Contacts of the helix formed by residues 218 - 228 (chain B) in PDB entry 2VN9
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 218 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216B ASP* 3.0 19.5 + - - +
217B GLU* 1.3 75.9 - - - +
219B GLN* 1.3 61.0 + - - +
220B HIS* 3.2 21.3 + - - +
221B ARG* 3.2 25.9 + - - +
222B LEU 2.9 23.7 + - - -
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Residues in contact with GLN 219 (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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178B PRO* 3.8 21.8 - - - +
216B ASP 4.8 0.9 - - - -
217B GLU 3.3 7.3 + - - +
218B ASP* 1.3 73.6 + - - +
220B HIS* 1.3 62.4 + - - +
222B LEU* 3.5 10.2 - - + +
223B TYR* 3.1 59.6 + - + -
303B ALA* 3.7 28.6 + - + +
304B ILE* 4.4 3.3 + - - +
308B MET* 5.5 3.6 - - - +
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Residues in contact with HIS 220 (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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218B ASP* 3.1 15.4 + - - +
219B GLN* 1.3 77.6 - - - +
221B ARG* 1.3 60.8 + - + +
223B TYR* 3.1 14.6 + + - +
224B GLN* 3.0 26.6 + - - +
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Residues in contact with ARG 221 (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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216B ASP* 3.1 37.6 + - - +
218B ASP* 3.2 29.4 + - + +
220B HIS* 1.3 75.6 - - + +
222B LEU* 1.3 64.6 + - - +
224B GLN* 3.9 8.7 - - - +
225B GLN* 3.2 28.8 + - - +
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Residues in contact with LEU 222 (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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178B PRO* 3.9 30.1 - - + +
179B GLY* 4.2 1.3 - - - +
214B PHE* 3.3 40.6 - - + +
215B TRP* 3.7 0.9 - - - +
216B ASP* 3.7 21.5 - - - +
218B ASP 2.9 13.6 + - - +
219B GLN* 3.5 14.1 - - - +
221B ARG* 1.3 77.4 - - - +
223B TYR* 1.3 66.5 + - + +
225B GLN* 3.5 5.9 - - - +
226B ILE* 3.2 29.5 + - + +
304B ILE* 3.7 32.3 - - + -
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Residues in contact with TYR 223 (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 PHE* 4.0 20.2 - + - -
178B PRO* 3.7 30.7 - - + +
181B LEU* 4.1 4.7 - - + +
186B LEU* 3.4 40.8 - - + +
219B GLN* 3.1 48.5 + - + -
220B HIS* 3.1 16.4 + + - +
222B LEU* 1.3 78.9 - - + +
224B GLN* 1.3 59.1 + - - +
226B ILE* 3.2 6.3 + - + +
227B LYS* 2.9 46.1 + - - +
308B MET* 4.1 5.0 - - - -
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Residues in contact with GLN 224 (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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220B HIS 3.0 15.6 + - - +
221B ARG* 4.0 9.6 - - - +
222B LEU 3.4 0.2 - - - -
223B TYR* 1.3 72.1 - - - +
225B GLN* 1.3 64.1 + - - +
227B LYS* 4.0 12.0 - - - +
228B ALA* 3.0 27.2 + - - +
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Residues in contact with GLN 225 (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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213B PRO 4.0 2.6 - - - +
214B PHE* 3.5 15.8 - - + -
215B TRP 3.0 44.4 + - - -
216B ASP* 3.7 17.8 + - - +
221B ARG* 3.2 14.8 + - - +
222B LEU* 3.5 9.6 - - - +
224B GLN* 1.3 76.6 - - - +
226B ILE* 1.3 56.3 + - - +
228B ALA* 3.5 1.3 + - - -
229B GLY* 3.0 6.8 + - - -
230B ALA* 2.9 53.9 + - + +
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Residues in contact with ILE 226 (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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178B PRO 3.4 25.6 - - - +
179B GLY 4.5 5.8 - - - +
181B LEU 3.2 24.9 - - - +
183B PRO* 3.6 26.3 - - + +
186B LEU* 3.3 23.3 - - + -
198B TRP* 4.0 6.7 - - + -
214B PHE* 3.7 31.4 - - + -
222B LEU* 3.2 24.8 + - + +
223B TYR* 3.2 9.9 + - + +
225B GLN* 1.3 76.0 - - - +
227B LYS* 1.3 60.4 + - - +
229B GLY* 2.9 19.9 + - - -
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Residues in contact with LYS 227 (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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183B PRO* 4.2 16.1 - - + +
186B LEU* 3.8 35.0 + - + -
187B ARG* 4.3 21.9 + - + +
223B TYR* 2.9 37.5 + - - +
224B GLN* 4.1 7.7 - - - +
226B ILE* 1.3 74.9 - - - +
228B ALA* 1.3 56.0 + - - +
255B ILE* 3.4 23.4 - - - +
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Residues in contact with ALA 228 (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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224B GLN 3.0 20.4 + - - +
225B GLN* 3.9 2.9 - - - +
227B LYS* 1.3 74.9 - - - +
229B GLY* 1.3 65.2 + - - +
230B ALA* 3.2 12.2 + - + +
255B ILE* 3.5 12.3 - - - +
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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