Contacts of the helix formed by residues 209 - 223 (chain A) in PDB entry 2VGZ
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 THR 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A SER* 4.0 26.0 + - - +
207A SER 3.8 2.2 + - - +
208A LEU* 1.3 77.2 - - - +
210A SER* 1.3 63.3 + - - +
211A GLU* 3.7 15.8 + - - +
212A ARG* 3.4 26.9 + - - +
213A LYS* 3.0 21.5 + - - +
243A VAL* 4.0 6.3 - - - -
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Residues in contact with SER 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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209A THR* 1.3 73.7 - - - +
211A GLU* 1.3 84.6 + - - +
213A LYS* 3.3 7.6 + - - +
214A LYS* 2.9 42.1 + - - +
243A VAL* 3.6 11.1 - - - +
244A PRO* 3.9 32.3 - - - -
249A MET* 4.7 2.4 - - - +
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Residues in contact with GLU 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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209A THR* 3.7 14.5 - - - +
210A SER* 1.3 98.6 + - - +
212A ARG* 1.3 66.6 + - + +
214A LYS* 3.4 26.1 + - - +
215A GLU* 3.2 25.0 + - - +
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Residues in contact with ARG 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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162A ASP* 2.7 42.7 + - - -
164A SER* 3.5 26.5 + - - -
165A GLY 3.0 17.8 + - - -
166A ILE 3.3 15.4 + - - -
167A VAL* 3.7 9.2 - - - +
168A PRO* 3.9 26.3 - - + +
208A LEU* 3.7 13.7 - - + -
209A THR* 3.4 17.4 + - - +
210A SER 3.4 0.4 - - - -
211A GLU* 1.3 75.1 - - + +
213A LYS* 1.3 67.8 + - - +
215A GLU* 3.1 6.2 + - - +
216A ILE* 2.8 28.8 + - - +
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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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198A PRO* 3.6 31.1 - - - +
199A ASN* 4.4 12.5 + - - +
208A LEU* 4.0 14.8 + - + -
209A THR 3.0 14.4 + - - +
210A SER* 3.5 9.0 - - - +
212A ARG* 1.3 75.7 - - - +
214A LYS* 1.3 56.9 + - - +
216A ILE* 3.1 0.8 + - - +
217A TYR* 2.8 27.5 + - - +
229A GLU* 4.3 6.5 + - - -
243A VAL* 3.6 24.1 + - + +
244A PRO 2.7 33.5 + - - +
245A THR* 3.9 13.3 - - - +
246A PHE* 3.5 29.1 - - + +
249A MET* 3.8 14.4 - - + -
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Residues in contact with LYS 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 SER* 2.9 29.9 + - - +
211A GLU* 3.5 38.4 + - - +
212A ARG 3.3 0.2 - - - -
213A LYS* 1.3 71.6 - - - +
215A GLU* 1.3 61.9 + - - +
217A TYR* 3.4 3.1 + - - +
218A GLU* 3.1 26.0 + - - +
249A MET* 3.9 19.5 - - + -
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Residues in contact with GLU 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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168A PRO* 3.6 28.2 - - + +
169A ASP* 4.1 4.5 - - - +
172A ARG* 3.5 36.4 + - - +
211A GLU* 3.2 13.1 + - - +
212A ARG* 3.1 11.7 + - - +
214A LYS* 1.3 75.3 - - - +
216A ILE* 1.3 65.4 + - - +
218A GLU* 3.3 6.6 + - - +
219A LEU* 3.1 27.9 + - - +
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Residues in contact with ILE 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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166A ILE* 3.9 24.0 - - + +
168A PRO* 4.2 11.4 - - + -
171A LEU* 4.0 17.0 - - + -
194A LEU* 3.5 30.3 - - + -
208A LEU* 3.8 34.1 - - + -
212A ARG* 2.8 23.6 + - + +
213A LYS* 3.7 3.6 - - - +
215A GLU* 1.3 77.2 - - - +
217A TYR* 1.3 58.9 + - - +
219A LEU* 3.2 8.8 + - - +
220A ALA* 2.9 26.6 + - + +
225A PHE* 4.9 0.6 - - + -
227A ILE* 4.8 5.2 - - + -
246A PHE* 3.9 15.9 - - + -
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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 LYS 2.8 17.1 + - - +
214A LYS* 3.7 5.2 - - - +
216A ILE* 1.3 79.0 - - - +
218A GLU* 1.3 66.6 + - - +
220A ALA* 3.1 4.0 + - - +
221A ARG* 2.9 33.4 + - + +
227A ILE* 3.6 21.1 - - + -
246A PHE* 4.3 5.4 - + + -
249A MET* 3.5 39.3 - - + -
250A ASP* 2.5 37.7 + - - -
251A VAL* 3.1 4.3 + - + -
252A ASP* 2.9 37.2 + - - +
254A ARG* 3.7 16.1 - - + +
255A VAL* 3.9 8.5 - - + -
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Residues in contact with GLU 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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214A LYS 3.1 18.4 + - - +
215A GLU* 3.7 7.0 - - - +
216A ILE 3.2 0.2 - - - -
217A TYR* 1.3 85.1 - - - +
219A LEU* 1.3 56.6 + - - +
221A ARG* 3.3 35.5 + - - +
222A LYS* 2.9 28.3 + - - +
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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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168A PRO* 3.7 26.0 - - + +
171A LEU* 3.8 20.4 - - + -
172A ARG* 3.8 49.8 - - + +
175A LEU* 4.1 9.0 - - + -
215A GLU 3.1 16.3 + - - +
216A ILE* 3.4 10.3 - - - +
218A GLU* 1.3 73.5 - - - +
220A ALA* 1.3 64.3 + - - +
222A LYS* 3.2 10.0 + - + -
223A TYR* 3.0 51.8 + - + +
225A PHE* 3.9 3.0 - - + -
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Residues in contact with ALA 220 (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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216A ILE 2.9 14.1 + - - +
217A TYR 3.3 9.2 - - - +
219A LEU* 1.3 73.1 - - - +
221A ARG* 1.3 57.5 + - - +
224A ASP* 2.8 23.0 + - - -
225A PHE* 3.1 44.2 + - + +
227A ILE* 3.7 21.5 - - + -
254A ARG* 3.5 15.4 + - - -
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Residues in contact with ARG 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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217A TYR* 2.9 18.9 + - + +
218A GLU* 3.4 37.0 + - - +
219A LEU 3.1 0.2 - - - -
220A ALA* 1.3 75.4 - - - +
222A LYS* 1.3 66.6 + - - +
224A ASP* 3.4 12.6 + - - +
251A VAL* 3.8 25.5 - - - +
252A ASP* 2.8 40.9 + - - +
254A ARG* 3.9 15.0 + - - +
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Residues in contact with LYS 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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180A PRO* 3.6 42.5 - - + +
218A GLU 2.9 17.0 + - - +
219A LEU* 3.2 14.1 + - + +
221A ARG* 1.3 80.4 - - - +
223A TYR* 1.3 87.5 + - + +
224A ASP* 3.8 1.2 + - - +
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Residues in contact with TYR 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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5A ARG* 4.5 0.9 + - - -
172A ARG* 4.8 4.1 + - + +
175A LEU* 3.2 57.2 + - + +
176A SER* 4.1 8.1 + - - -
178A TRP* 3.3 24.8 + - + -
179A LYS 4.6 0.7 - - - -
180A PRO* 4.1 23.1 - - + +
183A ALA* 3.5 13.0 - - - +
190A THR* 5.0 6.1 + - + -
191A PRO* 5.1 5.2 - - + +
219A LEU* 3.0 30.7 + - + +
220A ALA 3.8 0.2 - - - -
222A LYS* 1.3 110.6 + - + +
224A ASP* 1.3 70.7 + - - +
225A PHE* 3.4 20.2 + - + +
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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