Contacts of the helix formed by residues 190 - 206 (chain D) in PDB entry 5LF4
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 THR 190 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D THR* 4.0 1.1 - - - -
44D GLU* 3.3 23.3 - - - +
188D SER 4.5 4.9 - - - +
189D MET* 1.3 79.2 - - - +
191D LEU* 1.3 60.6 + - - +
192D LYS* 3.5 7.6 + - - +
193D GLU* 3.0 45.0 + - - +
194D ALA* 3.0 24.1 + - - +
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Residues in contact with LEU 191 (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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42D THR* 3.7 18.3 + - + +
44D GLU* 2.9 25.4 + - + +
45D GLY* 3.9 24.2 - - - +
46D VAL 4.1 14.4 - - - +
47D CYS* 4.1 15.9 - - + +
190D THR* 1.3 71.0 - - - +
192D LYS* 1.3 57.4 + - - +
194D ALA* 3.2 2.6 + - - +
195D ILE* 2.9 37.6 + - + +
219D THR* 4.4 11.2 - - + -
221D GLN* 3.7 40.8 - - + +
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Residues in contact with LYS 192 (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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44D GLU* 4.6 0.6 + - - -
190D THR* 3.3 7.8 + - - +
191D LEU* 1.3 77.6 - - - +
193D GLU* 1.3 62.4 + - + +
195D ILE* 3.4 12.9 + - - +
196D LYS* 3.1 23.4 + - - +
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Residues in contact with GLU 193 (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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186D HIS* 4.1 11.3 - - - +
188D SER 4.9 0.2 - - - +
189D MET* 3.6 21.7 - - + +
190D THR* 3.0 45.5 + - - +
192D LYS* 1.3 76.9 - - + +
194D ALA* 1.3 56.7 + - - +
196D LYS* 3.3 6.9 + - - +
197D SER* 2.8 32.7 + - - -
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Residues in contact with ALA 194 (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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40D ILE* 3.4 27.5 - - + +
42D THR* 3.6 29.4 - - + -
47D CYS* 4.0 8.5 - - - -
189D MET* 3.6 13.8 - - - +
190D THR 3.0 5.8 + - - +
191D LEU* 3.2 8.9 + - + +
193D GLU* 1.3 76.1 - - - +
195D ILE* 1.3 62.5 + - - +
198D SER* 3.0 24.8 + - - -
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Residues in contact with ILE 195 (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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47D CYS* 4.0 20.2 - - + -
191D LEU* 2.9 36.8 + - + +
192D LYS* 3.6 11.7 - - - +
194D ALA* 1.3 75.3 - - - +
196D LYS* 1.3 62.7 - - - +
198D SER* 3.1 8.3 + - - -
199D LEU* 3.0 45.9 + - + +
217D LEU* 3.7 18.4 - - + -
219D THR* 4.0 7.2 - - + -
229D PHE* 4.0 20.9 - - + -
237D VAL* 3.8 18.6 - - + -
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Residues in contact with LYS 196 (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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192D LYS 3.1 14.0 + - - +
193D GLU* 3.7 8.5 - - - +
195D ILE* 1.3 75.1 - - - +
197D SER* 1.3 58.5 + - - +
199D LEU* 3.0 4.2 + - - +
200D ILE* 2.8 39.7 + - + +
237D VAL* 4.7 3.3 - - + +
240D ASP* 6.3 0.9 - - + -
241D ILE* 3.7 23.7 - - + +
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Residues in contact with SER 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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40D ILE* 4.4 4.5 - - - -
184D VAL* 3.8 27.2 - - - +
189D MET* 3.2 21.7 - - - +
193D GLU* 2.8 21.7 + - - +
194D ALA* 3.6 5.2 - - - -
196D LYS* 1.3 74.4 - - - +
198D SER* 1.3 56.6 + - - +
200D ILE* 3.4 11.8 + - - +
201D ILE* 3.0 34.7 + - - +
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Residues in contact with SER 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ILE* 3.7 32.2 - - - +
40D ILE* 3.9 7.6 - - - -
47D CYS* 4.0 9.1 - - - -
49D ALA* 4.1 13.9 - - - +
194D ALA 3.0 14.3 + - - -
195D ILE* 3.1 14.9 + - - -
197D SER* 1.3 74.7 - - - +
199D LEU* 1.3 61.3 + - - +
201D ILE* 4.0 6.9 - - - +
202D LEU* 3.0 32.3 + - - +
217D LEU* 4.4 1.9 - - - +
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Residues in contact with LEU 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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49D ALA* 4.7 2.0 - - + -
195D ILE* 3.0 44.7 + - + +
196D LYS 3.0 1.6 + - - -
198D SER* 1.3 76.7 + - - +
200D ILE* 1.3 64.6 + - - +
202D LEU* 3.5 15.6 + - + -
203D LYS* 3.0 24.6 + - - +
210D LEU* 3.7 11.2 - - + +
215D ILE* 3.3 33.9 - - + -
217D LEU* 4.1 20.4 - - + -
234D LEU* 5.5 2.7 - - + -
237D VAL* 3.6 16.4 - - + -
238D ILE* 5.2 7.2 - - + -
241D ILE* 3.6 22.6 - - + +
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Residues in contact with ILE 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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196D LYS* 2.8 28.9 + - + +
197D SER* 3.7 11.2 - - - +
199D LEU* 1.3 74.4 - - - +
201D ILE* 1.3 64.7 + - + +
203D LYS* 3.3 5.9 + - - +
204D GLN* 3.1 36.2 + - + +
241D ILE* 3.5 27.3 - - + +
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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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38D ILE* 3.6 22.2 - - + -
177D ALA* 3.7 27.1 - - + +
180D SER* 3.6 31.6 - - - +
181D LEU* 3.5 33.9 - - + +
184D VAL* 4.3 11.7 - - + -
197D SER 3.0 18.5 + - - +
198D SER* 4.0 0.9 - - - +
199D LEU 3.2 0.2 - - - -
200D ILE* 1.3 77.0 - - + +
202D LEU* 1.3 66.5 + - - +
204D GLN* 3.2 15.4 + - - +
205D VAL* 3.1 22.6 + - + +
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Residues in contact with LEU 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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36D THR* 3.9 34.5 - - + +
38D ILE* 4.1 18.6 - - + -
49D ALA* 4.0 13.0 - - + -
50D VAL* 3.9 31.9 - - - +
51D GLU* 4.1 9.6 - - + +
198D SER 3.0 19.6 + - - +
199D LEU* 3.9 11.7 - - + +
201D ILE* 1.3 76.4 - - - +
203D LYS* 1.3 58.9 + - - +
205D VAL* 3.9 4.3 - - + -
206D MET* 2.9 40.2 + - - +
210D LEU* 4.0 8.3 - - + -
215D ILE* 4.2 13.5 - - + -
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Residues in contact with LYS 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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199D LEU 3.0 18.2 + - - +
200D ILE* 3.4 7.6 - - - +
202D LEU* 1.3 77.8 - - - +
204D GLN* 1.3 63.6 + - - +
206D MET* 3.8 11.5 + - - +
208D GLU 4.9 2.3 - - - +
209D LYS* 4.9 6.1 - - - +
210D LEU* 3.8 52.7 + - + +
238D ILE* 6.2 1.8 - - - -
241D ILE* 4.5 28.0 - - + -
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Residues in contact with GLN 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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176D GLY 5.3 0.8 + - - -
180D SER* 3.3 27.2 + - - -
200D ILE* 3.1 34.9 + - + +
201D ILE* 3.5 15.5 + - - +
203D LYS* 1.3 80.1 - - + +
205D VAL* 1.4 69.6 + - + +
206D MET 4.0 3.8 - - - +
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Residues in contact with VAL 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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36D THR* 4.1 20.6 - - + +
51D GLU* 5.7 0.4 - - - +
173D ALA* 3.5 34.8 - - + +
176D GLY* 4.8 4.9 - - - -
177D ALA* 4.3 23.6 - - + +
201D ILE* 3.1 22.5 + - + +
202D LEU* 3.7 12.1 - - + +
204D GLN* 1.4 88.7 - - + +
206D MET* 1.3 69.0 + - + +
207D GLU* 3.6 1.6 + - - -
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Residues in contact with MET 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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51D GLU* 3.7 37.7 - - + +
53D ARG 6.0 0.4 - - - +
202D LEU* 2.9 29.4 + - + +
203D LYS* 4.0 9.4 - - - +
204D GLN 3.4 3.7 - - - +
205D VAL* 1.3 80.8 - - + +
207D GLU* 1.3 63.4 + - - +
208D GLU* 3.5 19.4 - - + +
210D LEU* 4.0 20.2 - - - -
214D ASN* 3.6 44.6 - - + +
215D ILE* 3.7 20.4 - - - -
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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