Contacts of the helix formed by residues 195 - 206 (chain A) in PDB entry 4UC5
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 LEU 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A ASN* 4.0 13.0 - - + -
193A GLY 2.9 7.5 + - - +
194A ASN* 1.3 71.6 - - - +
196A LYS* 1.3 66.7 + - - +
197A ILE 3.3 2.7 - - - -
198A ALA* 3.1 12.6 + - + +
199A ILE* 3.2 27.0 + - + +
233A VAL* 4.5 19.5 - - + -
234A ILE 5.8 0.2 - - - +
235A LEU* 4.1 23.1 - - + -
242A ASN* 6.3 0.4 - - - +
250A GLU* 6.0 0.2 - - + -
251A ALA* 3.6 35.2 - - + -
254A GLN* 3.7 22.9 - - - +
255A LEU* 5.9 0.9 - - + -
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Residues in contact with LYS 196 (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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194A ASN* 2.8 18.7 + - - +
195A LEU* 1.3 74.4 - - - +
197A ILE* 1.3 57.2 + - + +
199A ILE* 3.0 12.0 + - - +
200A ASP* 2.8 43.1 + - - +
254A GLN* 4.8 4.2 + - - +
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Residues in contact with ILE 197 (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 ALA 4.5 4.7 - - - +
169A THR* 3.6 24.2 - - + +
170A GLU* 3.4 44.4 - - + +
175A ARG* 2.8 31.6 + - - +
188A LYS 4.6 0.2 - - - +
189A ASN 4.7 0.2 - - - -
190A GLY* 3.6 29.6 - - - +
194A ASN* 2.8 42.3 + - + +
196A LYS* 1.3 71.9 - - + +
198A ALA* 1.3 60.0 + - - +
200A ASP* 4.4 3.6 - - - +
201A ALA* 2.9 14.4 + - - +
191B THR* 4.9 2.0 - - - +
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Residues in contact with ALA 198 (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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169A THR* 3.7 9.2 - - + -
187A PHE* 4.0 12.3 - - + +
188A LYS 3.8 22.9 - - - +
189A ASN* 4.2 5.8 - - - +
195A LEU* 3.1 11.1 + - + +
196A LYS 3.1 0.6 - - - -
197A ILE* 1.3 77.2 - - - +
199A ILE* 1.3 67.1 + - - +
201A ALA* 3.3 3.0 + - - +
202A ILE* 3.0 28.8 + - - +
233A VAL* 3.9 19.5 - - + -
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Residues in contact with ILE 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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195A LEU* 3.2 28.0 + - + +
196A LYS* 3.0 10.4 + - - +
198A ALA* 1.3 76.9 - - - +
200A ASP* 1.3 66.5 + - - +
202A ILE* 3.4 8.6 + - - +
203A GLY* 3.3 16.6 + - - -
233A VAL* 4.5 4.3 - - + -
254A GLN* 3.5 47.3 - - + +
255A LEU* 3.8 18.4 - - + +
258A ALA* 3.4 32.7 - - + +
260A VAL* 4.4 10.0 - - + +
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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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175A ARG* 3.7 15.7 + - - +
196A LYS* 2.8 33.1 + - - +
197A ILE* 4.4 2.8 - - - +
199A ILE* 1.3 74.8 - - - +
201A ALA* 1.3 60.4 + - - +
203A GLY* 3.1 4.2 + - - -
204A ALA* 2.8 28.9 + - - +
102B THR* 3.7 31.3 + - + +
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Residues in contact with ALA 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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169A THR 3.7 3.4 - - - +
175A ARG* 3.7 23.1 - - + +
187A PHE* 3.6 35.3 - - + -
197A ILE 2.9 20.5 + - - +
198A ALA* 3.3 8.3 + - - +
200A ASP* 1.3 76.4 - - - +
202A ILE* 1.3 56.2 + - - +
204A ALA* 3.4 1.2 + - - +
205A ALA* 2.8 33.6 + - - +
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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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187A PHE* 4.3 8.7 - - + -
198A ALA 3.0 13.9 + - - +
199A ILE* 3.5 7.0 - - - +
200A ASP 3.2 0.2 - - - -
201A ALA* 1.3 72.7 - - - +
203A GLY* 1.3 68.0 + - - +
205A ALA* 3.1 2.1 + - - +
206A SER* 3.0 26.3 + - - -
231A CYS* 4.1 20.1 - - + +
232A HIS* 3.6 31.0 - - - +
233A VAL* 3.3 31.4 - - + -
255A LEU* 4.2 13.2 - - + -
260A VAL* 3.6 26.5 - - + -
261A THR* 4.7 5.2 - - + +
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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 ILE 3.3 6.5 + - - -
200A ASP* 3.1 6.1 + - - -
202A ILE* 1.3 78.8 - - - +
204A ALA* 1.3 60.4 + - - +
206A SER* 2.8 25.0 + - - -
207A HIS* 3.2 17.2 + - - -
260A VAL* 4.2 14.1 - - - +
102B THR* 5.4 0.7 - - - -
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Residues in contact with ALA 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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175A ARG* 4.4 23.8 - - + +
200A ASP 2.8 19.2 + - - +
201A ALA 3.6 4.3 - - - +
203A GLY* 1.3 71.5 - - - +
205A ALA* 1.3 58.0 + - - +
207A HIS* 2.9 21.1 + - - +
209A HIS* 2.9 29.9 + - + +
101B ARG 5.8 0.7 - - - +
102B THR* 3.9 27.0 + - + +
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Residues in contact with ALA 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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175A ARG 3.8 23.1 - - - +
178A ALA* 4.0 7.0 - - + -
179A SER* 3.2 16.4 - - - +
187A PHE* 3.9 21.1 - - + -
201A ALA 2.8 22.7 + - - +
202A ILE 3.1 2.7 + - - +
204A ALA* 1.3 74.1 - - - +
206A SER* 1.3 57.2 + - - +
207A HIS 3.2 0.2 - - - -
228A ASN* 2.9 23.3 + - - +
231A CYS* 4.0 9.0 - - - -
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Residues in contact with SER 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* 3.0 15.3 + - - -
203A GLY* 2.8 20.6 + - - -
205A ALA* 1.3 77.7 - - - +
207A HIS* 1.3 69.1 + - - +
226A GLY 4.5 1.7 - - - +
227A GLY* 3.4 13.1 - - - -
228A ASN 3.6 19.4 + - - +
229A PRO* 4.8 6.2 - - - +
260A VAL* 6.0 0.6 - - - +
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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