Contacts of the helix formed by residues 212 - 223 (chain R) in PDB entry 5VAI
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 HIS 212 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24P ALA* 5.4 3.8 - - + -
27P GLU* 5.3 2.2 - - + -
28P PHE* 3.0 51.9 - + + +
31P TRP* 3.2 41.6 - + + -
32R LEU* 4.7 16.3 - - + +
36R VAL* 5.5 5.4 - - + +
207R THR 4.4 0.2 - - - -
208R ALA* 4.1 29.6 - - + -
211R GLN* 1.3 77.8 - - - +
213R GLN* 1.3 70.1 + - - +
214R TRP 3.1 2.9 - - - -
215R ASP* 3.1 30.1 + - + +
216R GLY* 3.5 5.7 + - - -
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Residues in contact with GLN 213 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28P PHE* 6.0 2.2 - - - -
31P TRP* 4.8 13.7 - - + -
37P GLY 6.0 0.8 - - - -
36R VAL* 4.6 10.0 - - - +
39R TRP* 5.6 5.1 - - - -
40R ARG* 2.5 33.7 + - - +
211R GLN* 2.9 25.7 - - + +
212R HIS* 1.3 81.9 + - - +
214R TRP* 1.3 71.4 + - + +
216R GLY* 4.1 4.7 + - - -
217R LEU* 4.3 6.4 + - - +
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Residues in contact with TRP 214 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207R THR* 6.0 0.4 - - - +
211R GLN* 4.8 11.8 + - + +
212R HIS 3.1 0.4 - - - -
213R GLN* 1.3 90.2 - - + +
215R ASP* 1.3 52.8 + - - +
216R GLY 3.1 2.7 - - - -
217R LEU* 2.8 39.6 + - + +
218R LEU* 2.3 61.8 + - + -
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Residues in contact with ASP 215 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24P ALA* 5.7 1.7 - - - +
32R LEU* 4.3 13.0 - - + +
203R TRP* 5.8 2.1 - - - -
204R MET* 3.2 37.2 - - - +
207R THR* 3.4 30.8 + - + +
208R ALA* 4.9 1.6 + - - +
211R GLN 4.9 1.0 + - - -
212R HIS* 3.1 22.0 + - + +
214R TRP* 1.3 78.8 - - - +
216R GLY* 1.3 56.7 + - - +
218R LEU* 3.9 12.7 - - - +
219R SER* 2.7 30.3 + - - -
222R ASP* 4.8 3.8 - - - +
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Residues in contact with GLY 216 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32R LEU* 4.0 17.5 - - - +
33R SER* 6.3 2.2 - - - -
36R VAL* 5.8 4.9 - - - -
212R HIS 3.5 8.2 + - - -
213R GLN 4.1 2.8 + - - -
214R TRP 3.1 0.8 - - - -
215R ASP* 1.3 78.6 - - - +
217R LEU* 1.3 57.4 + - - +
219R SER* 3.2 8.6 - - - -
220R TYR* 2.9 22.5 + - - +
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Residues in contact with LEU 217 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213R GLN 4.3 4.8 + - - +
214R TRP* 2.8 49.0 + - + +
216R GLY* 1.3 67.8 - - - +
218R LEU* 1.3 61.4 + - + +
219R SER 2.9 1.6 - - - -
220R TYR* 2.4 45.0 + - + +
221R GLN* 2.9 22.5 + - + +
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Residues in contact with LEU 218 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203R TRP* 4.5 23.8 - - + +
207R THR* 5.1 7.9 - - - +
214R TRP* 2.3 61.6 + - + +
215R ASP* 3.9 9.4 - - - +
217R LEU* 1.3 71.1 - - + +
219R SER* 1.3 56.0 + - - +
221R GLN* 3.5 25.1 + - - +
222R ASP* 2.8 35.3 + - - +
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Residues in contact with SER 219 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32R LEU* 5.8 2.0 - - - -
204R MET* 5.0 6.8 - - - +
215R ASP* 2.7 26.8 + - - -
216R GLY* 3.2 10.8 - - - -
217R LEU 2.9 0.4 - - - -
218R LEU* 1.3 74.2 - - - +
220R TYR* 1.3 52.8 + - - +
222R ASP* 3.1 14.7 + - - +
223R SER* 2.6 31.0 + - - -
226R CYS* 4.9 0.5 - - - -
295R GLY* 5.3 5.2 - - - -
296R CYS* 4.3 15.7 + - - -
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Residues in contact with TYR 220 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216R GLY 2.9 9.0 + - - +
217R LEU* 2.4 44.6 + - + +
219R SER* 1.3 66.7 - - - +
221R GLN* 1.3 65.6 + - + -
223R SER* 2.9 36.2 + - - -
224R LEU* 3.4 20.5 + - + +
289R TYR* 5.8 0.4 - - - -
293R ASP* 5.7 1.6 - - - -
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Residues in contact with GLN 221 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217R LEU* 2.9 21.4 + - + +
218R LEU* 3.7 27.6 - - - +
220R TYR* 1.3 82.6 - - + +
222R ASP* 1.3 53.8 + - - +
224R LEU* 3.0 10.7 + - - +
225R GLY* 2.4 32.3 + - - -
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Residues in contact with ASP 222 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203R TRP* 5.5 6.6 - - - -
204R MET* 5.5 2.9 - - - +
215R ASP* 4.8 4.0 - - - +
218R LEU* 2.8 29.1 + - - +
219R SER* 3.1 21.5 + - - +
221R GLN* 1.3 74.4 - - - +
223R SER* 1.3 51.3 + - - +
224R LEU 2.9 7.2 + - - -
225R GLY* 4.8 1.7 - - - -
226R CYS* 2.4 54.7 + - + +
227R ARG 2.7 15.9 + - - -
296R CYS* 3.9 4.0 - - - -
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Residues in contact with SER 223 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219R SER 2.6 16.4 + - - -
220R TYR* 2.9 30.3 + - - -
222R ASP* 1.3 72.1 - - - +
224R LEU* 1.3 58.8 + - - +
226R CYS* 4.2 3.6 - - - -
227R ARG* 3.4 9.1 - - - +
289R TYR* 2.4 58.8 + - - -
293R ASP* 2.8 17.7 + - - -
295R GLY* 5.6 7.9 - - - -
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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