Contacts of the helix formed by residues 169 - 180 (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 169 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167C TYR* 3.4 8.6 + - - +
168C TYR* 1.3 83.4 - - - +
170C PRO* 1.3 78.1 - - + +
171C GLU* 2.9 15.4 + - - +
172C GLU* 3.0 38.8 + - - +
173C LEU* 2.9 12.9 + - - +
202C GLY* 5.0 3.8 - - - -
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Residues in contact with PRO 170 (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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169C THR* 1.3 88.7 - - + +
171C GLU* 1.3 64.6 + - - +
174C ALA* 2.6 41.0 + - - +
194C LEU* 4.9 7.0 - - + +
197C GLY* 3.8 16.7 - - - +
198C ARG* 4.3 34.1 - - + +
202C GLY* 6.4 0.2 - - - -
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Residues in contact with GLU 171 (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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169C THR* 2.9 14.1 + - - +
170C PRO* 1.3 96.1 - - - +
172C GLU* 1.3 55.9 + - + +
174C ALA* 2.9 5.6 + - - +
175C GLN* 2.4 40.2 + - - +
194C LEU* 4.8 12.9 - - + +
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Residues in contact with GLU 172 (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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15C ILE* 3.4 17.5 - - + +
16C GLY* 3.4 32.5 + - - +
17C GLN* 3.6 4.5 + - - -
168C TYR* 3.7 27.0 - - + +
169C THR* 3.0 29.1 + - - +
171C GLU* 1.3 80.8 - - + +
173C LEU* 1.3 60.4 + - - +
175C GLN* 3.0 19.2 - - - +
176C GLY 2.9 23.2 + - - -
204C MET* 5.1 0.2 - - - +
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Residues in contact with LEU 173 (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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15C ILE* 5.8 1.1 - - + -
168C TYR* 2.8 38.1 - - + +
169C THR 2.9 11.3 + - - +
170C PRO 4.4 2.0 - - - +
172C GLU* 1.3 70.9 - - - +
174C ALA* 1.3 60.9 + - - +
176C GLY* 3.3 1.4 + - - -
177C VAL* 2.8 33.2 + - - +
197C GLY* 4.4 10.3 - - - +
200C SER* 3.3 15.9 - - - +
202C GLY* 3.5 2.5 - - - -
203C THR* 2.8 48.5 - - - +
204C MET* 3.2 37.6 - - + +
207C ALA* 4.1 7.9 - - + +
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Residues in contact with ALA 174 (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 2.6 23.9 + - - +
171C GLU 3.3 2.7 - - - +
173C LEU* 1.3 74.2 - - - +
175C GLN* 1.3 69.4 + - - +
177C VAL* 3.1 24.7 - - - +
178C MET* 3.1 6.6 + - - +
190C GLU* 4.4 6.8 - - - +
193C ALA* 3.8 13.9 - - - +
194C LEU* 4.0 22.2 - - + +
197C GLY* 3.8 15.7 - - - -
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Residues in contact with GLN 175 (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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15C ILE* 4.0 24.5 - - + +
171C GLU 2.4 22.7 + - - +
172C GLU* 3.0 24.7 - - - +
174C ALA* 1.3 69.4 - - - +
176C GLY* 1.3 73.5 + - - +
178C MET* 2.8 27.2 + - + +
179C ARG* 3.6 4.0 + - - +
190C GLU* 5.3 5.8 - - - -
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Residues in contact with GLY 176 (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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15C ILE* 4.5 19.7 - - - -
172C GLU 2.9 14.5 + - - -
173C LEU 3.3 3.3 + - - -
175C GLN* 1.3 77.5 - - - +
177C VAL* 1.3 54.2 + - - +
178C MET 2.5 14.7 + - - -
179C ARG* 2.6 15.0 + - - +
180C ASP* 2.6 21.3 - - - +
204C MET* 4.9 10.1 - - - -
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Residues in contact with VAL 177 (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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173C LEU 2.8 25.9 + - - +
174C ALA* 3.1 14.6 - - - +
176C GLY* 1.3 71.2 - - - +
178C MET* 1.3 56.3 + - - +
180C ASP* 2.9 36.3 + - + +
181C ALA* 3.1 8.3 + - - +
188C ILE* 4.8 6.0 - - + +
193C ALA* 4.3 11.7 - - + -
196C ILE* 4.2 37.5 - - + -
197C GLY* 5.1 1.1 - - - +
204C MET* 5.6 0.4 - - - +
207C ALA* 4.1 24.0 - - + +
208C LYS* 5.3 0.4 - - - +
211C PHE* 4.9 6.7 - - + -
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Residues in contact with MET 178 (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 3.1 8.6 + - - +
175C GLN* 2.8 21.1 + - + +
176C GLY 2.5 4.4 + - - -
177C VAL* 1.3 66.8 - - - +
179C ARG* 1.3 88.7 + - - +
180C ASP 2.8 4.0 - - - -
181C ALA* 2.5 38.2 + - - +
182C ARG* 3.9 17.6 + - - +
187C ARG* 5.0 13.0 - - - +
188C ILE* 5.3 3.4 - - - -
190C GLU* 3.8 29.2 - - - +
193C ALA* 5.5 3.1 - - + -
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Residues in contact with ARG 179 (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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15C ILE* 5.9 6.7 - - + -
175C GLN* 3.6 3.5 + - - +
176C GLY* 2.6 14.2 + - - +
178C MET* 1.3 96.3 - - - +
180C ASP* 1.3 62.7 + - - +
181C ALA 3.1 0.8 + - - -
182C ARG* 2.7 74.2 + - - +
183C LEU* 4.9 0.9 - - - +
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Residues in contact with ASP 180 (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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176C GLY* 2.6 19.5 - - - +
177C VAL* 2.9 26.0 + - + +
178C MET 2.8 0.6 - - - -
179C ARG* 1.3 81.2 - - - +
181C ALA* 1.3 54.6 + - - +
182C ARG 3.1 5.6 - - - -
183C LEU* 2.8 45.2 - - + +
186C VAL* 5.2 1.0 - - - +
204C MET* 5.7 0.2 - - - +
207C ALA 5.1 0.3 - - - +
208C LYS* 2.8 36.9 + - + +
313C ANP 6.1 1.4 - - - -
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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