Contacts of the helix formed by residues 218 - 230 (chain A) in PDB entry 3VLN
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 SER 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A LEU 4.1 1.2 + - - -
217A THR* 1.3 77.9 - - - +
219A GLU* 1.3 64.5 + - - +
220A LYS* 3.4 30.4 - - - +
221A ASP* 3.3 33.7 + - - +
222A TRP* 3.1 20.8 + - - +
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Residues in contact with GLU 219 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A GLU* 4.8 10.6 - - + +
186A ALA* 3.8 26.2 - - + +
188A LYS* 3.2 25.4 + - - -
217A THR 3.8 1.8 + - - -
218A SER* 1.3 71.8 - - - +
220A LYS* 1.3 65.8 + - - +
222A TRP* 3.2 5.9 + - - +
223A GLN* 2.9 55.3 + - + +
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Residues in contact with LYS 220 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A SER* 3.4 30.4 - - - +
219A GLU* 1.3 86.6 - - - +
221A ASP* 1.3 64.5 + - - +
223A GLN* 3.8 7.2 - - - +
224A GLY* 3.0 24.3 + - - -
239A TYR* 4.3 5.7 + - - -
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Residues in contact with ASP 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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31A PHE* 3.7 10.2 - - + -
217A THR* 3.7 16.4 - - + +
218A SER* 3.3 21.5 + - - +
220A LYS* 1.3 80.6 - - - +
222A TRP* 1.3 65.5 + - - +
224A GLY 3.3 0.7 + - - -
225A PHE* 3.1 21.3 + - - +
239A TYR* 3.6 26.6 - - + -
240A GLY* 5.5 3.6 - - - -
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Residues in contact with TRP 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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31A PHE* 4.1 19.9 + + + -
127A VAL* 5.9 0.4 - - + -
131A ILE* 4.4 12.1 - - + -
183A ARG* 3.6 44.9 - - + +
186A ALA* 3.3 36.3 - - + -
187A MET* 3.8 26.2 - - + -
217A THR* 4.0 10.0 - - + +
218A SER 3.1 16.2 + - - +
219A GLU* 3.9 4.5 - - - +
221A ASP* 1.3 76.9 - - - +
223A GLN* 1.3 61.7 + - + +
225A PHE* 3.3 24.7 + + - +
226A LEU* 2.9 65.4 + - + +
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Residues in contact with GLN 223 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A ALA* 3.2 28.7 + - + +
188A LYS* 4.1 6.7 - - - +
219A GLU* 2.9 48.6 + - + +
220A LYS* 3.8 7.4 - - - +
222A TRP* 1.3 79.3 - - + +
224A GLY* 1.3 64.8 + - - +
226A LEU* 3.3 8.6 + - + +
227A GLU* 3.1 24.4 + - - +
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Residues in contact with GLY 224 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A LYS 3.0 11.8 + - - -
221A ASP 3.8 0.2 - - - -
223A GLN* 1.3 74.4 - - - +
225A PHE* 1.3 67.3 + - - +
227A GLU* 3.6 4.6 + - - +
228A LEU* 3.4 19.2 + - - +
239A TYR* 3.6 41.2 - - - -
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Residues in contact with PHE 225 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A MET* 3.6 30.1 - - + -
31A PHE* 3.3 48.2 - + + -
221A ASP 3.1 13.1 + - - +
222A TRP* 3.4 24.7 - + - +
224A GLY* 1.3 77.0 - - - +
226A LEU* 1.3 69.2 + - + +
228A LEU* 3.2 5.6 + - - +
229A TYR* 2.8 72.4 + + + +
236A ALA* 3.4 18.2 - - + -
237A CYS* 4.4 0.4 - - - -
239A TYR* 3.8 9.4 - - - -
908A ACT 5.4 1.1 - - - -
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Residues in contact with LEU 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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131A ILE* 3.8 35.9 - - + -
186A ALA 5.8 0.9 - - - +
187A MET* 5.5 1.8 - - + -
222A TRP* 2.9 59.0 + - + +
223A GLN* 3.8 8.1 - - + +
224A GLY 3.3 0.4 - - - -
225A PHE* 1.3 88.9 - - + +
227A GLU* 1.3 64.2 + - - +
229A TYR* 3.1 7.8 + - + +
230A LEU* 2.9 44.8 + - + +
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Residues in contact with GLU 227 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A GLN 3.1 16.1 + - - +
224A GLY* 4.0 4.8 - - - +
225A PHE 3.3 0.2 - - - -
226A LEU* 1.3 77.7 - - - +
228A LEU* 1.3 81.5 + - - +
230A LEU* 3.8 8.9 + - - +
231A GLN* 2.8 44.2 + - - +
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Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A GLY 3.4 4.0 + - - +
225A PHE 3.2 4.8 + - - +
227A GLU* 1.3 93.2 + - - +
229A TYR* 1.3 66.6 + - - +
231A GLN* 3.1 13.4 + - - +
233A SER* 3.0 41.8 + - - +
235A GLU* 3.9 27.8 - - + +
236A ALA* 3.6 18.4 - - + -
239A TYR* 3.9 27.4 - - + -
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Residues in contact with TYR 229 (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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29A MET* 4.4 3.4 - - + -
56A LEU* 3.8 23.8 + - + +
57A LYS* 3.6 36.4 + - + -
131A ILE* 6.4 1.1 - - + -
225A PHE* 2.8 54.5 + + + +
226A LEU* 3.1 11.6 + - + +
228A LEU* 1.3 78.4 - - - +
230A LEU* 1.3 61.5 + - + +
231A GLN 3.1 0.2 - - - -
232A ASN* 2.9 24.9 + - - +
233A SER 4.8 0.9 - - - +
236A ALA* 3.5 11.6 - - + +
237A CYS* 4.4 11.9 - - - -
908A ACT 4.3 11.9 + - + +
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Residues in contact with LEU 230 (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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131A ILE* 3.2 42.4 - - + +
132A ARG* 5.6 2.2 - - + -
226A LEU* 2.9 42.2 + - + +
227A GLU* 4.0 8.5 - - - +
229A TYR* 1.3 79.6 - - + +
231A GLN* 1.3 62.5 + - + +
232A ASN* 3.4 5.3 + - - +
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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