Contacts of the helix formed by residues 185 - 201 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A GLY 3.5 9.8 + - - -
166A GLY* 3.7 2.7 - - - -
167A TYR* 3.4 32.3 + - - -
182A GLY* 3.5 17.9 + - - -
183A VAL 3.6 0.4 - - - +
184A ASP* 1.3 86.2 + - - +
186A ALA* 1.3 63.4 + - - +
187A GLY* 3.3 4.1 + - - -
188A ALA* 3.0 26.2 + - - +
189A LYS* 3.4 18.9 + - - +
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Residues in contact with ALA 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ASP* 3.8 6.2 - - - +
185A ASN* 1.3 76.3 - - - +
187A GLY* 1.3 63.4 + - - +
189A LYS* 3.8 6.0 - - - +
190A ALA* 3.5 17.3 + - - +
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Residues in contact with GLY 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ILE 3.8 3.3 - - - +
164A ASP* 3.2 45.6 - - - +
165A GLY* 3.8 4.5 - - - -
185A ASN* 3.3 7.0 + - - -
186A ALA* 1.3 78.3 - - - +
188A ALA* 1.3 65.1 + - - +
189A LYS 3.2 0.3 + - - -
191A GLY 3.2 16.8 + - - -
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Residues in contact with ALA 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A TRP* 5.3 1.3 - - + -
161A ILE* 3.2 35.1 - - + +
166A GLY* 3.8 12.8 - - - +
182A GLY 4.4 0.7 - - - +
183A VAL* 3.3 30.1 - - - +
185A ASN* 3.0 15.7 + - - +
187A GLY* 1.3 74.0 - - - +
189A LYS* 1.3 63.5 + - - +
191A GLY 3.3 0.3 + - - -
192A LEU* 3.0 21.7 + - - +
361A LEU* 3.8 2.1 - - + +
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Residues in contact with LYS 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ASP 5.1 2.7 - - - +
185A ASN 3.4 18.1 + - - +
186A ALA* 3.8 8.3 - - - +
187A GLY 3.2 0.4 - - - -
188A ALA* 1.3 76.2 - - - +
190A ALA* 1.3 65.3 + - + +
191A GLY 3.0 1.2 + - - -
192A LEU 3.0 3.6 + - - -
193A THR* 2.9 48.2 + - - -
357A VAL* 3.4 15.8 - - + +
358A ASP* 3.3 41.8 + - - +
361A LEU* 3.7 15.1 - - + +
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Residues in contact with ALA 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ASP* 4.2 12.6 - - - +
186A ALA 3.5 10.8 + - - +
187A GLY 3.5 2.0 + - - -
189A LYS* 1.3 83.9 - - + +
191A GLY* 1.3 60.4 + - - +
193A THR* 3.7 11.7 - - - -
194A PHE* 3.3 15.2 + - - +
250A PHE* 3.3 13.5 - - + -
251A LYS* 4.3 17.9 - - - -
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Residues in contact with GLY 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A LEU* 3.9 26.9 - - - +
161A ILE* 4.2 8.3 - - - -
164A ASP* 5.1 0.2 - - - -
187A GLY 3.2 13.2 + - - -
188A ALA 3.6 4.7 - - - -
189A LYS 3.0 1.8 + - - -
190A ALA* 1.3 76.5 - - - +
192A LEU* 1.3 62.4 + - - +
194A PHE* 3.2 14.2 + - - +
195A LEU 3.2 8.8 + - - -
250A PHE* 4.0 11.8 - - - -
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Residues in contact with LEU 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ILE* 3.9 29.0 - - + +
188A ALA 3.0 15.6 + - - +
189A LYS 3.7 3.6 - - - +
191A GLY* 1.3 73.2 - - - +
193A THR* 1.3 55.2 + - - +
195A LEU* 3.2 17.5 + - + -
196A VAL* 2.7 46.4 + - + +
346A ALA 4.7 5.4 - - - +
347A VAL* 4.1 20.0 - - + +
350A ALA* 3.7 24.5 - - + -
357A VAL* 3.8 19.1 - - + -
360A ALA* 5.3 1.3 - - + -
361A LEU* 3.8 25.6 - - + -
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Residues in contact with THR 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LYS* 2.9 34.8 + - - -
190A ALA* 3.7 10.8 - - - -
191A GLY 3.2 0.2 - - - -
192A LEU* 1.3 76.7 - - - +
194A PHE* 1.3 56.6 + - - +
196A VAL* 3.4 2.1 + - - +
197A ASP* 3.0 48.5 + - - +
357A VAL* 3.4 27.5 - - + +
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Residues in contact with PHE 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A TRP* 3.3 47.1 - + + -
130A GLU* 3.6 16.8 - - + -
133A PRO* 4.1 7.6 - - + -
160A LEU* 4.0 15.7 - - + -
190A ALA 3.3 3.8 + - - +
191A GLY 3.2 10.1 + - - +
193A THR* 1.3 77.5 - - - +
195A LEU* 1.3 64.1 + - - +
197A ASP* 3.3 10.6 + - + +
198A LEU* 3.1 60.1 + - + +
250A PHE* 3.6 31.4 - + + -
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Residues in contact with LEU 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A TRP* 5.4 0.4 - - + -
149A PHE* 3.9 11.9 - - + -
151A LEU* 3.7 25.1 - - + -
157A THR* 3.9 29.2 - - + +
160A LEU* 3.8 24.6 - - + +
161A ILE* 4.7 5.8 - - + -
191A GLY 3.2 5.1 + - - +
192A LEU* 3.2 27.2 + - + +
194A PHE* 1.3 79.7 - - - +
196A VAL* 1.3 61.8 + - + +
198A LEU* 3.9 7.4 + - + +
199A ILE* 3.5 25.6 + - + +
204A MET* 3.8 14.6 - - + -
347A VAL* 4.5 7.6 - - + -
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Residues in contact with VAL 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LEU* 2.7 30.8 + - + +
193A THR* 3.7 5.8 - - - +
195A LEU* 1.3 72.7 - - + +
197A ASP* 1.3 67.4 + - - +
199A ILE* 3.1 12.6 + - + +
200A LYS* 3.0 36.1 + - + +
350A ALA* 3.6 44.6 - - + +
351A ALA* 4.5 2.9 - - - +
357A VAL* 4.3 14.8 - - + -
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Residues in contact with ASP 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A THR* 3.0 33.9 + - - +
194A PHE* 3.3 12.7 + - + +
196A VAL* 1.3 77.4 - - - +
198A LEU* 1.3 58.4 + - + +
200A LYS* 3.6 27.2 + - - -
201A ASN* 2.8 52.2 + - - +
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Residues in contact with LEU 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A TRP* 4.3 16.8 - - + -
132A ILE* 4.5 12.8 - - + -
133A PRO* 3.7 33.7 - - + -
147A LEU* 5.8 0.2 - - + -
194A PHE* 3.1 44.3 + - + +
195A LEU* 4.1 5.2 - - - +
197A ASP* 1.3 77.7 - - + +
199A ILE* 1.3 59.0 + - - +
201A ASN* 4.0 0.8 + - - +
203A HIS* 2.8 46.6 + - + +
204A MET* 3.1 35.2 + - + -
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Residues in contact with ILE 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A LEU* 4.9 15.9 - - + -
195A LEU* 3.5 21.5 + - + +
196A VAL* 3.1 9.7 + - - +
197A ASP 3.1 0.6 - - - -
198A LEU* 1.3 76.0 - - - +
200A LYS* 1.3 58.9 + - + +
201A ASN 3.1 4.3 - - - -
202A LYS* 2.9 26.3 + - - +
204A MET* 3.8 31.0 - - + +
205A ASN 4.8 0.4 - - - -
206A ALA* 4.3 21.3 - - + +
351A ALA* 3.9 43.7 - - + +
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Residues in contact with LYS 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A VAL* 3.0 25.8 + - + +
197A ASP* 3.8 28.8 + - - +
199A ILE* 1.3 77.2 - - + +
201A ASN* 1.3 69.1 + - - +
202A LYS* 3.3 7.5 + - - +
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Residues in contact with ASN 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A ASP* 2.8 32.1 + - - +
198A LEU* 4.9 1.0 - - - +
200A LYS* 1.3 89.0 + - - +
202A LYS* 1.3 71.0 + - - +
203A HIS* 3.2 35.1 + - + +
450A ZN 3.9 13.5 - - - -
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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