Contacts of the helix formed by residues 199 - 213 (chain A) in PDB entry 2VK2
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 ASN 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A SER* 3.6 8.7 - - - -
170A PHE* 2.9 40.6 + - + +
197A ALA* 3.3 20.0 - - - +
198A HIS* 1.3 78.6 - - - +
200A ASP* 1.3 64.3 + - - +
201A ASP* 3.8 6.9 - - - +
202A MET* 3.0 30.5 + - - +
225A SER* 3.7 5.3 - - - -
226A ILE 3.1 6.7 - - - +
227A ASP* 3.4 16.7 + - - +
1298A GZL 3.0 20.9 + - - +
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Residues in contact with ASP 200 (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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199A ASN* 1.3 73.6 - - - +
201A ASP* 1.3 58.9 + - - +
203A VAL* 3.0 4.6 + - - +
204A ILE* 2.8 31.7 + - + +
225A SER* 2.6 30.3 + - - -
226A ILE 2.8 18.6 + - - +
227A ASP* 3.5 3.8 + - + +
228A GLY* 2.6 28.8 + - - -
229A VAL* 3.0 29.2 + - + -
232A ILE* 3.4 15.6 - - + +
244A SER* 2.8 17.5 + - - -
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Residues in contact with ASP 201 (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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13A GLU 4.2 1.7 - - - +
14A SER* 3.3 12.5 - - - -
15A GLY* 3.0 31.2 + - - -
170A PHE 4.1 3.6 - - - +
172A ARG* 3.3 43.1 + - - +
199A ASN* 3.3 14.7 + - - +
200A ASP* 1.3 74.2 - - - +
202A MET* 1.3 63.9 + - - +
204A ILE* 3.2 9.6 + - - +
205A GLY 3.1 18.0 + - - -
227A ASP* 5.2 0.9 + - - +
229A VAL* 3.9 23.6 - - - +
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Residues in contact with MET 202 (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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134A LEU* 3.2 35.8 - - + +
135A GLN 3.2 25.1 - - - +
168A GLY* 3.4 16.6 - - - +
170A PHE* 3.4 22.9 - - + -
171A THR 3.3 29.6 - - - +
175A GLY* 3.7 10.1 - - - -
197A ALA* 4.1 4.9 - - + -
198A HIS* 3.6 2.5 - - + +
199A ASN* 3.0 40.2 + - - +
201A ASP* 1.3 75.8 - - - +
203A VAL* 1.3 57.2 + - - +
205A GLY* 3.3 3.5 + - - -
206A ALA* 2.9 24.8 + - - +
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Residues in contact with VAL 203 (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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195A VAL* 3.8 34.1 - - + +
197A ALA* 3.6 22.8 - - + +
199A ASN 3.5 2.2 + - - -
200A ASP 3.0 11.4 + - - +
202A MET* 1.3 77.3 - - - +
204A ILE* 1.3 59.4 + - - +
206A ALA* 3.2 5.5 + - - +
207A ILE* 2.8 41.0 + - + +
223A THR* 3.9 15.9 - - - -
224A GLY 4.3 0.4 - - - +
225A SER* 3.5 23.8 - - - +
232A ILE* 3.5 18.2 - - + -
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Residues in contact with ILE 204 (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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172A ARG* 3.5 37.5 - - - +
200A ASP* 2.8 25.3 + - + +
201A ASP* 3.2 8.0 + - - +
203A VAL* 1.3 74.1 - - - +
205A GLY* 1.3 63.3 + - - +
207A ILE* 3.4 14.0 + - + +
208A GLN* 3.3 25.0 + - + +
229A VAL* 4.1 8.3 - - + -
231A ASP* 3.6 33.2 - - + +
232A ILE* 4.0 24.2 - - + +
235A ALA* 5.5 1.8 - - + -
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Residues in contact with GLY 205 (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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172A ARG* 3.4 26.5 - - - +
176A LYS* 3.3 16.4 - - - +
201A ASP 3.1 10.5 + - - -
202A MET 3.7 1.8 - - - -
203A VAL 3.3 0.2 - - - -
204A ILE* 1.3 75.3 - - - +
206A ALA* 1.3 59.8 + - - +
208A GLN* 3.2 20.6 + - - +
209A ALA 3.1 16.6 + - - -
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Residues in contact with ALA 206 (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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134A LEU* 3.8 12.3 - - + -
176A LYS* 4.1 1.0 - - - +
179A MET* 3.6 35.0 - - + -
195A VAL* 4.4 11.7 - - + -
202A MET 2.9 14.7 + - - +
203A VAL* 3.2 12.3 + - - +
205A GLY* 1.3 76.4 - - - +
207A ILE* 1.3 55.4 - - - +
209A ALA* 3.1 3.9 + - - +
210A ILE* 2.8 35.2 + - - +
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Residues in contact with ILE 207 (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 VAL* 2.8 32.4 + - + +
204A ILE* 3.5 15.3 - - + +
205A GLY 3.3 0.2 - - - -
206A ALA* 1.3 71.8 - - - +
208A GLN* 1.3 62.7 + - + +
210A ILE* 3.4 9.0 + - - +
211A LYS* 3.0 30.1 + - - +
217A PRO* 3.8 19.7 - - + +
223A THR* 4.0 13.7 - - + -
232A ILE* 4.7 1.1 - - + -
235A ALA* 4.2 12.6 - - + -
240A GLU* 3.4 39.7 - - + +
241A ALA* 4.0 17.5 - - + -
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Residues in contact with GLN 208 (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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172A ARG* 3.9 20.8 - - - +
176A LYS* 3.3 33.8 + - - +
204A ILE* 3.3 10.5 + - + +
205A GLY* 3.2 25.4 + - - +
207A ILE* 1.3 78.6 - - + +
209A ALA* 1.3 56.2 + - - +
211A LYS* 3.3 13.3 + - - +
212A GLU* 2.9 38.8 + - - +
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Residues in contact with ALA 209 (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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176A LYS* 3.8 16.1 - - + +
179A MET* 3.9 14.6 - - + -
180A GLU* 3.7 31.9 - - + +
183A ILE* 3.5 11.9 - - + +
205A GLY 3.1 6.0 + - - +
206A ALA 3.1 9.0 + - - +
208A GLN* 1.3 78.6 - - - +
210A ILE* 1.3 62.4 + - - +
212A GLU* 3.4 6.5 + - - +
213A ALA* 3.1 18.4 + - - +
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Residues in contact with ILE 210 (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 MET* 3.9 21.8 - - + -
183A ILE* 3.9 7.4 - - + -
195A VAL* 4.3 10.3 - - + -
206A ALA 2.8 25.5 + - - +
207A ILE* 3.7 10.1 - - - +
208A GLN 3.3 0.2 - - - -
209A ALA* 1.3 76.3 - - - +
211A LYS* 1.3 62.5 + - - +
213A ALA* 3.2 9.8 + - - +
215A LEU* 3.1 42.4 + - + +
216A LYS 4.1 1.1 - - - -
217A PRO* 3.7 30.1 - - + -
221A ILE* 3.8 39.0 - - + +
223A THR* 4.9 2.2 - - + -
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Residues in contact with LYS 211 (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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207A ILE* 3.0 29.0 + - - +
208A GLN* 3.7 9.6 - - - +
210A ILE* 1.3 76.0 - - - +
212A GLU* 1.3 58.7 + - + +
214A GLY* 3.0 20.6 + - - -
215A LEU 3.6 8.0 + - - +
217A PRO* 3.5 18.6 - - + -
240A GLU* 2.9 39.9 + - - +
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Residues in contact with GLU 212 (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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176A LYS* 2.9 39.2 + - - -
180A GLU* 3.8 9.8 - - + +
208A GLN* 2.9 20.9 + - - +
209A ALA* 3.8 5.7 - - - +
211A LYS* 1.3 74.9 - - + +
213A ALA* 1.3 57.9 + - - +
214A GLY 3.2 1.3 + - - -
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Residues in contact with ALA 213 (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 ILE* 3.8 30.7 - - + -
188A ASN* 4.6 13.0 - - + +
209A ALA 3.1 16.2 + - - +
210A ILE* 3.6 7.4 - - - +
211A LYS 3.2 0.4 - - - -
212A GLU* 1.3 76.0 - - - +
214A GLY* 1.3 59.0 + - - +
215A LEU* 3.4 7.5 + - + +
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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