 - - - +
189C THR* 1.3 73.7 + - - +
191C GLU* 1.3 61.7 + - + +
192C ALA 2.8 1.1 - - - -
193C ALA* 2.4 38.3 + - - +
194C LEU* 2.7 30.9 + - + +
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Residues in contact with GLU 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C THR* 2.4 45.1 + - - +
190C GLU* 1.3 77.8 - - + +
192C ALA* 1.3 66.9 + - - +
194C LEU* 2.8 31.1 - - - +
195C GLU 3.3 0.3 + - - -
228C ARG* 2.5 61.7 + - - +
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Residues in contact with ALA 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C ILE* 4.4 3.6 - - + -
189C THR* 3.2 18.6 - - + +
190C GLU 2.6 3.2 + - - -
191C GLU* 1.3 75.7 + - - +
193C ALA* 1.3 54.5 + - - +
194C LEU 2.6 3.5 + - - -
195C GLU* 2.3 40.2 + - - +
196C ILE 3.6 0.3 + - - -
227C THR* 3.3 5.4 - - - -
228C ARG* 2.9 45.1 - - - +
231C ALA* 3.3 11.7 - - + -
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Residues in contact with ALA 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C ALA* 3.8 11.2 - - - +
177C VAL* 4.3 14.7 - - + +
178C MET* 5.3 3.8 - - + +
188C ILE* 3.6 25.2 - - + +
189C THR 2.8 16.3 + - - +
190C GLU* 2.4 30.0 + - - +
192C ALA* 1.3 70.3 - - - +
194C LEU* 1.3 54.9 + - - -
196C ILE* 3.3 9.8 + - - +
197C GLY* 2.9 24.9 + - - -
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Residues in contact with LEU 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C PRO* 4.6 9.4 - - + +
171C GLU* 4.8 16.2 - - + +
174C ALA* 4.0 17.5 - - + -
190C GLU* 2.7 59.3 + - + +
191C GLU* 2.8 19.5 - - - +
192C ALA 2.6 2.8 + - - -
193C ALA* 1.3 71.2 - - - +
195C GLU* 1.3 67.7 + - - +
197C GLY* 3.2 7.8 + - - -
198C ARG* 3.3 11.4 + - - +
228C ARG* 4.4 8.1 - - - +
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Residues in contact with GLU 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C GLU 4.1 1.8 - - - +
192C ALA 2.3 39.9 + - - +
194C LEU* 1.3 70.1 - - - +
196C ILE* 1.3 63.7 + - - +
198C ARG* 3.0 4.7 + - - +
199C ARG* 2.7 35.7 + - - +
228C ARG* 3.8 33.1 + - + +
231C ALA* 4.0 15.7 - - + -
232C LEU* 2.3 47.1 - - + +
235C LEU* 4.2 13.9 - - + -
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Residues in contact with ILE 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C VAL* 4.2 20.9 - - + -
188C ILE* 3.3 35.0 - - + -
192C ALA 4.7 1.8 - - - +
193C ALA* 3.4 10.8 - - - +
195C GLU* 1.3 78.1 - - + +
197C GLY* 1.3 56.7 + - - +
199C ARG* 2.6 34.6 + - - +
200C SER* 3.3 18.8 + - - +
207C ALA 4.5 0.4 - - - +
210C LEU* 4.2 7.2 - - + -
211C PHE* 3.0 58.1 - - + -
231C ALA* 5.2 10.8 - - + +
235C LEU* 4.6 5.5 - - + +
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Residues in contact with GLY 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C PRO* 3.8 16.3 - - - +
173C LEU* 4.4 6.5 - - - +
174C ALA* 3.8 25.7 - - - +
177C VAL* 5.3 0.4 - - - -
193C ALA 2.9 14.9 + - - -
194C LEU 3.4 6.5 - - - -
195C GLU 3.1 0.4 + - - -
196C ILE* 1.3 77.9 - - - +
198C ARG* 1.3 57.3 + - - +
199C ARG 3.5 0.5 + - - -
200C SER* 3.6 19.9 + - - +
202C GLY 5.2 0.2 + - - -
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Residues in contact with ARG 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C PRO* 4.3 27.3 - - + +
194C LEU 3.3 6.0 + - - +
195C GLU 3.0 10.8 + - - +
196C ILE 2.9 1.2 + - - -
197C GLY* 1.3 70.1 - - - -
199C ARG* 1.3 65.6 + - - +
200C SER 3.3 3.6 - - - -
201C ARG* 4.9 2.6 + - - -
243C LEU* 3.2 44.3 - - + +
244C GLY 4.8 0.2 + - - -
288C TYR* 3.9 14.3 + - - -
292C GLN* 3.2 33.5 - - - +
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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