Contacts of the helix formed by residues 217 - 226 (chain A) in PDB entry 5VLR
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 MET 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A PRO* 2.9 20.2 + - + +
214A LEU* 2.8 33.1 + - + +
216A LEU* 1.4 77.8 - - - +
218A ALA* 1.4 55.0 + - + +
219A CYS 2.8 3.3 + - - -
220A ALA* 2.7 34.4 + - - +
221A LEU* 3.4 4.5 + - - +
237A GLU* 5.9 6.7 - - - -
238A ASP 4.0 8.3 - - - +
239A TYR 3.2 34.1 - - - +
240A THR* 3.8 11.7 - - + -
241A LEU* 4.6 12.1 - - + +
250A LEU 5.1 2.9 - - - +
251A TYR* 5.7 1.8 - - + -
276A MET* 3.7 25.2 - - + +
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Residues in contact with ALA 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A LEU* 3.1 12.9 + - + +
217A MET* 1.4 73.7 - - - +
219A CYS* 1.4 55.3 + - - +
220A ALA 3.4 0.2 - - - -
221A LEU* 3.3 14.6 + - + +
222A ARG* 2.9 49.6 + - - +
237A GLU 5.2 11.9 - - - +
276A MET* 5.3 1.3 - - - +
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Residues in contact with CYS 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A PHE* 4.9 15.9 - - - -
214A LEU 4.2 0.6 + - - -
215A ALA* 3.2 24.1 + - - +
216A LEU* 5.1 2.7 - - - -
217A MET 2.8 5.6 + - - +
218A ALA* 1.4 73.5 - - - +
220A ALA* 1.4 53.1 + - - +
222A ARG* 3.2 14.1 + - - +
223A LYS* 2.8 33.3 + - - +
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Residues in contact with ALA 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A VAL* 3.8 37.2 - - + -
196A PHE* 4.0 12.8 - - + -
203A PHE* 4.5 8.6 - - + -
205A PHE* 5.4 4.0 - - + -
216A LEU 4.1 7.6 + - - +
217A MET 2.7 15.6 + - - +
219A CYS* 1.4 74.6 - - - +
221A LEU* 1.4 57.1 + - - +
222A ARG 3.4 0.2 - - - -
223A LYS* 3.6 11.2 - - - +
224A LYS* 3.2 24.4 + - - +
276A MET* 5.8 0.9 - - + -
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Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A PHE* 4.2 16.9 - - + -
217A MET 3.4 3.5 + - - +
218A ALA* 3.3 20.2 + - + +
219A CYS 3.3 0.2 - - - -
220A ALA* 1.4 76.2 - - - +
222A ARG* 1.4 60.6 + - + +
224A LYS* 3.7 4.8 + - - +
225A ALA* 3.4 21.5 + - - +
276A MET* 4.7 10.5 - - + -
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Residues in contact with ARG 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ALA* 2.9 32.5 + - + +
219A CYS* 3.4 13.0 - - - +
221A LEU* 1.4 75.7 - - + +
223A LYS* 1.4 58.3 + - - +
224A LYS 3.3 0.7 - - - -
225A ALA* 3.7 6.1 + - - +
226A THR* 3.2 30.3 + - - -
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Residues in contact with LYS 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A PHE* 3.3 24.1 - - + -
219A CYS* 2.8 19.8 + - - +
220A ALA* 3.7 13.5 - - - +
221A LEU 3.4 0.2 - - - -
222A ARG* 1.4 74.5 - - - +
224A LYS* 1.3 60.3 + - - +
226A THR* 3.9 14.2 - - - +
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Residues in contact with LYS 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A PHE* 4.7 13.0 - - + -
203A PHE* 3.6 23.6 - - + -
220A ALA 3.2 14.8 + - - +
221A LEU* 3.8 7.4 - - - +
222A ARG 3.3 0.2 - - - -
223A LYS* 1.3 76.3 - - - +
225A ALA* 1.4 64.1 + - - +
226A THR 3.4 8.7 - - - +
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Residues in contact with ALA 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A LEU 3.4 14.5 + - - +
222A ARG* 4.1 7.0 - - - +
224A LYS* 1.4 79.7 - - - +
226A THR* 1.4 57.4 + - - +
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Residues in contact with THR 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A ARG 3.2 17.7 + - - -
223A LYS* 3.9 12.6 - - - +
224A LYS 3.3 12.7 - - - +
225A ALA* 1.4 76.3 - - - +
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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