Contacts of the helix formed by residues 191 - 212 (chain D) in PDB entry 2VUU
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 ASP 191 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D ASN* 3.7 18.6 + - - +
155D ASN* 4.9 3.3 + - - +
190D LEU* 1.3 77.4 - - - +
192D ALA* 1.3 55.0 + - - +
193D GLU* 3.7 2.4 + - - +
194D HIS* 2.9 23.0 + - - +
195D ASP* 2.8 50.1 + - - +
220D PHE* 5.6 0.6 - - - +
329D ARG* 2.7 54.7 + - - +
334D TYR* 3.8 10.6 - - - -
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Residues in contact with ALA 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ARG* 3.8 26.9 - - + +
20D SER* 3.4 5.5 + - - -
153D TYR* 4.0 22.9 - - + -
155D ASN* 3.9 17.1 - - - +
190D LEU* 3.5 7.9 + - - +
191D ASP* 1.3 71.6 + - - +
193D GLU* 1.3 62.6 + - - +
196D VAL* 3.1 41.7 + - + +
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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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16D ARG* 4.2 27.9 - - + +
20D SER* 3.1 25.6 + - - -
23D ARG* 4.3 18.1 + - - +
43D ILE* 5.6 2.8 - - - +
155D ASN* 4.8 10.1 - - - +
191D ASP* 3.4 4.1 + - - +
192D ALA* 1.3 75.3 - - + +
194D HIS* 1.3 61.1 + - - +
198D PRO* 5.2 0.3 - - - +
329D ARG* 4.9 7.6 - - - +
342D GLU* 5.1 9.0 - - - +
708L ARG* 5.7 0.2 + - - -
711L SER* 2.6 36.8 + - - +
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Residues in contact with HIS 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D ASP* 2.9 26.9 + - - +
193D GLU* 1.3 79.9 - - - +
195D ASP* 1.3 81.7 + - - +
198D PRO* 3.5 19.2 - - - +
325D TRP* 3.9 2.7 + + - -
327D GLY 3.0 27.1 - - - -
328D TRP 4.2 0.4 - - - -
329D ARG* 3.4 46.9 - - + +
333D GLU* 4.5 7.5 + - - -
694L CYS* 5.4 0.8 - - - -
696L ALA* 3.5 14.6 - - + +
708L ARG* 3.2 40.9 + - - +
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Residues in contact with ASP 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D LEU* 4.3 4.3 - - + -
191D ASP* 2.8 33.1 + - - +
194D HIS* 1.3 98.5 + - - +
196D VAL* 1.3 62.9 + - - +
197D GLY 3.4 2.2 - - - -
198D PRO* 3.8 1.6 - - - -
199D ALA* 3.3 24.4 + - - +
220D PHE* 4.0 18.1 - - + +
325D TRP* 2.8 28.1 + - + +
328D TRP* 3.1 18.7 - - - +
329D ARG 2.9 18.9 + - - +
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Residues in contact with VAL 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D GLN* 3.2 47.3 - - + +
20D SER* 3.8 1.6 - - - +
78D PHE* 4.5 1.1 - - + -
190D LEU* 3.9 21.3 - - + -
191D ASP 4.0 0.6 + - - -
192D ALA* 3.1 34.8 + - - +
195D ASP* 1.3 75.1 - - - +
197D GLY* 1.3 66.4 + - - +
199D ALA* 3.8 2.5 - - - +
200D LEU* 3.0 45.6 + - + +
218D LEU* 4.3 12.6 - - + -
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Residues in contact with GLY 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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20D SER* 2.5 27.2 + - - -
21D LEU* 3.5 25.4 - - - +
24D VAL* 4.1 7.6 - - - +
196D VAL* 1.3 74.6 - - - +
198D PRO* 1.3 67.5 - - - +
200D LEU* 3.3 2.3 + - - +
201D LEU* 3.0 23.4 + - - +
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Residues in contact with PRO 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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20D SER* 4.2 1.3 - - - +
24D VAL* 3.9 20.2 - - + -
193D GLU 5.2 0.2 - - - +
194D HIS 3.5 26.2 - - - +
195D ASP 3.8 3.8 - - - -
197D GLY* 1.3 87.7 - - - +
199D ALA* 1.3 61.4 + - - +
201D LEU* 3.3 8.8 + - + +
202D GLN* 3.0 22.0 + - - +
324D LEU 4.8 0.2 - - - +
325D TRP* 3.4 44.6 - - + +
700L PHE* 4.3 13.7 - - + -
704L HIS* 5.0 6.1 + - - +
708L ARG* 5.3 3.6 - - + -
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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 ASP 3.3 18.6 + - - +
196D VAL 3.8 2.9 - - - +
197D GLY 3.3 0.6 - - - -
198D PRO* 1.3 76.7 - - - +
200D LEU* 1.3 66.8 + - - +
202D GLN* 3.0 9.0 + - - +
203D ILE* 3.0 26.5 + - + +
218D LEU* 3.9 25.6 - - + -
220D PHE* 4.2 13.0 - - + -
321D ALA* 6.4 0.2 - - - -
324D LEU* 4.4 8.5 - - + +
325D TRP* 4.1 10.4 - - + +
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Residues in contact with LEU 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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21D LEU* 4.2 15.7 - - + -
78D PHE* 3.3 49.1 - - + -
109D ILE* 4.3 9.8 - - + +
148D VAL* 4.0 29.6 - - + -
196D VAL* 3.0 31.0 + - + +
197D GLY 3.9 2.2 - - - +
199D ALA* 1.3 76.4 - - - +
201D LEU* 1.3 57.6 + - - +
203D ILE* 3.2 13.4 + - + +
204D PHE* 2.9 39.2 + - + -
218D LEU* 4.2 12.8 - - + -
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Residues in contact with LEU 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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8D ILE* 5.3 0.7 - - + -
21D LEU* 4.9 6.4 - - + +
24D VAL* 3.2 27.4 - - + -
25D ALA* 4.5 10.5 - - + -
28D VAL* 4.1 14.1 - - + -
30D HIS* 3.7 32.5 - - + +
197D GLY 3.0 13.5 + - - +
198D PRO 3.4 10.1 - - - +
199D ALA 3.1 0.2 - - - -
200D LEU* 1.3 78.8 - - - +
202D GLN* 1.3 55.9 + - - +
204D PHE* 3.4 13.3 + - + +
205D LYS* 2.9 34.4 + - + +
704L HIS* 3.5 34.3 - - + +
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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 PRO 3.0 11.1 + - - +
199D ALA 3.0 9.7 + - - +
201D LEU* 1.3 75.2 - - - +
203D ILE* 1.3 59.2 + - - +
205D LYS* 3.1 28.6 - - - +
206D ASP* 2.9 55.9 + - - +
323D LYS 5.4 0.4 - - - +
324D LEU* 3.2 45.4 + - + +
703L LEU* 4.5 18.0 - - - +
704L HIS* 4.8 4.4 + - - -
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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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107D HIS* 3.5 15.2 - - + -
109D ILE* 3.6 17.9 - - + -
146D THR* 4.2 7.0 - - + -
148D VAL* 4.0 22.4 - - + -
199D ALA* 3.0 20.3 + - + +
200D LEU* 3.5 17.9 - - + +
202D GLN* 1.3 73.8 - - - +
204D PHE* 1.3 61.2 + - - +
206D ASP* 3.2 3.5 + - - +
207D GLY 2.9 22.2 + - - -
211D TRP* 3.8 17.5 - - + +
216D ILE* 3.8 22.4 - - + -
218D LEU* 5.6 2.5 - - + -
324D LEU* 3.6 26.5 - - + -
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Residues in contact with PHE 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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6D LYS* 5.9 0.7 + - - -
8D ILE* 4.2 32.8 - - + -
21D LEU* 4.6 13.9 - - + -
30D HIS* 6.3 1.8 - - + +
76D LEU* 4.0 28.8 - - + +
77D ALA 3.2 34.1 - - - -
78D PHE* 4.3 2.7 - - + -
107D HIS* 3.8 25.0 + - + -
109D ILE* 3.2 34.3 - - + -
200D LEU* 2.9 23.3 + - + +
201D LEU* 3.6 12.1 - - + +
203D ILE* 1.3 74.6 - - - +
205D LYS* 1.3 67.4 + - - +
207D GLY* 3.2 13.0 + - - -
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Residues in contact with LYS 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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5D LYS* 6.5 1.1 - - - +
30D HIS* 6.4 0.2 - - - +
201D LEU* 2.9 22.9 + - + +
202D GLN* 3.1 32.6 - - - +
204D PHE* 1.3 77.7 - - - +
206D ASP* 1.3 58.2 + - - +
207D GLY* 4.8 0.2 - - - -
209D GLN* 5.3 1.6 + - - -
703L LEU* 3.9 14.0 + - - +
704L HIS* 3.1 36.8 + - + +
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Residues in contact with ASP 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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202D GLN* 2.9 35.2 + - - +
203D ILE 3.4 1.6 - - - +
204D PHE 3.1 0.2 - - - -
205D LYS* 1.3 80.1 - - - +
207D GLY* 1.3 58.1 + - - +
209D GLN* 3.0 27.1 + - - +
210D LYS* 3.4 26.9 + - + +
211D TRP* 2.7 39.1 + - + -
324D LEU* 3.5 14.0 - - - +
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Residues in contact with GLY 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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107D HIS* 3.4 19.5 - - - -
203D ILE 2.9 8.3 + - - -
204D PHE 3.2 8.7 + - - -
206D ASP* 1.3 80.2 - - - +
208D PRO* 1.3 74.7 - - - +
209D GLN* 3.2 10.3 + - - -
211D TRP* 3.2 17.2 + - - +
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Residues in contact with PRO 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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106D GLN* 3.6 21.5 - - + +
107D HIS* 3.7 23.1 - - + +
144D PRO* 4.2 13.2 - - + -
207D GLY* 1.3 79.0 - - - +
209D GLN* 1.3 76.0 + - - +
210D LYS 3.1 2.5 - - - -
212D ASN* 2.7 57.1 + - + +
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Residues in contact with GLN 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 LYS 5.3 2.0 + - - -
206D ASP 3.0 28.1 + - - +
207D GLY* 3.9 8.4 - - - -
208D PRO* 1.3 91.3 - - - +
210D LYS* 1.3 60.2 + - + +
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Residues in contact with LYS 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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206D ASP* 3.4 39.0 + - + +
207D GLY 3.4 0.6 + - - -
208D PRO 3.1 0.4 - - - -
209D GLN* 1.3 84.1 - - + +
211D TRP* 1.3 101.0 + - + +
212D ASN 3.8 0.4 - - - -
214D HIS* 3.9 13.7 + - - -
320D GLU* 5.6 0.6 + - - -
323D LYS* 4.5 26.0 - - - +
324D LEU* 5.5 2.0 - - - +
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Residues in contact with TRP 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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146D THR* 2.8 28.3 + - + +
203D ILE* 3.8 17.7 - - + -
206D ASP* 2.7 43.5 + - + +
207D GLY 3.2 10.3 + - - +
208D PRO* 4.3 0.4 - - - -
210D LYS* 1.3 112.3 - - + +
212D ASN* 1.3 67.6 + - - +
214D HIS* 3.0 46.5 + + + +
215D ARG 5.4 0.9 - - - -
216D ILE* 3.7 24.7 - - + -
320D GLU* 3.8 35.0 - - + -
324D LEU* 4.0 23.1 - - + +
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Residues in contact with ASN 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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143D LEU 4.2 1.7 - - - +
144D PRO* 3.5 10.4 - - - +
145D SER* 3.0 30.6 + - - -
208D PRO* 2.7 39.3 + - + +
210D LYS 3.8 0.6 - - - -
211D TRP* 1.3 70.1 - - - +
213D GLY* 1.3 64.9 + - - +
214D HIS* 3.1 18.4 + - - -
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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
------------------------------------------------------------
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