Contacts of the helix formed by residues 208 - 226 (chain A) in PDB entry 3URZ
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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202A VAL* 5.0 6.7 - - - +
203A ILE* 3.7 8.1 - - - +
206A PHE 4.5 2.5 - - - -
207A PRO* 1.3 78.5 - - - +
209A THR* 1.3 60.6 + - - +
210A GLU* 3.5 10.7 + - - +
211A ALA* 3.4 27.1 + - - +
212A GLN* 3.0 32.8 + - - +
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Residues in contact with THR 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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208A SER* 1.3 73.1 + - - +
210A GLU* 1.3 58.7 + - - +
212A GLN* 4.4 3.5 - - - +
213A LYS* 3.0 38.6 + - + +
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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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149A ASN* 5.6 12.4 + - - +
199A LEU* 5.6 0.5 - - - +
208A SER* 3.3 9.3 + - - +
209A THR* 1.3 79.6 - - - +
211A ALA* 1.3 57.9 + - - +
213A LYS* 3.5 24.7 + - - +
214A THR* 3.1 23.8 + - - +
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Residues in contact with ALA 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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199A LEU* 4.5 23.1 - - + +
202A VAL* 4.4 12.6 - - + -
203A ILE* 3.3 29.2 - - + -
208A SER* 3.4 13.3 + - - +
209A THR 3.3 0.4 - - - -
210A GLU* 1.3 77.7 - - - +
212A GLN* 1.3 63.5 + - - +
214A THR* 3.3 6.6 + - - -
215A LEU* 3.2 26.0 + - - +
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Residues in contact with GLN 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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203A ILE* 3.2 31.9 - - + +
208A SER 3.0 18.6 + - - +
209A THR* 4.4 3.8 - - - +
211A ALA* 1.3 76.6 - - - +
213A LYS* 1.3 62.9 + - - +
215A LEU* 3.4 13.1 + - - +
216A ASP* 3.3 25.6 + - - +
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Residues in contact with LYS 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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209A THR* 3.0 31.5 + - + +
210A GLU* 3.5 27.1 + - - +
212A GLN* 1.3 76.5 - - - +
214A THR* 1.3 71.7 + - - +
216A ASP* 2.9 29.1 - - - +
217A LYS* 3.4 40.8 - - - +
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Residues in contact with THR 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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149A ASN* 5.0 7.3 + - - +
152A TYR* 3.7 39.4 - - + -
199A LEU* 3.5 27.1 - - + -
210A GLU* 3.1 16.1 + - - +
211A ALA* 3.3 9.3 + - - -
212A GLN 3.3 0.4 - - - -
213A LYS* 1.3 85.3 - - - +
215A LEU* 1.3 59.8 + - - +
217A LYS* 3.2 12.7 + - - +
218A ILE* 3.0 27.5 + - + +
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Residues in contact with LEU 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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196A ARG* 3.8 35.9 - - + +
199A LEU* 3.7 29.8 - - + +
200A GLN* 4.4 11.7 - - + +
203A ILE* 3.3 35.4 - - + -
211A ALA 3.2 16.3 + - - +
212A GLN* 3.4 19.7 + - - +
214A THR* 1.3 76.6 - - - +
216A ASP* 1.3 56.9 + - - +
218A ILE* 3.5 6.3 + - + +
219A LEU* 3.0 26.7 + - - +
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Residues in contact with ASP 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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212A GLN* 3.3 16.2 + - - +
213A LYS* 2.9 27.4 - - - +
215A LEU* 1.3 75.7 - - - +
217A LYS* 1.3 75.6 + - - +
219A LEU* 3.4 14.0 + - + +
220A ARG* 2.9 36.0 + - - +
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Residues in contact with LYS 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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152A TYR* 3.2 36.4 + - - +
213A LYS* 3.4 46.7 + - - +
214A THR* 3.2 14.1 + - - +
216A ASP* 1.3 82.2 + - - +
218A ILE* 1.3 60.3 + - - +
220A ARG* 3.3 30.7 + - - +
221A ILE* 3.0 36.9 + - + +
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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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152A TYR* 3.7 26.7 - - + -
188A PHE* 3.9 23.2 - - + -
192A TYR* 4.0 15.7 - - + +
195A ALA* 4.2 6.7 - - + -
196A ARG* 4.1 47.6 - - + +
199A LEU* 4.2 16.8 - - + -
214A THR 3.0 19.4 + - - +
215A LEU* 3.7 9.9 - - - +
217A LYS* 1.3 75.3 - - - +
219A LEU* 1.3 57.6 + - - +
221A ILE* 3.5 6.1 + - - +
222A GLU* 3.0 27.5 + - - +
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Residues in contact with LEU 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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196A ARG* 4.9 6.5 - - - +
215A LEU 3.0 18.1 + - - +
216A ASP* 3.5 13.7 - - + +
217A LYS 3.3 0.2 - - - -
218A ILE* 1.3 74.8 - - - +
220A ARG* 1.3 61.9 + - - +
222A GLU* 3.7 22.1 - - - +
223A LYS* 3.5 23.2 + - + +
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Residues in contact with ARG 220 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A ASP* 2.9 24.3 + - - +
217A LYS* 3.4 34.0 - - - +
218A ILE 3.3 0.2 - - - -
219A LEU* 1.3 76.9 - - - +
221A ILE* 1.3 65.5 + - - +
222A GLU 3.4 0.3 + - - -
223A LYS* 3.2 40.1 + - - +
224A GLU* 3.5 24.4 - - - +
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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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152A TYR* 4.8 4.5 - - + +
156A GLU* 3.7 14.8 - - - +
159A LYS* 3.6 33.4 - - + +
188A PHE* 4.7 7.6 - - + -
192A TYR* 3.2 43.7 - - + +
217A LYS* 3.0 23.0 + - + +
218A ILE* 3.9 5.2 - - - +
220A ARG* 1.3 78.2 - - + +
222A GLU* 1.3 61.9 + - - +
224A GLU* 3.6 10.4 + - - +
225A VAL* 3.2 32.0 + - + +
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Residues in contact with GLU 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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188A PHE* 3.5 31.1 - - + -
196A ARG* 2.9 39.4 + - - -
218A ILE 3.0 16.2 + - - +
219A LEU* 3.7 22.9 - - + +
220A ARG 3.3 0.2 - - - -
221A ILE* 1.3 78.6 - - - +
223A LYS* 1.3 57.3 + - - +
224A GLU 3.4 0.2 + - - -
225A VAL* 3.5 2.5 + - - +
226A ASN* 3.1 35.3 + - - +
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Residues in contact with LYS 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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219A LEU* 3.5 11.5 + - + +
220A ARG* 3.2 40.0 + - - +
222A GLU* 1.3 75.8 - - - +
224A GLU* 1.3 73.7 + - + +
226A ASN* 3.0 22.7 - - - +
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Residues in contact with GLU 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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159A LYS* 4.8 12.3 + - - -
181A ARG* 3.7 21.0 + - - -
184A LEU* 6.1 0.2 - - - -
220A ARG* 3.5 35.2 - - - +
221A ILE* 3.6 13.1 + - + +
222A GLU 3.3 0.6 - - - -
223A LYS* 1.3 89.4 + - + +
225A VAL* 1.3 65.7 + - + +
226A ASN* 3.5 6.1 + - - +
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Residues in contact with VAL 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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159A LYS* 5.3 2.7 - - - -
181A ARG* 4.2 13.9 + - - +
184A LEU* 3.5 62.6 - - + +
185A SER* 3.6 11.8 - - - +
188A PHE* 5.2 7.6 - - + -
221A ILE* 3.2 31.4 + - + +
222A GLU* 4.1 3.8 - - - +
224A GLU* 1.3 76.6 - - + +
226A ASN* 1.3 71.9 + - - +
174B LYS* 4.9 9.9 + - - -
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Residues in contact with ASN 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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181A ARG* 3.7 20.2 - - - +
185A SER* 6.2 0.9 - - - -
188A PHE* 6.1 0.9 - - - -
222A GLU* 3.1 23.6 + - - +
223A LYS* 3.0 21.2 - - - +
224A GLU 3.3 4.3 + - - +
225A VAL* 1.3 82.4 + - - +
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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