Contacts of the helix formed by residues 185 - 201 (chain C) in PDB entry 3IO6
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 ASN 185 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165C GLY* 3.3 19.6 + - - -
166C GLY 3.7 2.1 + - - -
167C TYR* 3.7 9.1 - - - -
182C GLY* 3.0 35.2 + - - -
184C ASP* 1.3 85.7 - - - +
186C ALA* 1.3 59.9 + - - +
187C GLY* 3.1 5.7 + - - +
188C ALA* 2.8 34.0 + - - +
189C LYS* 3.0 25.1 + - - +
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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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164C ASP* 4.2 3.6 - - - +
185C ASN* 1.3 74.6 - - - +
187C GLY* 1.3 59.4 + - - +
189C LYS* 3.5 9.9 - - - +
190C ALA* 3.3 24.1 + - - +
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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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161C ILE 3.4 10.3 - - - +
164C ASP* 3.4 29.7 + - - +
165C GLY* 3.6 17.0 - - - -
185C ASN* 3.1 7.5 + - - +
186C ALA* 1.3 76.9 - - - +
188C ALA* 1.3 62.7 + - - +
190C ALA* 4.4 0.2 - - - -
191C GLY* 3.2 17.3 + - - -
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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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158C TRP* 5.4 0.9 - - + -
161C ILE* 3.4 31.4 + - + +
166C GLY* 3.9 11.5 - - - +
182C GLY 4.3 0.2 - - - +
183C VAL* 3.4 31.0 - - - +
185C ASN* 2.8 20.0 + - - +
187C GLY* 1.3 70.2 - - - +
189C LYS* 1.3 64.7 + - - +
192C LEU* 3.0 23.0 + - - +
361C LEU* 3.7 4.1 - - + +
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Residues in contact with LYS 189 (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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74B GLY* 5.7 3.6 - - - -
184C ASP* 3.7 30.0 + - - -
185C ASN 3.0 14.0 + - - +
186C ALA* 3.5 12.6 - - - +
188C ALA* 1.3 76.7 - - - +
190C ALA* 1.3 62.6 + - - +
192C LEU 3.2 0.2 + - - -
193C THR* 2.7 31.8 + - - +
357C VAL* 3.5 7.5 - - + +
358C ASP* 3.3 49.2 + - - +
361C LEU* 3.8 15.2 - - + +
362C ALA* 5.8 0.6 - - - +
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Residues in contact with ALA 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C ASP* 5.1 1.8 - - - +
186C ALA 3.3 12.2 + - - +
187C GLY 4.5 1.3 - - - +
189C LYS* 1.3 79.5 - - - +
191C GLY* 1.3 62.5 + - - +
193C THR* 3.4 8.7 + - - -
194C PHE* 3.0 24.4 + - - +
250C PHE* 3.6 6.7 - - + -
251C LYS* 3.7 31.6 - - - +
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Residues in contact with GLY 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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160C LEU* 4.0 20.2 - - - +
161C ILE* 4.2 8.5 - - - -
187C GLY 3.2 17.0 + - - -
188C ALA 3.8 1.6 - - - -
189C LYS 3.1 1.2 - - - -
190C ALA* 1.3 79.1 - - - +
192C LEU* 1.3 61.2 + - - +
194C PHE* 3.3 10.0 + - - +
195C LEU* 3.4 11.8 + - - +
250C PHE* 3.6 18.5 - - - -
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Residues in contact with LEU 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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161C ILE* 4.3 17.0 - - + +
188C ALA 3.0 17.2 + - - +
191C GLY* 1.3 71.3 - - - +
193C THR* 1.3 60.6 + - - +
195C LEU* 3.1 27.1 + - + +
196C VAL* 2.8 40.2 + - + +
346C ALA 4.3 7.9 - - - +
347C VAL* 4.5 22.0 - - + +
350C ALA* 3.8 21.3 - - + -
351C ALA* 6.2 0.2 - - + -
357C VAL* 3.8 15.9 - - + +
361C LEU* 3.8 33.0 - - + +
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Residues in contact with THR 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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189C LYS* 2.7 28.0 + - - +
190C ALA* 3.6 8.9 - - - -
191C GLY 3.3 0.2 - - - -
192C LEU* 1.3 76.9 - - - +
194C PHE* 1.3 56.9 + - - +
196C VAL* 3.2 4.8 + - + +
197C ASP* 2.8 40.5 + - - +
357C VAL* 3.4 29.7 - - + +
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Residues in contact with PHE 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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129C TRP* 3.6 36.8 - - + -
130C GLU* 3.8 24.5 - - + -
133C PRO* 4.6 3.8 - - + -
160C LEU* 4.5 10.3 - - + -
190C ALA 3.0 12.9 + - - +
191C GLY 3.5 9.0 - - - +
192C LEU 3.2 0.2 - - - -
193C THR* 1.3 76.5 - - - +
195C LEU* 1.3 61.9 + - - +
197C ASP* 3.1 13.1 + - + +
198C LEU* 3.0 61.4 + - + +
250C PHE* 3.8 26.9 - + + -
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Residues in contact with LEU 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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129C TRP* 5.3 0.2 - - + -
149C PHE* 3.9 10.8 - - + -
151C LEU* 3.8 27.8 - - + -
157C THR* 4.3 19.1 - - + +
160C LEU* 3.8 28.0 - - + +
161C ILE* 5.4 3.1 - - + -
191C GLY 3.4 5.9 + - - +
192C LEU* 3.1 29.3 + - + +
194C PHE* 1.3 78.2 - - - +
196C VAL* 1.3 63.1 + - + +
198C LEU* 3.2 16.5 + - - +
199C ILE* 3.3 25.8 + - + +
204C MET* 3.8 14.5 - - + +
347C VAL* 4.3 10.5 - - + -
351C ALA* 5.5 1.6 - - + -
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Residues in contact with VAL 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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192C LEU* 2.8 29.1 + - + +
193C THR* 3.5 12.3 - - + +
195C LEU* 1.3 72.5 - - + +
197C ASP* 1.3 61.8 - - - +
199C ILE* 3.2 11.8 + - + +
200C LYS* 3.1 40.0 + - + +
350C ALA* 3.8 43.5 - - + +
351C ALA* 4.3 5.8 - - + +
357C VAL* 4.5 11.7 - - + -
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Residues in contact with ASP 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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193C THR* 2.8 29.4 + - - +
194C PHE* 3.1 17.1 + - + +
196C VAL* 1.3 73.0 - - - +
198C LEU* 1.3 59.7 + - + +
199C ILE 3.0 5.4 + - - -
200C LYS* 3.3 25.5 + - - +
201C ASN* 2.8 46.4 + - - +
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Residues in contact with LEU 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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129C TRP* 4.2 16.8 - - + -
132C ILE* 4.5 12.8 - - + -
133C PRO* 3.5 37.9 - - + -
160C LEU* 5.2 0.4 - - + -
194C PHE* 3.0 46.1 + - + +
195C LEU* 3.2 9.2 + - - +
197C ASP* 1.3 76.5 - - + +
199C ILE* 1.3 58.2 + - - +
201C ASN* 4.3 1.6 - - - +
203C HIS* 2.9 43.2 + - + +
204C MET* 3.0 34.2 + - + -
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Residues in contact with ILE 199 (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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151C LEU* 4.5 16.4 - - + -
195C LEU* 3.3 32.3 + - + +
196C VAL* 3.2 10.7 + - + +
197C ASP 3.0 0.6 - - - -
198C LEU* 1.3 80.0 - - - +
200C LYS* 1.3 63.4 + - + +
201C ASN 3.3 0.2 - - - -
202C LYS* 3.2 21.1 + - - +
204C MET* 3.6 30.4 - - + +
206C ALA* 4.3 14.1 - - + +
351C ALA* 3.7 44.2 - - + +
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Residues in contact with LYS 200 (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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196C VAL* 3.1 33.1 + - + +
197C ASP* 3.7 23.9 + - - +
199C ILE* 1.3 74.5 - - + +
201C ASN* 1.3 69.7 + - - +
202C LYS* 3.1 11.8 + - - +
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Residues in contact with ASN 201 (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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133C PRO* 6.0 0.5 - - - +
197C ASP* 2.8 29.1 + - - +
198C LEU* 6.0 0.3 - - - +
200C LYS* 1.3 82.9 + - - +
202C LYS* 1.3 68.3 + - - +
203C HIS* 3.3 27.3 + - + +
451C ZN 3.6 18.4 - - - -
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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