Contacts of the helix formed by residues 212 - 227 (chain A) in PDB entry 1UWV
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 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A GLN* 2.9 27.2 + - - -
185A ALA* 5.8 0.6 - - - +
210A PRO 3.8 2.4 + - - -
211A LEU* 1.3 77.1 - - - +
213A SER* 1.3 58.6 + - - +
214A ALA* 3.7 2.2 + - - -
215A ASP* 3.0 24.8 + - - +
216A ARG* 2.8 27.3 + - - +
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Residues in contact with SER 213 (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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212A SER* 1.3 71.0 - - - +
214A ALA* 1.3 61.0 + - - +
216A ARG* 3.8 9.7 - - - +
217A GLU* 2.9 30.9 + - - +
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Residues in contact with ALA 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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184A GLN* 3.8 17.7 - - - +
212A SER* 3.3 1.4 + - - -
213A SER* 1.3 80.5 + - - +
215A ASP* 1.3 63.0 + - - +
217A GLU* 3.3 6.5 + - - +
218A LYS* 3.0 37.9 + - - +
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Residues in contact with ASP 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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183A LEU* 3.4 22.4 - - + +
184A GLN* 2.8 30.7 + - - +
185A ALA* 2.7 37.0 + - - +
211A LEU* 4.5 11.4 - - + -
212A SER* 3.0 27.8 + - - +
214A ALA* 1.3 72.5 - - - +
216A ARG* 1.3 66.0 + - - +
218A LYS* 3.2 11.8 + - - +
219A LEU* 3.0 28.3 + - - +
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Residues in contact with ARG 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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207A HIS* 5.8 2.6 + - - -
211A LEU* 4.6 23.9 + - + +
212A SER 2.8 20.8 + - - +
213A SER* 3.8 9.3 - - - +
215A ASP* 1.3 71.6 - - - +
217A GLU* 1.3 57.9 + - - +
219A LEU* 3.2 11.8 + - + +
220A GLU* 2.8 57.1 + - + +
232A LEU* 3.5 26.1 - - + +
240A GLU* 2.9 39.6 + - - -
242A VAL* 4.4 6.1 - - + +
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Residues in contact with GLU 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 SER 2.9 19.1 + - - +
214A ALA* 3.6 8.0 - - - +
215A ASP 3.2 0.2 - - - -
216A ARG* 1.3 74.3 - - - +
218A LYS* 1.3 70.4 + - - +
220A GLU* 3.3 15.5 + - + +
221A ARG* 2.8 59.5 + - + +
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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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179A CYS* 4.3 4.3 - - - -
182A SER* 3.4 43.5 + - - +
183A LEU* 3.9 14.8 - - + -
184A GLN* 4.5 11.5 - - - +
214A ALA* 3.0 26.0 + - - +
215A ASP* 3.2 20.1 + - - +
217A GLU* 1.3 81.2 + - - +
219A LEU* 1.3 58.5 + - - +
221A ARG* 3.4 4.5 + - - +
222A PHE* 2.9 31.0 + - - +
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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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179A CYS* 4.0 17.5 - - - -
180A LEU* 4.0 19.3 - - + -
183A LEU* 4.1 15.0 - - + -
203A MSE 5.0 8.2 - - + +
205A LEU* 3.8 17.9 - - + -
211A LEU* 3.5 32.1 - - + -
215A ASP 3.0 17.4 + - - +
216A ARG* 3.6 8.3 - - + +
218A LYS* 1.3 76.0 - - - +
220A GLU* 1.3 57.6 + - - +
222A PHE* 3.4 4.8 + - - +
223A SER* 2.9 32.4 + - - -
230A LEU* 3.6 26.2 - - + +
232A LEU* 4.3 7.4 - - + -
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Residues in contact with GLU 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 ARG* 2.8 46.2 + - + +
217A GLU* 3.3 19.6 + - + +
219A LEU* 1.3 76.7 - - - +
221A ARG* 1.3 58.3 + - + +
223A SER* 3.2 6.5 + - - -
224A HIS* 2.9 32.7 + - - +
230A LEU* 4.4 2.9 - - + -
242A VAL* 3.8 27.4 - - + +
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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 GLU* 2.8 48.3 + - + +
218A LYS* 3.9 4.7 - - - +
220A GLU* 1.3 76.4 - - + +
222A PHE* 1.3 57.9 + - - +
224A HIS* 3.8 5.6 - - - +
225A SER* 2.9 36.6 + - - +
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Residues in contact with PHE 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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172A LEU* 4.7 2.0 - - + -
175A LYS* 3.5 44.2 - - + -
176A VAL* 3.8 13.9 - - + -
179A CYS* 3.7 28.3 - - + -
203A MSE 3.8 34.3 - - + -
218A LYS 2.9 18.2 + - - +
219A LEU* 3.7 3.6 - - - +
221A ARG* 1.3 75.1 - - - +
223A SER* 1.3 68.4 + - - +
224A HIS 3.3 0.2 + - - -
225A SER* 3.4 4.8 + - - -
226A GLU* 3.1 44.2 + - + +
228A LEU* 3.9 12.6 - - + -
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Residues in contact with SER 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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203A MSE 3.8 12.1 - - - -
219A LEU 2.9 18.7 + - - -
220A GLU* 3.2 6.1 + - - -
222A PHE* 1.3 80.9 - - - +
224A HIS* 1.3 65.4 + - - +
226A GLU 3.3 0.7 + - - -
227A GLY* 3.0 4.9 + - - -
228A LEU* 3.0 48.7 + - - +
230A LEU* 3.6 27.7 - - - +
242A VAL* 5.6 0.5 - - - +
243A SER* 4.4 4.5 + - - -
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Residues in contact with HIS 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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220A GLU 2.9 21.1 + - - +
221A ARG* 3.8 5.8 - - - +
223A SER* 1.3 80.0 + - - +
225A SER* 1.3 59.7 + - - +
227A GLY* 3.3 10.4 + - - -
228A LEU 5.2 0.9 - - - -
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Residues in contact with SER 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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221A ARG* 2.9 22.5 + - - +
222A PHE* 3.6 7.2 - - - -
224A HIS* 1.3 74.8 - - - +
226A GLU* 1.3 70.6 + - - +
227A GLY 3.4 0.6 + - - -
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Residues in contact with GLU 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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172A LEU* 3.9 9.9 - - + +
175A LYS* 3.4 39.9 + - - +
222A PHE* 3.1 41.0 + - + +
225A SER* 1.3 84.3 - - - +
227A GLY* 1.3 61.1 + - - +
228A LEU* 3.6 26.0 + - + +
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Residues in contact with GLY 227 (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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200A GLY* 5.9 0.5 - - - -
201A THR* 4.6 7.6 + - - +
223A SER 3.0 5.2 + - - -
224A HIS* 3.3 10.4 + - - -
225A SER 3.4 1.2 + - - -
226A GLU* 1.3 77.3 - - - +
228A LEU* 1.3 61.9 + - - +
229A ASP* 4.2 1.6 + - - +
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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