Contacts of the helix formed by residues 216 - 228 (chain A) in PDB entry 3VON
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 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A GLU* 5.3 3.5 - - - +
203A PHE* 4.5 1.8 - - - -
214A GLU 5.2 0.2 - - - +
215A SER* 1.3 73.9 - - - +
217A HIS* 1.3 79.0 + - + +
218A ILE* 3.1 29.1 - - - +
219A HIS* 2.9 36.7 + - - +
220A ILE* 3.3 15.5 + - - +
266A TYR* 4.0 4.0 - - - -
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Residues in contact with HIS 217 (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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193A PHE* 5.2 5.4 - + + -
195A GLU* 6.0 2.5 - - - -
216A ASP* 1.3 88.4 - - + +
218A ILE* 1.3 86.2 + - + +
220A ILE* 3.7 13.3 - - - +
221A ILE* 2.9 38.1 + - + +
235A TYR* 5.4 2.9 + - - +
249A PHE* 4.2 23.6 - - + -
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Residues in contact with ILE 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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183A LEU* 3.8 22.1 - - + +
190A PHE* 4.6 12.5 - - + -
193A PHE* 4.0 25.6 - - + +
194A ILE* 3.8 22.9 - - + -
195A GLU* 4.4 8.5 - - - +
203A PHE* 3.8 22.2 - - + -
216A ASP* 2.9 26.4 + - - +
217A HIS* 1.3 91.8 - - + +
219A HIS* 1.3 65.2 + - + +
221A ILE* 4.5 4.3 - - - +
222A ALA* 3.2 22.7 + - - +
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Residues in contact with HIS 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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92A PHE* 4.2 4.3 - - + -
93A TYR* 3.3 26.0 + - + +
179A THR* 3.5 14.0 - - + +
183A LEU* 5.4 0.7 - - - -
203A PHE* 3.7 20.1 - + - -
207A GLU* 3.1 33.7 - - + +
208A VAL* 4.2 7.8 - - + +
213A LYS 4.7 0.9 - - - -
214A GLU 3.2 19.6 + - - -
215A SER* 3.3 20.0 + - - -
216A ASP* 2.9 35.3 + - - +
218A ILE* 1.3 79.1 - - - +
220A ILE* 1.3 57.0 + - - +
222A ALA 3.4 0.3 + - - -
223A LEU* 3.1 28.8 + - - +
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Residues in contact with ILE 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE* 3.5 39.5 - - + -
215A SER* 5.3 0.2 - - - -
216A ASP 3.5 17.9 - - - +
217A HIS* 3.3 9.1 + - - +
219A HIS* 1.3 73.8 - - + +
221A ILE* 1.3 66.3 + - - +
222A ALA 3.1 1.1 - - - -
223A LEU* 4.4 0.3 - - - +
224A ALA* 3.1 26.9 + - - +
231A ILE* 4.1 13.7 - - + +
233A VAL* 4.1 23.1 - - + -
235A TYR* 4.7 5.2 - - + +
249A PHE* 3.6 30.7 - - + -
266A TYR* 3.6 25.4 - - + +
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Residues in contact with ILE 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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189A PHE* 5.6 1.8 - - + -
190A PHE* 3.7 32.1 - - + -
217A HIS* 2.9 22.4 + - + +
218A ILE* 4.5 3.4 - - - +
220A ILE* 1.3 75.6 - - - +
222A ALA* 1.3 63.1 + - - +
224A ALA* 3.7 3.0 - - - +
225A GLN* 3.2 39.4 + - + +
249A PHE* 3.7 39.9 - - + +
250A PRO* 4.6 12.3 - - + -
251A GLU* 5.5 3.8 - - + +
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Residues in contact with ALA 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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179A THR* 3.6 20.4 - - + +
182A TYR* 3.3 24.5 - - + -
183A LEU* 3.7 21.3 - - + -
190A PHE* 4.8 0.9 - - + -
218A ILE 3.2 18.7 + - - +
219A HIS 3.4 4.9 + - - +
220A ILE 3.1 1.0 - - - -
221A ILE* 1.3 79.1 - - - +
223A LEU* 1.3 66.0 + - - +
226A ALA* 3.1 19.9 + - - +
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Residues in contact with LEU 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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92A PHE* 3.7 24.5 - - + -
93A TYR* 4.2 13.2 - - + -
96A PHE* 3.5 36.7 - - + -
175A LEU* 3.8 29.2 - - + +
178A LEU* 4.2 10.5 - - + -
179A THR* 3.6 13.8 - - - +
219A HIS 3.1 11.6 + - - +
220A ILE 4.4 1.6 - - - +
222A ALA* 1.3 76.1 - - - +
224A ALA* 1.3 67.6 + - - +
226A ALA* 3.3 5.3 + - + +
227A LEU* 3.2 41.8 + - + +
231A ILE* 5.2 0.2 - - + -
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Residues in contact with ALA 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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96A PHE* 5.7 0.7 - - - -
220A ILE 3.1 20.9 + - - +
221A ILE* 3.7 4.7 - - - +
223A LEU* 1.3 77.9 - - - +
225A GLN* 1.3 57.1 + - - +
228A SER* 2.9 24.3 + - - -
229A VAL* 2.9 31.6 + - - +
231A ILE* 4.2 11.1 - - + +
249A PHE* 3.9 20.4 - - + +
250A PRO* 4.4 9.9 - - + -
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Residues in contact with GLN 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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182A TYR* 3.5 35.6 + - + +
189A PHE* 5.2 6.9 - - - -
190A PHE* 5.2 2.1 - - - -
221A ILE* 3.2 34.4 + - + +
224A ALA* 1.3 77.0 - - - +
226A ALA* 1.3 63.8 + - - +
228A SER* 3.6 14.1 + - - +
250A PRO* 4.0 30.6 - - + +
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Residues in contact with ALA 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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117A VAL* 3.9 13.5 - - - +
178A LEU* 4.1 25.7 - - + +
182A TYR* 3.9 26.6 - - + -
185A ARG* 4.8 6.4 + - - +
222A ALA 3.1 17.1 + - - +
223A LEU* 3.6 7.4 - - - +
224A ALA 3.3 0.2 - - - -
225A GLN* 1.3 79.5 - - - +
227A LEU* 1.3 61.2 + - + +
228A SER* 3.3 3.0 + - - -
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Residues in contact with LEU 227 (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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96A PHE* 3.7 30.1 - - + -
113A ARG* 3.3 19.5 + - - -
114A PHE* 3.8 26.4 - - + -
117A VAL* 4.3 19.4 - - + +
118A SER* 3.9 15.9 - - - +
142A PHE* 5.0 0.9 - - + -
175A LEU* 4.2 10.5 - - + -
178A LEU* 4.1 23.3 - - + -
223A LEU* 3.2 26.1 + - + +
226A ALA* 1.3 79.4 - - + +
228A SER* 1.3 70.7 + - - +
229A VAL* 3.4 15.8 - - + +
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Residues in contact with SER 228 (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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110A GLU* 4.7 3.6 - - - +
113A ARG* 3.8 22.5 + - - -
117A VAL* 5.5 2.1 - - - +
224A ALA 2.9 9.4 + - - -
225A GLN* 3.6 12.6 + - - +
226A ALA 3.3 4.3 + - - -
227A LEU* 1.3 81.4 - - - +
229A VAL* 1.3 59.2 + - - +
230A SER 4.1 1.3 + - - -
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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