Contacts of the helix formed by residues 181 - 196 (chain C) in PDB entry 1F9E
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 GLY 181 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179C ARG 3.0 0.6 + - - -
180C ASN* 1.3 74.6 - - - +
182C THR* 1.3 56.1 + - - +
183C HIS* 2.9 17.9 + - - -
184C LEU* 2.6 41.1 + - - +
185C ASP 3.6 1.7 + - - -
341D ARG* 4.8 3.6 - - - -
342D ASN 4.6 3.6 - - - -
343D PRO* 3.9 18.8 + - - -
346D GLY* 4.2 6.7 - - - -
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Residues in contact with THR 182 (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 ASN* 3.2 33.2 + - - +
170C ASN 3.5 4.3 + - - +
171C HIS* 4.1 4.5 - - - +
179C ARG* 2.5 58.7 + - - +
180C ASN 3.6 0.2 - - - -
181C GLY* 1.3 73.0 - - - +
183C HIS* 1.3 57.4 + - - +
185C ASP* 2.6 35.5 + - - +
186C ALA 2.8 11.4 + - - -
235C LEU* 3.4 20.4 - - + -
341D ARG* 4.6 2.6 - - - +
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Residues in contact with HIS 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C ASN* 4.2 10.5 - - - +
171C HIS* 3.3 45.3 + + + +
180C ASN* 4.1 1.6 - - - -
181C GLY* 3.2 30.1 + - - -
182C THR* 1.3 75.7 - - - +
184C LEU* 1.3 64.4 + - + +
186C ALA* 3.3 3.3 + - - +
187C GLY* 2.8 28.4 + - - -
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Residues in contact with LEU 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C GLY* 2.6 22.7 + - - +
183C HIS* 1.3 83.8 - - + +
185C ASP* 1.3 54.2 + - - +
187C GLY* 3.4 1.4 + - - -
188C ALA* 2.9 31.4 + - - +
343D PRO 3.7 12.6 - - - +
344D ALA* 3.6 33.2 - - - +
345D GLU* 3.8 10.8 - - - +
346D GLY 3.9 10.3 - - - +
351D GLN* 3.7 4.5 + - - +
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Residues in contact with ASP 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C ARG* 4.6 1.6 + - - -
181C GLY 5.2 0.2 - - - -
182C THR* 2.6 22.4 + - - +
184C LEU* 1.3 69.4 - - - +
186C ALA* 1.3 56.8 + - - +
188C ALA* 3.0 3.3 + - - +
189C LEU* 2.6 40.6 + - - +
235C LEU* 3.7 16.3 - - + +
283C GLN* 4.3 2.8 - - - +
346D GLY* 3.5 2.8 - - - -
347D THR* 3.0 54.6 + - - +
350D ILE* 3.4 19.9 - - + +
351D GLN* 3.2 17.3 + - - +
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Residues in contact with ALA 186 (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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167C ILE* 4.1 12.1 - - + +
169C ASN* 3.1 30.3 - - + +
182C THR 2.8 4.6 + - - -
183C HIS* 3.5 7.9 - - - +
185C ASP* 1.3 75.5 - - - +
187C GLY* 1.3 56.0 + - - +
189C LEU* 3.3 6.4 + - - +
190C THR* 2.4 37.6 + - - +
204C HIS* 5.1 7.6 - - + -
235C LEU* 3.8 8.2 - - + +
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Residues in contact with GLY 187 (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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183C HIS 2.8 20.0 + - - -
184C LEU* 3.7 2.0 - - - -
186C ALA* 1.3 74.4 - - - +
188C ALA* 1.3 63.2 + - - +
190C THR* 3.1 6.5 + - - -
191C THR* 2.9 29.4 + - - -
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Residues in contact with ALA 188 (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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184C LEU 2.9 17.8 + - - +
185C ASP* 3.4 3.6 - - - +
187C GLY* 1.3 73.2 - - - +
189C LEU* 1.3 60.3 + - - +
191C THR* 3.6 5.8 - - - -
192C THR* 2.6 35.1 + - - -
350D ILE* 5.2 0.2 - - + -
351D GLN* 3.9 21.5 - - - +
354D CYS* 3.6 18.6 - - + -
358D ARG* 4.8 9.4 - - - +
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Residues in contact with LEU 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C ILE* 3.7 17.3 - - + -
185C ASP 2.6 22.1 + - - +
186C ALA 3.6 3.8 - - - +
188C ALA* 1.3 73.0 - - - +
190C THR* 1.3 57.7 + - - +
192C THR* 3.5 1.0 - - - -
193C PHE* 2.8 65.8 + - + +
200C ILE* 5.4 0.2 - - - -
233C CYS* 4.0 23.1 - - + -
235C LEU* 4.0 33.7 - - + -
350D ILE* 3.8 21.8 - - + -
353D LEU* 4.9 7.2 - - + -
354D CYS* 3.8 15.0 - - - -
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Residues in contact with THR 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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167C ILE* 4.0 8.5 - - - +
186C ALA* 2.4 24.0 + - - +
187C GLY* 3.3 8.8 - - - -
189C LEU* 1.3 75.6 - - - +
191C THR* 1.3 52.1 - - - +
194C GLU* 2.7 54.7 + - - +
200C ILE* 3.6 36.0 - - + +
202C PRO* 6.0 1.9 - - + +
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Residues in contact with THR 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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187C GLY 2.9 15.3 + - - -
188C ALA* 3.6 9.0 - - - -
190C THR* 1.3 78.0 - - - +
192C THR* 1.3 59.1 + - - +
194C GLU* 3.4 7.9 - - - +
195C GLU* 2.8 58.4 + - + +
358D ARG* 4.3 13.9 - - - +
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Residues in contact with THR 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 ALA 2.6 25.2 + - - -
189C LEU* 3.5 2.5 - - - -
191C THR* 1.3 76.1 - - - +
193C PHE* 1.3 66.2 + - + +
195C GLU* 3.2 11.1 + - - +
196C LEU* 3.1 28.8 + - + +
354D CYS* 3.3 23.9 - - - +
357D LEU* 3.8 36.8 - - + -
358D ARG* 3.8 25.4 + - + +
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Residues in contact with PHE 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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165C CYS* 4.0 16.4 - - - -
189C LEU* 2.8 50.5 + - + +
192C THR* 1.3 74.8 - - - +
194C GLU* 1.3 67.4 + - - +
196C LEU* 3.0 25.6 + - + +
197C HIS 3.2 0.5 + - - -
198C PHE* 2.9 35.1 + + + +
200C ILE* 3.8 16.2 - - + -
231C ILE* 3.4 26.2 - - + -
233C CYS* 4.6 5.2 - - - -
281C PHE* 3.7 28.5 - + - -
353D LEU* 5.4 0.2 - - + -
357D LEU* 3.7 20.9 - - + -
400D PHE* 4.1 16.2 - + - -
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Residues in contact with GLU 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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190C THR* 2.7 38.7 + - - +
191C THR* 3.4 8.3 - - - +
193C PHE* 1.3 77.7 - - - +
195C GLU* 1.3 53.8 + - + +
197C HIS* 2.7 28.9 + - - -
198C PHE 3.8 11.6 + - - +
200C ILE* 3.8 10.9 - - + +
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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 THR* 2.8 46.9 + - + +
192C THR* 3.4 6.5 - - - +
193C PHE 3.2 0.2 - - - -
194C GLU* 1.3 77.9 - - + +
196C LEU* 1.3 57.9 + - + +
197C HIS* 3.1 18.8 + - - -
358D ARG* 3.8 31.1 + - - +
402D SER* 4.2 13.4 + - - +
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Residues in contact with LEU 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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162C ARG* 3.6 15.4 + - - -
192C THR* 3.1 17.9 + - + +
193C PHE* 3.0 27.9 + - + +
194C GLU 3.0 1.4 - - - -
195C GLU* 1.3 79.8 - - + +
197C HIS* 1.3 74.7 + - - +
198C PHE* 3.5 13.8 - - + -
357D LEU* 4.6 5.4 - - + +
361D CYS* 4.0 20.0 - - + -
362D PRO* 5.8 0.4 - - + -
400D PHE* 3.5 54.1 - - + +
401D PRO 4.1 8.7 - - - +
402D SER* 4.5 9.6 - - - +
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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