Contacts of the helix formed by residues 190 - 200 (chain A) in PDB entry 2O6S
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 ILE 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A LYS 5.4 1.1 - - - +
161A SER* 6.3 1.3 - - - -
183A TRP* 4.6 6.1 - - + -
184A ASP 3.5 25.0 + - - +
185A CYS* 3.6 34.1 - - - +
186A THR 3.2 6.3 + - - +
189A GLY* 1.3 74.6 - - - +
191A ARG* 1.3 66.8 + - - +
192A TYR 3.4 0.7 - - - -
193A LEU* 3.3 21.0 + - + +
194A SER* 3.0 19.8 + - - -
225A VAL* 3.7 33.0 - - + +
228A ILE* 3.7 10.8 - - + -
230A CYS* 3.5 23.3 - - - -
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Residues in contact with ARG 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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164A ASP* 4.4 16.2 + - - +
188A PRO* 3.0 23.0 + - + +
189A GLY 3.2 0.2 - - - -
190A ILE* 1.3 78.4 - - - +
192A TYR* 1.3 95.0 + - - +
194A SER* 3.9 2.6 - - - -
195A GLU* 2.8 66.5 + - + +
230A CYS* 4.3 21.1 - - + -
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Residues in contact with TYR 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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162A VAL* 4.2 8.7 - - + +
163A PRO 3.9 9.2 - - - -
164A ASP* 3.6 21.5 + - + +
165A GLY* 3.3 35.1 - - - -
166A VAL* 3.7 8.7 - - + -
167A PHE* 3.0 35.4 + + - -
168A ASP* 2.7 28.4 + - - -
189A GLY 4.4 3.4 + - - +
190A ILE 3.3 1.0 + - - -
191A ARG* 1.3 99.5 - - - +
193A LEU* 1.3 62.7 + - - +
195A GLU* 3.7 2.0 - - + +
196A TRP* 2.8 50.1 + + + +
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Residues in contact with LEU 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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161A SER* 5.9 0.4 - - - -
162A VAL* 4.3 16.6 - - + +
167A PHE* 3.9 29.4 - - + -
178A LEU* 4.3 10.3 - - + -
183A TRP* 3.6 46.2 - - + +
189A GLY 5.3 0.4 + - - -
190A ILE* 3.3 17.6 + - + +
192A TYR* 1.3 82.9 - - + +
194A SER* 1.3 63.9 + - - +
196A TRP* 3.8 2.9 - - + +
197A ILE* 2.9 48.8 + - + +
216A ALA* 5.6 0.2 - - + -
225A VAL* 4.1 13.0 - - + -
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Residues in contact with SER 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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190A ILE* 3.0 21.2 + - - -
191A ARG* 3.9 4.0 - - - -
193A LEU* 1.3 77.3 - - - +
195A GLU* 1.3 65.8 + - - +
197A ILE* 3.4 2.2 + - - +
198A ASN* 3.0 40.5 + - - -
225A VAL* 3.3 30.2 + - - +
226A ARG* 3.6 3.6 - - - +
228A ILE 2.8 25.6 + - - -
229A ILE* 4.9 0.3 - - - +
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Residues in contact with GLU 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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191A ARG* 2.8 56.2 + - + +
192A TYR* 3.9 3.8 - - + +
194A SER* 1.3 78.8 - - - +
196A TRP* 1.3 63.2 + - - +
198A ASN* 3.3 7.8 + - - +
199A LYS* 3.1 45.6 + - - +
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Residues in contact with TRP 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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167A PHE* 3.6 39.7 + + + +
168A ASP* 4.1 8.4 + - - +
173A LEU* 4.1 19.3 - - + -
176A ILE* 3.9 38.1 - - + -
178A LEU* 4.7 1.8 - - + -
192A TYR* 2.8 51.0 + + + +
193A LEU* 3.8 6.7 - - + +
195A GLU* 1.3 74.5 - - - +
197A ILE* 1.3 77.1 + - + +
199A LYS* 3.1 3.3 + - - -
200A HIS* 2.9 77.6 + + + -
203A VAL* 4.3 4.9 - - + -
204A VAL* 4.4 10.5 - - + -
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Residues in contact with ILE 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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178A LEU* 4.1 14.6 - - + -
193A LEU* 2.9 30.5 + - + +
194A SER 3.9 2.9 - - - +
196A TRP* 1.3 92.9 - - + +
198A ASN* 1.3 64.2 + - - +
200A HIS 3.1 11.8 + - - -
201A SER* 3.1 14.2 + - - -
204A VAL* 4.1 15.0 - - + -
213A PRO* 3.5 25.6 - - + +
216A ALA* 3.9 28.0 - - + -
225A VAL* 4.1 18.6 - - + -
226A ARG* 3.8 17.2 - - + +
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Residues in contact with ASN 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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194A SER* 3.0 31.6 + - - +
195A GLU* 3.6 9.0 - - - +
196A TRP 3.2 0.2 - - - -
197A ILE* 1.3 78.7 - - - +
199A LYS* 1.3 59.4 + - + +
200A HIS 3.8 0.2 + - - -
201A SER* 4.3 10.9 + - - -
226A ARG* 3.1 46.3 + - - +
229A ILE* 4.4 11.4 - - - +
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Residues in contact with LYS 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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195A GLU* 3.1 33.8 + - - +
196A TRP* 3.1 1.7 + - - -
198A ASN* 1.3 79.2 - - + +
200A HIS* 1.3 82.3 + - + +
201A SER 3.7 1.3 - - - -
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Residues in contact with HIS 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 TRP* 2.9 78.1 + + + +
197A ILE 3.1 4.9 + - - +
199A LYS* 1.3 96.4 + - + +
201A SER* 1.3 64.2 + - - +
202A GLY 3.2 3.4 - - - -
203A VAL* 3.0 30.0 + - + +
204A VAL* 3.9 9.2 + - - +
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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