Contacts of the helix formed by residues 196 - 212 (chain C) in PDB entry 1DXO
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 PRO 196 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194C HIS 3.9 6.1 - - - +
195C THR* 1.3 91.6 - - + +
197C ALA* 1.3 67.8 + - - +
198C ASP* 3.1 19.7 - - - +
199C ALA* 2.9 20.2 + - + +
200C ARG* 3.0 11.2 + - - +
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Residues in contact with ALA 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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195C THR 3.7 1.2 + - - -
196C PRO* 1.3 72.3 - - - +
198C ASP* 1.3 59.5 + - - +
200C ARG* 3.5 35.1 + - - +
201C ILE* 3.1 31.9 + - + +
301C FAD 4.9 1.2 - - - -
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Residues in contact with ASP 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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196C PRO* 3.1 23.7 - - - +
197C ALA* 1.3 72.9 - - - +
199C ALA* 1.3 74.4 + - - +
201C ILE* 3.3 21.2 + - - +
202C GLN* 3.3 18.9 + - - +
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Residues in contact with ALA 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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195C THR* 3.3 17.9 - - + -
196C PRO* 2.9 19.7 + - + +
198C ASP* 1.3 80.4 + - - +
200C ARG* 1.3 59.0 + - - +
202C GLN* 2.7 30.7 + - - +
203C ILE* 2.9 16.3 + - + +
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Residues in contact with ARG 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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17C PHE* 3.7 6.3 - - + -
192C ILE* 4.3 11.9 + - + -
195C THR* 2.8 34.9 + - + +
196C PRO* 3.0 11.5 + - - +
197C ALA* 3.5 36.0 - - - +
199C ALA* 1.3 76.1 - - - +
201C ILE* 1.3 61.5 + - - +
203C ILE* 3.2 14.8 + - - +
204C LEU* 3.1 25.1 + - - +
301C FAD 3.3 72.3 + - + +
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Residues in contact with ILE 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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197C ALA* 3.1 19.1 - - + +
198C ASP* 3.3 14.1 + - - +
199C ALA 3.1 1.0 - - - -
200C ARG* 1.3 77.4 - - - +
202C GLN* 1.3 69.2 + - - +
204C LEU* 3.6 13.0 + - + +
205C GLU* 3.2 32.8 + - + +
301C FAD 4.6 11.9 - - + +
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Residues in contact with GLN 202 (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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198C ASP* 3.4 18.0 + - - +
199C ALA* 2.7 18.2 + - - +
201C ILE* 1.3 84.4 + - - +
203C ILE* 1.3 54.3 + - + +
204C LEU 3.2 0.2 - - - -
205C GLU* 3.0 14.7 + - - +
206C GLY* 2.6 34.7 + - - -
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Residues in contact with ILE 203 (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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17C PHE* 3.7 20.6 - - + -
21C MET* 4.5 4.0 - - + -
187C GLN* 5.2 3.8 + - - +
189C THR* 3.8 30.1 - - + -
190C TYR 6.0 1.1 - - - +
192C ILE* 4.3 14.4 - - + -
195C THR* 4.1 28.3 - - + +
199C ALA* 2.9 15.4 + - + +
200C ARG* 3.2 11.2 + - - +
202C GLN* 1.3 77.2 - - + +
204C LEU* 1.3 61.1 + - - +
206C GLY* 3.3 2.0 + - - +
207C TRP* 3.0 24.1 + - - +
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Residues in contact with LEU 204 (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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17C PHE* 3.8 18.2 - - + -
20C ALA* 3.7 30.1 - - + +
21C MET* 4.0 7.2 - - - +
24C ALA* 3.9 14.5 - - + +
200C ARG 3.1 15.8 + - - +
201C ILE* 3.6 14.1 - - + +
202C GLN 3.2 0.2 - - - -
203C ILE* 1.3 77.9 - - - +
205C GLU* 1.3 66.9 + - - +
207C TRP* 3.3 4.8 + - - +
208C LYS* 3.0 31.7 + - + +
301C FAD 3.3 39.5 - - + +
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Residues in contact with GLU 205 (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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201C ILE* 3.2 24.5 + - + +
202C GLN* 3.0 22.1 + - - +
204C LEU* 1.3 84.4 - - - +
206C GLY* 1.3 64.0 + - - +
208C LYS* 3.4 22.4 + - - +
209C LYS* 3.0 24.8 + - - +
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Residues in contact with GLY 206 (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 GLN* 5.3 3.1 - - - -
202C GLN 2.6 18.7 + - - -
203C ILE* 3.8 2.2 - - - -
205C GLU* 1.3 72.0 - - - +
207C TRP* 1.3 62.7 + - - +
209C LYS* 3.3 6.8 + - - +
210C ARG* 3.0 23.1 + - - +
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Residues in contact with TRP 207 (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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21C MET* 3.4 49.5 + - + -
24C ALA* 4.4 7.6 - - + -
25C ALA* 3.8 6.8 - - - +
98C ILE* 4.0 17.5 - - + -
100C GLN* 4.0 8.7 + - - -
143C VAL* 4.6 15.0 - - + -
145C SER* 4.0 20.6 - - - -
187C GLN* 3.5 45.1 - - + +
203C ILE 3.0 11.8 + - - +
204C LEU 3.4 9.9 - - - +
206C GLY* 1.3 75.4 - - - +
208C LYS* 1.3 61.3 + - - +
210C ARG* 3.1 22.2 + - - -
211C LEU* 3.1 54.9 + - + +
214C ILE* 5.2 0.9 - - + -
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Residues in contact with LYS 208 (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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24C ALA* 3.3 41.4 - - + +
27C ALA* 3.9 11.1 - - - +
28C ALA* 3.6 20.8 - - + +
31C LYS* 2.7 35.1 - - - +
204C LEU* 3.0 20.1 + - + +
205C GLU* 3.8 25.9 + - - +
207C TRP* 1.3 75.5 - - - +
209C LYS* 1.3 62.4 + - - +
210C ARG 3.4 0.2 + - - -
211C LEU* 3.4 11.0 + - - +
212C GLU* 3.2 17.7 + - - +
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Residues in contact with LYS 209 (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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205C GLU 3.0 18.3 + - - +
206C GLY* 3.7 6.7 - - - +
207C TRP 3.2 0.2 - - - -
208C LYS* 1.3 77.1 - - - +
210C ARG* 1.3 62.5 + - - +
212C GLU* 3.0 46.1 + - - +
213C ASN* 4.1 16.9 + - - +
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Residues in contact with ARG 210 (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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143C VAL* 4.1 3.6 - - - +
184C LEU* 3.9 4.0 - - - +
185C GLU* 2.6 46.5 + - - +
186C PRO 4.0 1.6 + - - -
187C GLN* 3.1 40.6 + - - +
206C GLY 3.0 13.2 + - - +
207C TRP* 3.1 20.2 + - + +
209C LYS* 1.3 74.2 - - - +
211C LEU* 1.3 58.0 + - - +
212C GLU 3.0 6.0 + - - -
213C ASN* 3.2 5.5 + - - +
214C ILE* 3.1 36.5 + - + +
217C GLU* 2.6 39.2 + - - +
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Residues in contact with LEU 211 (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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25C ALA* 3.6 32.3 - - + +
28C ALA* 4.4 5.6 - - + -
29C LEU* 3.5 32.3 - - + +
32C LYS* 5.2 2.0 - - - +
34C TRP* 4.5 5.5 + - - -
96C LEU* 5.0 0.9 - - + -
98C ILE* 4.2 11.7 - - + -
207C TRP* 3.1 60.7 + - + +
208C LYS* 3.8 9.4 - - - +
209C LYS 3.3 0.4 - - - -
210C ARG* 1.3 74.8 - - - +
212C GLU* 1.3 63.9 + - - +
213C ASN 3.2 0.8 + - - -
214C ILE* 3.4 33.7 - - + +
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Residues in contact with GLU 212 (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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28C ALA* 5.7 3.6 - - + +
32C LYS* 3.6 49.6 + - + +
34C TRP* 5.6 1.4 + - - -
208C LYS 3.2 16.4 - - - +
209C LYS* 3.0 44.5 + - - +
210C ARG 3.0 0.6 - - - -
211C LEU* 1.3 80.2 - - - +
213C ASN* 1.3 68.1 + - - +
214C ILE 3.7 0.2 - - - -
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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