Contacts of the helix formed by residues 191 - 212 (chain H) in PDB entry 2VUT
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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154H ASN* 3.1 30.1 + - - +
155H ASN* 5.5 2.9 - - - +
190H LEU* 1.3 74.5 - - - +
192H ALA* 1.3 60.6 + - - +
193H GLU* 4.2 3.5 + - - +
194H HIS* 3.2 9.3 + - + +
195H ASP* 2.9 40.2 + - - +
220H PHE* 5.3 1.2 - - - -
329H ARG* 2.8 64.5 + - - +
334H TYR* 3.7 11.8 - - - +
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Residues in contact with ALA 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H ARG* 3.9 26.2 - - + +
17H GLN 4.9 0.2 - - - +
20H SER* 3.1 8.7 + - - -
153H TYR* 3.7 35.5 - - + +
154H ASN 5.1 0.2 - - - +
155H ASN* 5.3 5.3 - - + +
190H LEU* 3.3 7.5 + - - -
191H ASP* 1.3 71.6 + - - +
193H GLU* 1.3 64.4 + - - +
196H VAL* 3.1 37.9 + - + +
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Residues in contact with GLU 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H ARG* 4.7 9.3 - - + +
20H SER* 3.0 23.0 + - - -
23H ARG* 4.5 16.3 + - - +
155H ASN* 4.2 18.1 + - + +
191H ASP* 4.2 2.0 - - - +
192H ALA* 1.3 79.7 - - - +
194H HIS* 1.3 60.6 + - - +
198H PRO* 5.3 1.6 - - - +
329H ARG* 3.7 21.5 + - - +
338H VAL* 4.7 5.0 - - - +
342H GLU* 4.3 14.0 - - - +
708P ARG* 5.4 1.0 + - - -
711P SER* 3.6 24.2 + - - +
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Residues in contact with HIS 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191H ASP* 3.2 20.7 + - - +
192H ALA 3.3 0.6 - - - -
193H GLU* 1.3 80.6 - - - +
195H ASP* 1.3 87.3 + - - +
198H PRO* 3.4 16.1 - - - +
325H TRP* 4.0 1.1 + + - -
327H GLY 2.9 27.4 - - - -
328H TRP 4.0 0.7 - - - -
329H ARG* 3.3 47.8 - - + +
333H GLU* 4.4 9.5 + - - -
694P CYS* 5.6 1.0 - - - -
696P ALA* 3.5 15.3 - - + +
708P ARG* 3.6 41.8 + - - +
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Residues in contact with ASP 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190H LEU* 4.5 0.2 - - + -
191H ASP* 2.9 25.1 + - - +
194H HIS* 1.3 106.8 + - - +
196H VAL* 1.3 66.0 + - - +
197H GLY 3.4 1.8 - - - -
198H PRO* 3.7 5.4 - - - +
199H ALA* 3.2 25.8 + - - +
220H PHE* 3.8 22.7 - - + -
325H TRP* 2.8 18.8 + - + -
328H TRP* 3.0 18.3 - - - +
329H ARG 2.8 22.2 + - - +
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Residues in contact with VAL 196 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H GLN* 3.7 32.8 - - + +
20H SER* 3.9 3.6 - - - +
78H PHE* 4.9 0.7 - - + -
190H LEU* 3.8 25.1 - - + -
192H ALA* 3.1 34.1 + - + +
195H ASP* 1.3 78.3 - - - +
197H GLY* 1.3 66.8 + - - +
199H ALA* 3.7 3.6 - - - +
200H LEU* 2.9 47.4 + - + +
218H LEU* 4.2 15.5 - - + -
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Residues in contact with GLY 197 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H SER* 2.8 28.6 + - - -
21H LEU* 3.8 6.6 - - - +
24H VAL* 3.6 22.1 - - - +
196H VAL* 1.3 73.9 - - - +
198H PRO* 1.3 69.9 - - - +
200H LEU* 3.1 2.6 + - - +
201H LEU* 3.0 24.1 + - - +
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Residues in contact with PRO 198 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H SER* 4.6 1.8 - - - +
24H VAL* 4.2 16.4 - - + -
193H GLU 5.3 0.9 - - - +
194H HIS 3.4 26.5 - - - +
195H ASP 3.7 3.4 - - - +
197H GLY* 1.3 85.6 - - - +
199H ALA* 1.3 61.1 + - - +
201H LEU* 3.2 9.4 + - + +
202H GLN* 3.0 22.9 + - - +
325H TRP* 3.5 47.4 - - + +
700P PHE* 4.4 12.8 - - + -
704P HIS* 4.8 4.8 + - - +
708P ARG* 5.9 2.7 - - + -
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Residues in contact with ALA 199 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195H ASP 3.2 19.8 + - - +
196H VAL 3.7 2.9 - - - +
198H PRO* 1.3 78.1 - - - +
200H LEU* 1.3 62.9 + - - +
202H GLN* 3.2 6.7 + - - +
203H ILE* 3.1 29.2 + - + +
218H LEU* 3.9 23.8 - - + -
220H PHE* 4.0 11.4 - - + -
321H ALA* 6.2 0.2 - - - -
324H LEU* 4.8 11.1 - - + +
325H TRP* 4.1 12.5 - - + +
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Residues in contact with LEU 200 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H LEU* 3.8 20.6 - - + -
78H PHE* 3.4 53.2 - - + -
109H ILE* 3.9 22.3 - - + +
148H VAL* 4.1 15.5 - - + -
196H VAL* 2.9 37.6 + - + +
197H GLY 3.7 3.1 - - - +
199H ALA* 1.3 73.0 - - - +
201H LEU* 1.3 65.8 + - - +
203H ILE* 3.3 8.3 + - + +
204H PHE* 3.0 31.8 + - + -
218H LEU* 4.8 5.2 - - + -
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Residues in contact with LEU 201 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H ILE* 5.1 0.7 - - + -
21H LEU* 4.2 9.4 - - + +
24H VAL* 3.3 41.7 - - + +
25H ALA* 4.2 10.8 - - + -
28H VAL* 4.2 10.8 - - + -
30H HIS* 4.0 31.2 - - + +
197H GLY 3.0 13.8 + - - +
198H PRO* 3.2 7.6 + - + +
200H LEU* 1.3 76.7 - - - +
202H GLN* 1.3 58.2 + - - +
204H PHE* 3.4 9.8 + - + +
205H LYS* 2.8 31.5 + - + +
700P PHE* 4.4 0.2 - - + -
704P HIS* 4.0 27.1 - - + +
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Residues in contact with GLN 202 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198H PRO 3.0 12.3 + - - +
199H ALA 3.5 8.7 - - - +
200H LEU 3.2 0.2 - - - -
201H LEU* 1.3 77.2 - - - +
203H ILE* 1.3 52.9 + - - +
205H LYS* 3.1 22.4 + - - +
206H ASP* 2.6 69.8 + - - +
324H LEU* 3.2 38.3 + - + +
325H TRP* 6.0 1.2 - - + -
703P LEU* 4.4 22.2 - - - +
704P HIS* 4.8 5.9 - - - -
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Residues in contact with ILE 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107H HIS* 3.5 24.0 - - + +
109H ILE* 3.8 13.2 - - + -
146H THR* 4.3 5.2 - - + -
148H VAL* 4.0 20.6 - - + -
199H ALA* 3.1 17.4 + - + +
200H LEU* 3.3 16.1 + - + +
202H GLN* 1.3 77.3 - - - +
204H PHE* 1.3 62.3 + - - +
206H ASP* 3.2 3.3 + - - +
207H GLY 3.0 17.8 + - - -
211H TRP* 3.8 22.1 - - + +
216H ILE* 3.4 30.1 - - + -
218H LEU* 5.9 2.0 - - + -
324H LEU* 3.9 18.6 - - + -
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Residues in contact with PHE 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H LYS* 4.9 10.3 + - - -
8H ILE* 4.4 14.4 - - + -
21H LEU* 4.2 25.6 - - + -
30H HIS* 5.7 3.8 - + + -
76H LEU* 3.7 41.0 - - + +
77H ALA 3.4 24.5 - - - -
78H PHE* 4.4 2.2 - - + -
107H HIS* 3.6 32.4 + - + -
109H ILE* 3.3 31.4 - - + -
200H LEU* 3.0 26.3 + - + +
201H LEU* 3.8 10.8 - - + +
203H ILE* 1.3 76.7 - - - +
205H LYS* 1.3 62.4 + - - +
207H GLY* 3.1 13.9 + - - -
208H PRO* 5.4 0.3 - - - +
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Residues in contact with LYS 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5H LYS* 3.9 21.6 - - - +
201H LEU 2.8 17.3 + - - +
202H GLN* 3.3 22.2 - - - +
204H PHE* 1.3 79.1 - - - +
206H ASP* 1.3 63.1 + - - +
207H GLY* 3.4 0.5 + - - -
703P LEU* 4.0 20.5 + - - -
704P HIS* 4.0 27.9 + - + +
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Residues in contact with ASP 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202H GLN* 2.6 42.3 + - - +
203H ILE 3.2 0.4 + - - +
205H LYS* 1.3 75.5 - - - +
207H GLY* 1.3 60.1 + - - +
209H GLN* 4.5 7.4 - - - +
210H LYS* 3.8 18.4 - - + +
211H TRP* 2.9 37.3 + - + +
324H LEU* 3.8 12.1 - - - +
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Residues in contact with GLY 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107H HIS* 3.7 11.0 - - - -
203H ILE 3.0 9.2 + - - -
204H PHE 3.1 13.0 + - - -
205H LYS 4.4 0.4 - - - -
206H ASP* 1.3 78.5 - - - +
208H PRO* 1.3 75.3 - - - +
209H GLN* 3.2 7.6 - - - -
210H LYS* 3.1 4.0 + - - +
211H TRP* 3.1 18.9 + - - -
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Residues in contact with PRO 208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H GLN* 3.4 27.6 - - + +
107H HIS* 3.6 25.1 - - + +
144H PRO* 4.1 16.6 - - + -
207H GLY* 1.3 76.8 - - - +
209H GLN* 1.3 75.7 + - - +
210H LYS 3.0 5.8 - - - -
212H ASN* 2.8 42.9 + - + +
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Residues in contact with GLN 209 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206H ASP 4.6 6.7 - - - +
207H GLY* 3.3 5.9 - - - -
208H PRO* 1.3 100.5 - - + +
210H LYS* 1.3 59.2 + - + +
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Residues in contact with LYS 210 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206H ASP* 3.8 20.2 - - + +
207H GLY 3.1 9.0 + - - +
209H GLN* 1.3 83.2 - - + +
211H TRP* 1.3 108.5 + - + +
212H ASN 3.7 1.1 - - - -
214H HIS* 3.5 22.0 + - - -
320H GLU* 5.1 0.6 + - - -
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Residues in contact with TRP 211 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107H HIS* 4.4 0.9 - - + -
146H THR* 2.6 34.6 + - + +
203H ILE* 3.8 21.8 - - + -
206H ASP* 2.9 42.5 + - + +
207H GLY 3.1 9.1 + - - +
208H PRO* 4.6 0.7 - - - -
210H LYS* 1.3 110.0 - - + +
212H ASN* 1.3 62.8 + - - +
214H HIS* 3.2 32.7 + + - +
216H ILE* 3.7 20.4 - - + -
320H GLU* 3.3 37.9 - - + -
323H LYS* 6.5 2.2 - - + -
324H LEU* 3.5 31.9 - - + +
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Residues in contact with ASN 212 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143H LEU 4.1 1.9 - - - +
144H PRO* 3.5 10.2 - - - +
145H SER* 3.1 29.0 + - - +
146H THR* 4.2 1.1 - - - -
208H PRO* 2.8 34.5 + - + +
209H GLN 4.9 0.2 - - - -
210H LYS 3.7 1.2 - - - -
211H TRP* 1.3 71.8 - - - +
213H GLY* 1.3 65.8 + - - +
214H HIS* 3.0 15.8 + - - -
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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
------------------------------------------------------------
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