Contacts of the helix formed by residues 196 - 212 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194D HIS 4.0 6.3 - - - +
195D THR* 1.3 92.7 - - + +
197D ALA* 1.3 66.4 + - - +
198D ASP* 3.5 23.6 - - - +
199D ALA* 2.9 20.0 + - + +
200D ARG* 3.0 11.7 + - - +
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Residues in contact with ALA 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D PRO* 1.3 72.1 - - - +
198D ASP* 1.3 62.6 + - - +
200D ARG* 3.5 37.4 + - - +
201D ILE* 3.0 32.5 + - + +
301D FAD 5.0 0.7 - - - -
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Residues in contact with ASP 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D PRO* 3.5 22.0 - - - +
197D ALA* 1.3 74.6 + - - +
199D ALA* 1.3 69.8 + - - +
201D ILE* 3.4 15.5 + - - +
202D GLN* 3.3 27.7 + - - +
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Residues in contact with ALA 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D THR* 3.5 18.8 - - + -
196D PRO* 2.9 19.6 + - + +
198D ASP* 1.3 80.6 - - - +
200D ARG* 1.3 67.6 + - - +
202D GLN* 2.8 22.1 + - - +
203D ILE* 2.8 17.5 + - + +
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Residues in contact with ARG 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D PHE* 3.7 5.6 - - + -
192D ILE* 4.1 19.8 + - + -
195D THR* 3.0 23.6 + - + +
196D PRO* 3.0 11.4 + - - +
197D ALA* 3.5 43.4 - - - +
198D ASP 3.3 0.2 - - - -
199D ALA* 1.3 75.5 - - - +
201D ILE* 1.3 62.2 - - - +
203D ILE* 3.2 14.6 + - - +
204D LEU* 3.1 25.4 + - - +
301D FAD 3.3 71.5 + - + +
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Residues in contact with ILE 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D ALA* 3.0 20.4 - - + +
198D ASP* 3.4 15.3 - - - +
199D ALA 3.0 0.6 - - - -
200D ARG* 1.3 77.3 - - - +
202D GLN* 1.3 68.7 + - - +
204D LEU* 3.5 13.6 + - + +
205D GLU* 3.2 31.8 + - + +
301D FAD 4.7 10.5 - - + +
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Residues in contact with GLN 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D ASP* 3.4 20.9 + - - +
199D ALA* 2.8 12.9 + - - +
201D ILE* 1.3 85.3 - - - +
203D ILE* 1.3 55.2 + - + +
205D GLU* 2.8 14.5 + - - +
206D GLY* 2.6 34.1 + - - -
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Residues in contact with ILE 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D PHE* 3.8 19.5 - - + -
21D MET* 4.3 4.5 - - + -
187D GLN* 5.6 3.8 + - - +
189D THR* 3.9 29.4 - - + -
190D TYR 6.1 1.1 - - - +
192D ILE* 4.1 15.3 - - + -
195D THR* 3.9 20.6 - - + +
199D ALA* 2.8 14.7 + - + +
200D ARG* 3.2 24.0 + - - +
202D GLN* 1.3 75.8 - - + +
204D LEU* 1.3 62.9 + - - +
206D GLY* 3.3 1.4 + - - +
207D TRP* 3.0 23.2 + - - +
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Residues in contact with LEU 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D PHE* 3.4 22.9 - - + -
20D ALA* 3.8 28.9 - - + +
21D MET* 3.9 9.9 - - - -
24D ALA* 4.3 8.2 - - + +
200D ARG 3.1 11.3 + - - +
201D ILE* 3.6 13.2 - - + +
202D GLN 3.1 0.4 - - - -
203D ILE* 1.3 75.4 - - - +
205D GLU* 1.3 69.1 + - - +
207D TRP* 3.3 7.5 + - - +
208D LYS* 3.0 29.8 + - + +
301D FAD 3.2 41.3 - - + +
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Residues in contact with GLU 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D ILE* 3.2 26.9 + - + +
202D GLN* 2.8 19.6 + - - +
204D LEU* 1.3 83.4 - - - +
206D GLY* 1.3 59.2 + - - +
208D LYS* 3.4 22.1 + - - +
209D LYS* 3.0 28.9 + - - +
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Residues in contact with GLY 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D GLN* 5.7 2.5 - - - -
202D GLN 2.6 18.3 + - - -
203D ILE* 3.8 2.7 - - - -
205D GLU* 1.3 71.5 - - - +
207D TRP* 1.3 64.9 + - - +
209D LYS* 3.4 7.1 + - - +
210D ARG* 3.1 23.4 + - - +
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Residues in contact with TRP 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D MET* 3.2 49.4 + - + -
24D ALA* 4.2 11.0 - - + -
25D ALA* 3.7 8.3 - - - +
98D ILE* 3.9 21.5 - - + +
100D GLN* 4.4 1.4 + - - -
143D VAL* 4.6 11.0 - - + -
145D SER* 3.9 23.2 + - - -
187D GLN* 3.3 51.2 - - + +
203D ILE 3.0 18.1 + - - +
204D LEU 3.5 5.2 - - - +
205D GLU 3.2 0.2 - - - -
206D GLY* 1.3 76.7 - - - +
208D LYS* 1.3 62.3 + - - +
210D ARG* 3.2 23.1 + - - +
211D LEU* 3.2 55.2 + - + +
214D ILE* 4.8 0.9 - - + -
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Residues in contact with LYS 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ALA* 3.5 37.8 - - + +
27D ALA* 3.9 10.5 - - - +
28D ALA* 3.7 18.1 - - + +
31D LYS* 2.6 36.8 - - - +
204D LEU* 3.0 16.1 + - + +
205D GLU* 3.7 27.4 + - - +
207D TRP* 1.3 77.2 - - - +
209D LYS* 1.3 61.8 + - - +
211D LEU* 3.2 15.3 + - - +
212D GLU* 3.4 15.2 + - - +
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Residues in contact with LYS 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D GLU 3.0 16.6 + - - +
206D GLY* 3.7 8.1 - - - +
207D TRP 3.3 0.2 - - - -
208D LYS* 1.3 76.4 - - - +
210D ARG* 1.3 62.0 + - - +
212D GLU* 3.1 53.6 + - - +
213D ASN* 4.1 12.7 + - - +
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Residues in contact with ARG 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D VAL* 3.6 13.2 - - - +
184D LEU* 3.8 3.6 - - - +
185D GLU* 2.7 41.0 + - - +
186D PRO 4.0 1.2 + - - -
187D GLN* 3.0 41.5 + - - +
206D GLY 3.1 14.0 + - - +
207D TRP* 3.2 17.9 + - + +
209D LYS* 1.3 74.3 - - - +
211D LEU* 1.3 58.0 + - - +
212D GLU 3.0 6.5 + - - -
213D ASN* 3.2 6.4 + - - +
214D ILE* 3.0 32.6 + - + +
217D GLU* 2.7 39.4 + - - +
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Residues in contact with LEU 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ALA* 3.7 20.0 - - + -
28D ALA* 4.5 4.7 - - + -
29D LEU* 3.3 36.4 - - + +
32D LYS* 4.9 3.5 - - - +
34D TRP* 4.6 8.3 + - - -
96D LEU* 4.9 0.2 - - + -
98D ILE* 4.1 9.6 - - + -
207D TRP* 3.2 54.4 + - + +
208D LYS* 3.2 10.9 + - - +
210D ARG* 1.3 73.8 - - - +
212D GLU* 1.3 65.3 + - - +
213D ASN 3.2 0.6 + - - -
214D ILE* 3.5 45.7 - - + +
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Residues in contact with GLU 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ALA* 5.8 2.2 - - + +
32D LYS* 3.6 51.8 + - + +
34D TRP* 5.7 0.7 + - - -
208D LYS 3.4 9.8 + - - +
209D LYS* 3.1 56.0 + - - +
210D ARG 3.0 0.4 - - - -
211D LEU* 1.3 79.2 - - - +
213D ASN* 1.3 69.4 + - - +
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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