Contacts of the helix formed by residues 195 - 213 (chain D) in PDB entry 4HYY
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 195 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D ALA 3.6 0.2 - - - -
194D TYR* 1.3 91.6 + - + +
196D SER* 1.3 53.9 + - - +
197D GLU* 3.2 8.3 + - - +
198D HIS* 2.8 26.2 + - + +
199D GLN 2.8 30.3 + - - -
228D LEU* 3.3 15.0 - - - +
232D ASP* 3.6 18.2 - - - +
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Residues in contact with SER 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D THR* 1.3 71.7 - - - +
197D GLU* 1.3 65.4 + - - +
199D GLN* 3.1 16.5 + - - +
200D MET* 3.2 13.2 + - - +
228D LEU* 3.2 34.1 + - - +
229D PHE* 3.5 29.5 - - - -
232D ASP* 2.6 28.5 + - - +
233D PHE* 3.9 11.6 - - - -
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Residues in contact with GLU 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D THR* 3.2 7.1 + - - +
196D SER* 1.3 83.4 - - - +
198D HIS* 1.3 57.8 - - - +
200D MET* 3.1 9.0 + - - +
201D GLU* 2.9 38.9 + - - +
232D ASP* 5.1 1.8 - - - +
233D PHE* 5.3 9.5 - - + -
245D LYS* 4.0 25.5 + - + -
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Residues in contact with HIS 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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192D ARG 3.3 14.5 + - - -
193D ALA* 3.4 7.0 - - + -
194D TYR* 3.0 43.3 - + + -
195D THR* 2.8 27.3 + - + +
197D GLU* 1.3 76.0 - - - +
199D GLN* 1.3 61.8 + - - +
201D GLU* 3.1 22.5 + - + +
202D LEU* 3.0 43.5 + - + +
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Residues in contact with GLN 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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159D ILE* 4.8 10.6 - - + +
161D THR* 3.9 13.5 - - - +
193D ALA* 4.0 16.7 - - + +
195D THR 2.8 14.3 + - - +
196D SER 3.1 10.5 + - - +
198D HIS* 1.3 73.6 - - - +
200D MET* 1.3 60.3 + - - +
202D LEU* 3.3 6.2 + - - +
203D LEU* 3.3 26.0 + - + +
222D ILE* 4.0 8.5 - - + +
224D SER 4.3 0.6 + - - -
225D ILE* 2.9 31.7 + - - +
228D LEU* 3.6 31.7 - - - +
229D PHE* 3.8 13.4 - - + -
249D MET* 3.4 18.4 - - - +
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Residues in contact with MET 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 SER 3.2 7.7 + - - +
197D GLU* 3.1 10.8 + - - +
199D GLN* 1.3 75.3 - - - +
201D GLU* 1.3 65.7 + - - +
202D LEU 3.2 0.5 + - - -
203D LEU* 3.3 19.3 + - - +
204D ASP* 3.3 27.2 + - - +
229D PHE* 5.6 2.7 - - + -
245D LYS* 5.3 4.7 - - + +
248D GLN* 3.7 28.5 - - + +
249D MET* 3.6 43.0 - - + +
252D ARG* 3.7 23.3 - - + -
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Residues in contact with GLU 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D GLU* 2.9 27.7 + - - +
198D HIS* 3.1 24.5 + - + +
200D MET* 1.3 77.5 - - - +
202D LEU* 1.3 61.4 + - + +
204D ASP* 3.1 17.0 + - - +
205D TYR* 3.2 12.5 + - - +
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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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159D ILE* 4.0 24.7 - - + -
191D ALA* 4.2 21.8 - - + -
192D ARG 3.8 20.0 - - - +
193D ALA* 3.9 21.5 - - + -
198D HIS* 3.0 30.9 + - + +
199D GLN* 3.7 5.8 - - - +
200D MET 3.2 0.4 - - - -
201D GLU* 1.3 74.1 - - + +
203D LEU* 1.3 61.5 + - - +
205D TYR* 3.1 16.2 + - + +
206D VAL* 2.8 32.9 + - + +
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Residues in contact with LEU 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D ILE* 3.9 22.9 - - + -
199D GLN* 3.3 17.9 + - + +
200D MET* 3.3 16.3 + - - +
202D LEU* 1.3 78.2 - - - +
204D ASP* 1.3 62.7 + - - +
206D VAL* 3.3 5.2 + - + +
207D ALA* 2.8 31.0 + - - +
220D LEU* 4.3 16.2 - - + -
222D ILE* 4.3 17.0 - - + -
249D MET* 3.6 37.2 - - + +
252D ARG* 5.5 2.5 - - + -
253D LEU* 4.4 13.2 - - + +
256D ILE* 3.9 15.9 - - + +
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Residues in contact with ASP 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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200D MET* 3.3 26.2 + - - +
201D GLU* 3.1 10.5 + - - +
202D LEU 3.1 1.0 - - - -
203D LEU* 1.3 80.1 - - - +
205D TYR* 1.3 63.5 + - - +
207D ALA* 3.5 2.4 + - - +
208D ALA* 3.3 22.0 + - - +
252D ARG* 3.0 37.6 + - - +
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Residues in contact with TYR 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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205B TYR* 3.7 33.5 + + - -
208B ALA* 3.3 37.3 + - + -
209B LYS* 4.0 10.4 + - - +
212B GLU* 3.0 39.9 + - + +
157D ILE* 6.2 2.0 - - + -
189D LEU* 6.0 0.9 - - + -
201D GLU 3.2 10.4 + - - +
202D LEU* 3.1 19.7 + - + +
204D ASP* 1.3 78.2 - - - +
206D VAL* 1.3 62.7 + - + +
208D ALA* 3.3 5.1 + - - +
209D LYS* 2.9 39.7 + - + +
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Residues in contact with VAL 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D ILE* 4.0 29.2 - - + -
159D ILE* 4.3 11.7 - - + -
202D LEU* 2.8 22.6 + - + +
203D LEU* 3.4 10.8 - - + +
205D TYR* 1.3 73.6 - - + +
207D ALA* 1.3 68.4 + - - +
209D LYS* 2.8 11.1 + - - +
210D PHE* 2.8 56.2 + - + -
220D LEU* 4.2 15.7 - - + -
256D ILE* 4.8 4.0 - - + -
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Residues in contact with ALA 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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203D LEU 2.8 16.3 + - - +
204D ASP 3.9 2.5 - - - +
205D TYR 3.5 0.2 - - - -
206D VAL* 1.3 74.7 - - - +
208D ALA* 1.3 56.4 + - - +
210D PHE* 2.9 5.0 + - - +
211D HIS* 2.8 28.2 + - - +
252D ARG* 3.5 30.3 - - - +
256D ILE* 3.8 19.7 - - + +
260D TYR* 3.7 18.7 - - + +
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Residues in contact with ALA 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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84A GLY* 3.8 14.4 + - - +
205B TYR* 3.4 38.1 + - + -
204D ASP 3.3 11.1 + - - +
205D TYR 3.7 4.3 - - - +
206D VAL 3.1 0.8 - - - -
207D ALA* 1.3 75.8 - - - +
209D LYS* 1.3 65.9 + - - +
211D HIS* 3.4 11.1 + - - +
212D GLU* 3.2 19.2 + - - +
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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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205B TYR* 4.4 6.7 + - - +
209B LYS* 5.0 7.0 - - - +
212B GLU* 3.2 28.1 + - - -
157D ILE* 4.4 11.9 - - + -
189D LEU* 3.8 18.2 - - - +
205D TYR* 2.9 28.7 + - + +
206D VAL* 2.8 17.3 + - - +
208D ALA* 1.3 73.6 - - - +
210D PHE* 1.3 62.2 + - + +
212D GLU* 3.5 25.8 + - + +
213D GLU 4.2 3.1 + - - +
216D ILE* 5.2 4.7 - - + +
217D PHE* 3.9 33.3 - - + -
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Residues in contact with PHE 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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157D ILE* 4.0 20.0 - - + -
206D VAL* 2.8 36.3 + - + -
207D ALA 3.4 5.6 - - - +
209D LYS* 1.3 77.0 - - + +
211D HIS* 1.3 68.0 + - - +
212D GLU 3.0 3.0 + - - -
213D GLU 3.3 22.6 + - - +
214D ALA* 4.1 2.8 + - - -
217D PHE* 3.3 42.2 - + + -
219D LEU 4.8 3.1 - - - -
220D LEU* 4.6 12.6 - - + -
256D ILE* 3.9 26.2 - - + -
260D TYR* 3.6 34.6 - + + -
262D VAL* 3.9 20.2 - - + -
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Residues in contact with HIS 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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84A GLY* 3.8 29.6 + - - +
85A PHE 4.2 10.0 - - - +
207D ALA 2.8 13.0 + - - +
208D ALA* 3.4 15.9 - - - +
210D PHE* 1.3 76.1 - - - +
212D GLU* 1.3 60.0 + - - +
213D GLU* 3.4 2.3 + - - -
214D ALA 5.0 0.3 + - - -
259D GLU* 6.0 0.4 - - - -
260D TYR* 3.1 31.1 + - - +
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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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84A GLY 4.9 3.1 - - - +
85A PHE* 4.4 25.8 - - - +
86A LEU* 5.9 1.7 - - - -
90A GLU* 4.5 14.7 - - - +
189B LEU* 4.6 10.6 - - + +
205B TYR* 2.7 34.7 + - + +
209B LYS* 3.1 32.1 + - - -
208D ALA 3.2 7.0 + - - +
209D LYS* 3.7 22.8 + - + +
210D PHE 3.0 2.2 + - - -
211D HIS* 1.3 76.8 - - - +
213D GLU* 1.3 64.0 + - + +
216D ILE* 6.1 1.1 - - + -
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Residues in contact with GLU 213 (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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90A GLU* 5.7 4.9 - - - +
209D LYS 4.2 2.5 + - - +
210D PHE* 3.3 13.8 + - - +
211D HIS 4.2 1.1 - - - -
212D GLU* 1.3 82.0 - - + +
214D ALA* 1.3 74.9 + - - +
215D GLY 3.8 0.2 + - - -
216D ILE* 3.2 50.1 + - + +
217D PHE 4.9 0.5 + - - -
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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
------------------------------------------------------------
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