Contacts of the helix formed by residues 198 - 211 (chain A) in PDB entry 1VPE
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 VAL 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A GLY 4.8 0.2 - - - +
196A ALA 2.7 22.8 + - - +
197A LYS* 1.3 66.9 - - - +
199A SER* 1.3 57.9 + - - +
200A ASP 2.7 15.7 + - - -
201A LYS* 2.9 13.3 + - - -
202A ILE* 3.2 20.4 + - + +
220A ALA 4.5 3.6 - - - +
221A MET* 4.0 43.7 - - + +
224A THR* 4.0 20.0 - - + +
237A ARG* 4.0 18.7 - - - +
239A GLU* 3.7 24.2 - - + -
242A LYS* 5.0 2.9 - - + -
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Residues in contact with SER 199 (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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197A LYS 3.7 0.4 - - - -
198A VAL* 1.3 76.7 - - - +
200A ASP* 1.3 67.2 + - - +
202A ILE* 4.2 5.7 - - - +
203A GLY 5.1 0.9 + - - -
237A ARG* 5.4 0.2 - - - +
239A GLU* 3.1 31.1 + - - +
241A ASP* 6.0 0.7 - - - +
242A LYS* 4.0 33.4 + - - +
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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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62A ARG* 3.2 30.3 + - - -
151A ARG* 4.1 10.3 + - - +
197A LYS* 3.5 37.7 + - + +
198A VAL 2.7 5.9 + - - -
199A SER* 1.3 84.3 + - - +
201A LYS* 1.3 60.3 + - + +
203A GLY* 4.4 4.1 + - - -
204A VAL* 4.7 7.6 - - - +
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Residues in contact with LYS 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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193A LEU* 4.8 9.4 - - + +
194A GLY 3.6 21.9 + - - +
197A LYS* 3.3 19.7 - - + +
198A VAL 2.9 3.2 + - - -
200A ASP* 1.3 78.6 - - + +
202A ILE* 1.3 63.4 + - - +
203A GLY 3.0 3.6 - - - -
204A VAL* 2.9 32.3 + - + +
205A ILE* 3.9 3.0 + - - +
221A MET* 3.6 18.4 - - + -
317A ASN* 2.7 36.0 + - - +
318A GLY* 4.4 0.4 - - - -
377A GLY* 6.5 0.7 - - - -
380A LEU* 4.5 15.3 - - + -
400A ANP 3.1 50.3 + - - +
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Residues in contact with ILE 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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198A VAL* 3.2 20.1 + - + +
199A SER 4.2 7.9 - - - +
201A LYS* 1.3 76.6 - - - +
203A GLY* 1.3 63.8 + - - +
205A ILE* 3.2 22.1 + - - +
206A THR 4.4 0.2 + - - -
221A MET* 3.6 11.0 - - + +
224A THR* 4.7 6.1 - - + -
225A PHE* 4.2 17.7 - - + -
242A LYS* 3.8 49.1 - - + +
245A LEU* 4.0 15.9 - - + -
246A ALA* 4.1 22.2 - - + +
249A LEU* 3.6 20.1 - - + +
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Residues in contact with GLY 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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199A SER 5.1 0.6 + - - -
200A ASP 4.4 4.8 + - - -
201A LYS 3.0 1.8 + - - -
202A ILE* 1.3 85.5 - - - +
204A VAL* 1.3 62.4 + - - +
205A ILE 3.3 0.5 + - - -
206A THR* 3.5 23.6 - - - +
207A ASN* 3.9 5.1 + - - -
245A LEU* 4.9 7.9 - - - -
249A LEU* 5.7 0.2 - - - -
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Residues in contact with VAL 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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193A LEU* 4.8 3.6 - - + -
200A ASP 4.7 7.6 - - - +
201A LYS* 2.9 26.7 + - - +
203A GLY* 1.3 76.5 - - - +
205A ILE* 1.3 58.2 + - + +
206A THR 3.3 0.2 - - - -
207A ASN* 3.1 4.7 + - - +
208A LEU* 2.7 58.4 + - + +
377A GLY 5.7 0.2 - - - +
380A LEU* 4.0 35.9 - - + +
381A GLU* 4.5 13.5 - - + +
384A GLU* 3.5 22.7 - - - +
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Residues in contact with ILE 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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193A LEU* 3.7 31.2 - - + -
201A LYS 4.2 4.5 - - - +
202A ILE* 3.4 20.4 - - - +
203A GLY 3.1 0.6 - - - -
204A VAL* 1.3 77.4 - - - +
206A THR* 1.3 57.9 + - - +
208A LEU* 4.2 5.8 - - + -
209A MET* 2.8 55.1 + - + +
215A ILE* 4.2 17.0 - - + -
217A ILE* 4.1 9.0 - - + -
221A MET* 4.8 2.5 - - - -
225A PHE* 3.6 33.0 - - + -
249A LEU* 3.9 9.2 - - + -
260A ILE* 4.5 7.9 - - + -
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Residues in contact with THR 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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202A ILE 4.4 0.6 + - - -
203A GLY* 3.5 16.9 + - - +
205A ILE* 1.3 79.8 - - - +
207A ASN* 1.3 77.1 + - - +
209A MET* 3.5 15.4 - - - +
210A GLU* 3.8 14.2 - - - +
245A LEU* 6.3 0.7 - - - -
249A LEU* 4.0 23.6 - - - +
252A LYS* 3.1 30.6 + - - +
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Residues in contact with ASN 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 GLY 3.9 6.9 + - - -
204A VAL* 3.1 2.9 + - - +
206A THR* 1.3 91.3 - - - +
208A LEU* 1.3 64.8 + - - +
209A MET 3.0 1.1 - - - -
210A GLU* 2.9 28.9 + - - +
211A LYS* 4.1 3.8 + - - +
384A GLU* 3.3 45.9 + - + -
386A LYS* 3.7 18.9 + - - +
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Residues in contact with LEU 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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189A TYR* 4.2 14.8 - - + +
191A VAL* 3.9 39.0 - - + -
193A LEU* 4.5 5.6 - - + -
204A VAL* 2.7 51.0 + - + +
205A ILE* 3.8 7.2 - - - +
207A ASN* 1.3 72.6 - - - +
209A MET* 1.3 57.1 + - - +
210A GLU 3.0 5.2 + - - -
211A LYS* 3.1 10.5 + - + +
212A ALA* 3.0 27.2 + - - +
215A ILE* 4.6 10.1 - - + -
380A LEU* 4.3 13.7 - - + +
383A LEU* 4.6 19.3 - - + -
384A GLU* 5.4 4.7 - - + -
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Residues in contact with MET 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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205A ILE* 2.8 39.2 + - + +
206A THR* 3.5 10.3 - - - +
207A ASN 3.0 0.2 - - - -
208A LEU* 1.3 76.4 - - - +
210A GLU* 1.3 62.5 + - - +
211A LYS 3.5 0.4 + - - -
212A ALA 4.2 3.0 - - - +
215A ILE* 4.5 10.3 - - + +
249A LEU* 3.4 38.6 - - + +
252A LYS* 4.0 19.7 - - + +
253A ALA* 3.6 27.8 - - + -
256A LYS* 5.1 9.7 - - + +
258A VAL* 3.3 46.5 - - + +
260A ILE* 4.2 2.2 - - + -
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Residues in contact with GLU 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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187A LYS* 5.3 1.9 + - - -
206A THR 3.8 14.4 - - - +
207A ASN* 2.9 21.7 + - - +
209A MET* 1.3 81.9 - - - +
211A LYS* 1.3 58.6 + - + +
252A LYS* 4.5 7.4 + - - -
256A LYS* 4.0 27.3 - - - +
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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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181A VAL 3.2 22.1 + - - -
182A THR* 3.6 20.1 + - - +
185A PRO* 4.0 11.9 - - + -
187A LYS* 3.0 31.9 + - - +
189A TYR* 3.3 43.7 + - + +
207A ASN 4.7 4.5 - - - +
208A LEU* 3.1 12.5 + - + +
210A GLU* 1.3 81.2 - - + +
212A ALA* 1.3 60.6 + - - +
383A LEU* 3.3 32.0 + - + +
384A GLU* 5.2 4.0 - - - -
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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