Contacts of the helix formed by residues 208 - 219 (chain A) in PDB entry 2XVF
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 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A SER* 5.7 1.0 + - - -
67A TYR* 4.4 15.8 + - - -
186A ALA* 4.7 7.9 - - - -
206A SER* 3.0 2.4 + - - -
207A TYR* 1.3 88.1 - - - +
209A ALA* 1.3 58.6 + - - +
210A GLU 3.5 2.0 - - - -
211A ASP* 3.9 7.2 - - - +
212A ILE* 2.8 56.5 + - - +
271A CYS* 4.8 1.3 - - - +
274A TYR* 5.5 5.7 + - - -
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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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202A LEU* 4.6 10.3 - - + +
204A GLY 3.3 26.0 - - - +
205A SER* 3.8 7.4 - - - -
206A SER 3.1 16.1 + - - +
208A SER* 1.3 78.2 - - - +
210A GLU* 1.3 64.4 + - - +
212A ILE* 4.1 1.2 - - - +
213A GLY* 3.3 16.8 + - - -
241A TRP* 5.1 1.4 - - - -
271A CYS* 3.6 26.0 - - + +
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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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206A SER 4.8 0.6 + - - -
207A TYR 5.1 1.9 + - - +
208A SER 3.5 0.4 - - - -
209A ALA* 1.3 78.2 - - - +
211A ASP* 1.3 62.4 + - - +
213A GLY 3.6 0.3 + - - -
214A SER* 3.3 22.4 + - - -
235A TYR* 5.7 4.0 - - + -
237A TRP* 4.5 22.9 - - + -
241A TRP* 3.8 8.5 - - - -
404A LYS* 5.4 9.0 - - - +
408A ILE* 5.2 12.1 - - + +
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Residues in contact with ASP 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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67A TYR* 2.4 29.0 + - - +
70A LEU* 4.5 7.8 - - - +
71A TRP 4.7 2.6 + - - +
73A ASN* 5.8 8.0 + - - +
207A TYR 5.4 1.7 + - - +
208A SER* 3.4 9.4 + - - +
209A ALA 3.3 0.4 - - - -
210A GLU* 1.3 76.9 - - - +
212A ILE* 1.3 67.3 + - - +
214A SER* 3.0 14.4 + - - -
215A GLN* 2.8 33.0 + - - +
412A ARG* 3.1 29.3 + - - +
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Residues in contact with ILE 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TYR* 3.8 22.7 - - + -
186A ALA* 3.4 43.3 - - + +
189A PHE* 4.1 23.3 - - + -
202A LEU* 3.9 17.9 - - + -
208A SER* 2.8 31.9 + - - +
209A ALA 4.1 2.0 - - - +
211A ASP* 1.3 70.9 - - - +
213A GLY* 1.3 64.9 + - - +
215A GLN* 3.2 10.1 + - - +
216A CYS* 3.2 21.6 + - - -
269A ILE* 4.1 18.6 - - + -
271A CYS* 4.3 4.5 - - - -
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Residues in contact with GLY 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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202A LEU* 3.6 22.4 - - - +
209A ALA 3.3 8.5 + - - -
210A GLU 3.9 0.2 - - - -
212A ILE* 1.3 80.3 - - - +
214A SER* 1.3 55.6 + - - +
216A CYS* 3.3 3.6 + - - +
217A TYR 3.0 23.2 + - - -
224A LEU* 3.1 12.4 - - - +
241A TRP* 3.3 22.4 - - - -
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Residues in contact with SER 214 (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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210A GLU 3.3 14.7 + - - -
211A ASP* 3.0 23.6 + - - -
213A GLY* 1.3 72.8 - - - +
215A GLN* 1.3 59.9 + - - +
217A TYR* 3.8 4.2 - - - +
218A LYS* 3.0 30.0 + - - +
241A TRP* 3.4 7.1 - - - -
408A ILE* 5.6 2.2 - - - -
409A MSE 3.7 28.9 - - - -
411A PHE* 6.1 0.2 - - - -
412A ARG* 4.3 4.9 + - - -
432A TRP* 3.3 16.8 - - - -
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Residues in contact with GLN 215 (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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67A TYR* 3.8 22.8 - - + -
68A ARG 5.0 1.3 - - - +
69A TYR* 3.5 38.5 + - + +
70A LEU* 4.4 2.4 - - - +
71A TRP 4.7 2.6 - - - +
189A PHE* 4.6 6.1 - - + -
192A ALA* 3.7 13.7 - - + -
211A ASP* 2.8 40.4 + - - +
212A ILE* 3.2 7.2 + - - +
214A SER* 1.3 75.4 - - - +
216A CYS* 1.3 65.7 + - - +
218A LYS* 3.4 1.5 + - - +
219A TYR* 3.0 40.2 + - - +
412A ARG* 4.6 2.0 - - - +
432A TRP* 4.0 21.2 - - - +
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Residues in contact with CYS 216 (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* 3.9 27.1 - - - -
192A ALA* 4.0 9.8 - - - +
195A PHE* 4.2 18.4 - - + -
200A VAL* 4.6 5.4 - - + -
202A LEU* 5.5 0.2 - - - -
212A ILE* 3.2 15.2 + - - -
213A GLY* 3.6 8.1 - - - +
215A GLN* 1.3 78.0 - - - +
217A TYR* 1.3 59.9 + - - +
219A TYR 3.3 1.9 + - - -
220A GLY 3.2 6.8 + - - -
221A ALA* 2.9 32.9 + - + +
224A LEU* 3.8 17.3 - - + -
269A ILE* 4.4 12.6 - - - -
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Residues in contact with TYR 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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213A GLY 3.0 16.1 + - - +
214A SER* 3.8 6.5 - - - +
215A GLN 3.3 0.2 - - - -
216A CYS* 1.3 75.6 - - - +
218A LYS* 1.3 65.1 + - + +
220A GLY* 3.2 12.8 + - - -
221A ALA* 4.1 7.5 + - - +
224A LEU* 3.6 17.8 - - + +
238A PRO* 3.7 31.4 - - + +
240A ASN* 3.4 34.3 - - - +
241A TRP* 4.4 2.2 - + + -
409A MSE 3.9 28.9 - - + +
432A TRP* 5.1 0.4 - + - -
433A ILE* 3.8 24.3 - - + +
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Residues in contact with LYS 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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69A TYR 5.3 1.8 + - - -
71A TRP* 4.4 6.7 - - - +
214A SER 3.0 19.2 + - - +
215A GLN* 3.8 5.0 + - - +
217A TYR* 1.3 78.3 - - - +
219A TYR* 1.3 86.1 + - + +
220A GLY 3.2 2.6 + - - -
432A TRP* 2.9 64.7 + - + +
433A ILE* 3.6 37.5 - - + +
435A ALA 2.9 27.2 + - - -
436A LEU* 3.9 14.2 - - + +
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Residues in contact with TYR 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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69A TYR* 3.2 52.9 - + + +
71A TRP* 6.0 0.2 + - - -
192A ALA* 3.9 22.7 - - + +
193A LEU* 4.0 26.7 - - + +
196A LYS* 3.8 19.6 - - - +
215A GLN* 3.0 31.4 + - - +
216A CYS 3.3 3.1 + - - +
218A LYS* 1.3 104.7 + - + +
220A GLY* 1.3 59.1 + - - +
221A ALA 3.8 0.2 - - - -
435A ALA 4.0 1.4 + - - -
436A LEU* 2.7 54.4 + - + -
437A ASP 5.3 0.2 - - - -
438A ASP* 5.6 0.2 - - - -
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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