Contacts of the helix formed by residues 203 - 216 (chain A) in PDB entry 3OLJ
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 VAL 203 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A PHE* 3.8 42.8 - - + +
136A ALA* 5.4 2.7 - - + -
196A ALA* 3.3 34.1 - - + +
197A ILE* 4.0 11.9 - - + +
200A MET* 3.2 29.4 + - + +
201A PRO 3.1 0.6 - - - -
202A CYS* 1.3 82.1 - - - +
204A LYS* 1.3 61.5 + - - +
205A LYS 3.4 1.8 - - - -
206A LYS* 3.4 6.8 + - - +
207A ALA* 2.9 33.0 + - + +
303A PHE* 4.7 2.9 - - + -
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Residues in contact with LYS 204 (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 ILE 5.4 9.0 - - - +
200A MET 3.8 1.5 + - - +
201A PRO* 3.0 23.1 + - + +
202A CYS 3.4 0.2 - - - -
203A VAL* 1.3 80.7 - - - +
205A LYS* 1.3 59.0 + - + +
207A ALA* 4.5 4.3 - - - -
208A ASP* 2.9 70.2 + - - +
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Residues in contact with LYS 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A PRO 4.6 1.8 + - - +
202A CYS 4.9 3.3 + - - +
203A VAL 3.4 0.6 - - - -
204A LYS* 1.3 77.3 - - + +
206A LYS* 1.3 58.4 + - + +
208A ASP* 3.9 4.3 - - - +
209A TRP* 3.0 30.0 + - - +
212A ARG* 5.0 1.9 + - - -
299A ILE* 4.0 33.6 - - + +
302A GLU* 3.2 44.7 + - + +
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Residues in contact with LYS 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A PHE* 3.2 30.8 - - + -
137A SER* 5.6 0.2 - - - +
202A CYS 5.4 1.1 + - - +
203A VAL* 3.4 8.8 + - - +
205A LYS* 1.3 74.0 - - + +
207A ALA* 1.3 66.1 + - - +
209A TRP* 3.3 2.1 + - - +
210A ALA* 3.0 26.0 + - - +
235A PHE* 3.1 52.6 + - + -
299A ILE* 3.6 17.7 - - + -
300A GLU* 2.6 28.5 + - - +
303A PHE* 3.1 49.6 - - + -
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Residues in contact with ALA 207 (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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133A PHE* 5.8 0.4 - - - -
137A SER* 6.1 1.1 - - - -
140A ILE* 3.9 22.9 - - + -
197A ILE* 4.3 26.9 - - + -
203A VAL* 2.9 22.9 + - + +
204A LYS* 3.9 4.3 - - - +
206A LYS* 1.3 77.9 - - - +
208A ASP* 1.3 58.9 + - - +
210A ALA* 3.4 1.6 + - - +
211A LEU* 2.8 37.5 + - + +
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Residues in contact with ASP 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ILE* 6.1 1.2 - - - +
204A LYS* 2.9 59.6 + - - +
205A LYS* 3.9 4.7 - - - +
207A ALA* 1.3 75.0 - - - +
209A TRP* 1.3 63.5 + - - +
211A LEU* 3.8 10.2 - - - +
212A ARG* 2.9 47.1 + - - +
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Residues in contact with TRP 209 (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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205A LYS 3.0 19.9 + - - +
206A LYS 3.6 3.4 - - - +
207A ALA 3.3 0.2 - - - -
208A ASP* 1.3 77.9 - - - +
210A ALA* 1.3 63.9 + - - +
212A ARG* 3.3 32.3 + - - +
213A TRP* 3.0 55.0 - + - +
227A ALA* 3.5 25.4 - - - -
230A ALA* 4.2 3.6 - - + -
231A VAL* 3.9 8.3 - - + -
235A PHE* 3.6 28.9 - + + -
292A ILE* 3.7 41.1 - - + -
295A ASN* 2.8 27.4 - - - +
296A ALA* 4.1 12.8 - - + -
299A ILE* 3.4 21.5 - - + +
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Residues in contact with ALA 210 (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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140A ILE* 3.7 24.2 - - + -
206A LYS 3.0 16.8 + - - +
207A ALA 3.8 2.2 - - - +
209A TRP* 1.3 82.7 - - - +
211A LEU* 1.3 62.7 + - - +
213A TRP* 3.2 20.3 + - - +
214A ILE* 3.5 4.3 + - - +
228A PHE* 3.6 12.9 - - + -
231A VAL* 3.8 28.3 - - + -
235A PHE* 5.0 0.7 - - + -
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Residues in contact with LEU 211 (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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140A ILE* 4.0 27.1 - - + -
143A GLU* 3.7 24.7 - - - +
197A ILE* 4.9 13.5 - - + -
207A ALA* 2.8 33.3 + - + +
208A ASP* 4.0 11.0 - - - +
210A ALA* 1.3 72.9 - - - +
212A ARG* 1.3 61.5 - - - +
214A ILE* 3.1 21.3 + - + +
215A GLY* 3.1 10.9 + - - -
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Residues in contact with ARG 212 (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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205A LYS 5.0 1.4 + - - -
208A ASP* 2.9 35.1 + - - +
209A TRP* 3.5 41.0 - - - +
210A ALA 3.3 0.2 - - - -
211A LEU* 1.3 74.1 - - - +
213A TRP* 1.3 60.9 + - + +
215A GLY* 3.3 1.9 + - - +
216A ASP* 2.9 31.6 + - - +
299A ILE* 5.6 1.0 - - - +
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Residues in contact with TRP 213 (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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144A ASN* 4.7 1.4 - - - +
148A ARG* 3.6 1.6 + - - -
209A TRP* 3.0 62.9 + + - +
210A ALA* 3.2 9.9 + - - +
212A ARG* 1.3 80.4 - - + +
214A ILE* 1.3 60.6 + - - +
216A ASP* 3.9 11.2 + - - +
219A ALA* 3.9 22.7 - - + -
223A GLU* 4.2 13.9 - - + -
224A ARG* 3.4 43.6 - - + +
227A ALA* 3.5 21.1 - - + -
228A PHE* 3.9 16.2 - + + -
231A VAL* 5.8 0.2 - - + -
288A ARG* 3.6 24.5 - - - -
292A ILE* 3.9 28.9 - - + -
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Residues in contact with ILE 214 (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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140A ILE* 3.4 41.3 - - + +
143A GLU* 3.8 22.0 - - + +
144A ASN* 3.7 20.9 - - + +
147A GLU* 4.0 20.4 - - - +
148A ARG* 3.0 40.0 + - + +
210A ALA 3.8 4.5 - - - +
211A LEU* 3.1 11.8 + - + +
213A TRP* 1.3 78.4 - - - +
215A GLY* 1.3 58.7 + - - +
228A PHE* 3.7 18.2 - - + -
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Residues in contact with GLY 215 (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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211A LEU 3.1 12.1 + - - -
212A ARG* 3.7 3.8 - - - -
214A ILE* 1.3 75.8 - - - +
216A ASP* 1.3 62.5 + - - +
217A LYS* 3.1 22.6 + - - +
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Residues in contact with ASP 216 (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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148A ARG* 2.8 24.4 + - - -
212A ARG 2.9 17.6 + - - +
213A TRP* 4.1 18.7 - - + +
214A ILE 3.3 1.6 - - - -
215A GLY* 1.3 73.0 - - - +
217A LYS* 1.3 61.8 + - - +
218A GLU* 2.9 21.1 + - - +
219A ALA* 2.9 30.6 + - + +
224A ARG* 4.3 2.3 - - - -
288A ARG* 5.9 0.3 + - - -
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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