Contacts of the helix formed by residues 195 - 207 (chain B) in PDB entry 1VE3
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 GLY 195 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142B PHE* 4.5 0.9 - - - -
144B ASP* 5.5 3.4 - - - -
174B ARG* 4.7 4.4 - - - +
194B TRP* 1.3 76.8 - - - +
196B LYS* 1.3 66.4 + - - -
197B THR* 3.1 3.8 - - - -
198B GLY* 2.9 15.0 + - - +
199B VAL* 3.0 15.8 + - - +
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Residues in contact with LYS 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B PHE* 4.5 10.3 - - + -
144B ASP* 5.7 2.2 + - - -
194B TRP 4.3 0.2 + - - -
195B GLY* 1.3 69.4 - - - +
197B THR* 1.3 65.0 + - - +
199B VAL* 3.5 6.0 + - - +
200B GLU* 2.4 60.8 + - + +
209B LYS* 3.9 3.0 - - - +
212B GLU* 2.6 27.9 + - - -
218B TYR 5.7 1.1 - - - +
220B TYR* 3.3 56.5 - - + +
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Residues in contact with THR 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B GLY* 3.1 1.2 - - - -
196B LYS* 1.3 78.8 - - - +
198B GLY* 1.3 61.1 + - - +
200B GLU* 3.5 7.2 + - - +
201B LEU* 3.0 31.6 + - + +
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Residues in contact with GLY 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B ARG* 4.7 10.3 - - - -
194B TRP* 4.1 13.2 - - - -
195B GLY* 2.9 9.4 + - - -
197B THR* 1.3 80.4 - - - +
199B VAL* 1.3 64.5 + - - +
201B LEU* 3.2 20.4 + - - +
202B LEU* 3.3 16.8 + - - +
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Residues in contact with VAL 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ILE* 3.6 24.2 - - + -
121B LEU* 4.7 2.2 - - + -
125B PHE* 3.9 10.5 - - + -
140B MSE 3.8 33.9 - - + -
142B PHE* 3.7 18.2 - - + -
194B TRP* 3.7 19.7 - - + -
195B GLY 3.0 15.0 + - - +
196B LYS* 3.8 4.5 - - - +
198B GLY* 1.3 77.1 - - - +
200B GLU* 1.3 60.5 + - + +
202B LEU* 3.3 2.6 + - - +
203B ALA* 2.9 29.0 + - + +
224B TYR* 5.4 2.7 - - + +
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Residues in contact with GLU 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B LYS* 2.4 59.1 + - + +
197B THR* 3.8 7.2 - - - +
199B VAL* 1.3 77.5 - - + +
201B LEU* 1.3 66.9 + - - +
204B LYS* 2.8 52.8 + - - +
209B LYS* 3.5 21.2 + - + -
212B GLU* 3.5 2.8 - - - +
222B THR* 5.5 3.3 + - + +
224B TYR* 3.3 25.1 - - - +
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Residues in contact with LEU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B THR* 3.0 19.6 + - + +
198B GLY* 3.4 14.4 - - - +
200B GLU* 1.3 78.3 - - - +
202B LEU* 1.3 75.0 + - + +
204B LYS* 3.7 8.9 + - - +
205B LEU* 3.6 23.5 + - + +
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Residues in contact with LEU 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B PRO* 3.9 22.4 - - + +
121B LEU* 4.7 5.4 - - + -
122B ASN* 4.4 16.8 - - + +
125B PHE* 3.9 11.9 - - + -
194B TRP* 3.6 32.5 - - + -
198B GLY 3.3 8.5 + - - +
199B VAL 3.9 5.2 - - - +
200B GLU 3.2 0.4 - - - -
201B LEU* 1.3 87.2 - - + +
203B ALA* 1.3 69.2 + - - +
205B LEU* 3.2 36.4 + - + +
206B TYR* 3.5 10.2 - - - -
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Residues in contact with ALA 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B PHE* 3.6 21.7 - - + -
138B PHE* 5.6 0.4 - - + -
199B VAL* 2.9 19.4 + - + +
200B GLU 3.7 1.3 - - - +
202B LEU* 1.3 77.3 - - - +
204B LYS* 1.3 56.8 + - - +
205B LEU 3.0 3.6 + - - -
206B TYR* 3.0 3.8 + - - +
207B PHE* 2.9 36.0 + - + -
224B TYR* 3.5 39.7 - - + +
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Residues in contact with LYS 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B GLU* 2.8 46.7 + - + +
201B LEU* 4.1 6.3 - - - +
202B LEU 3.3 0.4 - - - -
203B ALA* 1.3 72.3 - - - +
205B LEU* 1.3 60.1 + - - +
206B TYR 3.2 0.7 - - - -
207B PHE 3.4 15.3 - - - +
208B THR* 5.7 0.2 - - - -
209B LYS* 4.2 27.6 - - - +
224B TYR* 4.6 9.4 - - + -
227B LYS* 3.0 22.3 + - - -
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Residues in contact with LEU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ASN* 4.2 2.2 - - - +
201B LEU* 3.6 20.0 - - + +
202B LEU* 3.4 36.8 - - + +
203B ALA 3.0 1.2 + - - -
204B LYS* 1.3 80.3 - - - +
206B TYR* 1.3 89.7 + - + +
227B LYS* 3.8 12.7 + - - +
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Residues in contact with TYR 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ASN* 2.7 37.8 + - - -
125B PHE* 3.9 21.5 - + + -
126B LYS* 3.3 34.7 - - + +
129B ARG* 3.3 44.1 + - + +
202B LEU 3.5 15.0 - - - -
203B ALA 3.0 1.7 + - - -
205B LEU* 1.3 105.5 - - + +
207B PHE* 1.3 75.1 + - + +
226B PRO* 3.8 0.7 - - - +
227B LYS* 3.7 19.7 + - - +
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Residues in contact with PHE 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B PHE* 3.5 39.3 - + + -
128B VAL* 3.7 7.2 - - + -
129B ARG* 3.6 25.1 - - + -
132B LEU* 4.2 5.4 - - + -
138B PHE* 3.7 36.1 - + + -
203B ALA* 2.9 22.2 + - + +
204B LYS* 3.4 27.1 - - - +
205B LEU 3.8 0.2 - - - -
206B TYR* 1.3 90.4 - - + +
208B THR* 1.3 64.3 + - - +
224B TYR* 3.6 28.0 - - + -
225B ASN 3.1 10.5 - - - +
226B PRO* 3.8 16.6 - - + -
227B LYS* 3.9 7.1 + - - -
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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