Contacts of the helix formed by residues 192 - 205 (chain A) in PDB entry 1UOU
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 VAL 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A LEU 3.5 24.5 - - - +
96A ALA 5.0 0.8 + - - -
99A GLY* 4.3 5.1 - - - -
100A GLN 5.4 0.4 + - - -
143A ILE* 5.1 2.9 - - + -
187A GLN* 3.7 8.1 - - + +
190A GLN 4.2 0.4 - - - -
191A LEU* 1.3 74.3 - - + +
193A PRO* 1.3 70.2 - - - +
194A ALA 3.2 2.0 - - - -
195A ASP* 3.1 33.8 + - + +
196A GLY 3.3 7.3 + - - -
220A SER* 3.7 20.9 - - - +
221A LYS* 4.2 13.5 - - + +
224A VAL* 4.0 35.4 - - + -
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Residues in contact with PRO 193 (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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62A VAL* 4.9 11.4 - - + -
98A SER* 3.1 39.7 - - - +
99A GLY* 3.8 3.8 - - - +
187A GLN* 5.1 0.4 - - + -
188A SER 3.2 24.5 - - - +
189A GLU* 3.6 16.4 - - - +
191A LEU 3.0 4.9 - - - -
192A VAL* 1.3 91.4 - - - +
194A ALA* 1.3 59.8 + - - +
196A GLY* 3.1 12.1 + - - +
197A ILE* 3.1 24.4 + - + +
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Residues in contact with ALA 194 (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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58A VAL* 3.9 9.9 - - + +
61A VAL* 4.6 10.1 - - + -
62A VAL* 3.8 21.0 - - + +
95A LEU* 3.7 21.5 - - + -
98A SER* 3.3 18.0 + - - +
192A VAL 3.2 0.8 - - - -
193A PRO* 1.3 78.1 - - - +
195A ASP* 1.3 59.4 + - - +
197A ILE* 3.5 2.8 + - - +
198A LEU* 3.1 34.5 + - + +
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Residues in contact with ASP 195 (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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95A LEU* 4.2 12.7 - - + +
187A GLN* 2.8 27.2 + - - -
192A VAL* 3.1 31.0 + - + +
194A ALA* 1.3 76.4 - - - +
196A GLY* 1.3 59.5 + - - +
198A LEU* 4.6 4.4 - - - +
199A TYR* 2.7 37.3 + - - +
202A ARG* 4.7 1.0 + - - -
217A SER* 2.4 38.6 + - - -
220A SER* 4.2 3.6 - - - +
221A LYS* 3.0 18.1 + - - +
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Residues in contact with GLY 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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187A GLN* 3.4 30.2 - - - +
192A VAL 3.3 5.1 + - - -
193A PRO 3.1 8.4 + - - -
195A ASP* 1.3 80.9 + - - +
197A ILE* 1.3 61.2 + - - +
199A TYR* 3.7 2.9 - - - +
200A ALA* 3.2 23.2 + - - +
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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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61A VAL* 3.8 42.6 - - + +
62A VAL* 4.5 10.1 - - - +
71A ILE* 4.4 15.9 - - + -
193A PRO* 3.1 23.0 + - + +
194A ALA* 3.5 0.9 + - - +
195A ASP 3.3 0.2 - - - -
196A GLY* 1.3 74.8 - - - +
198A LEU* 1.3 64.4 + - - +
200A ALA* 3.3 6.6 + - - +
201A ALA* 3.1 22.2 + - + +
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Residues in contact with LEU 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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57A PHE* 4.6 13.2 - - + -
58A VAL* 5.5 1.6 - - + -
61A VAL* 3.4 34.1 - - + -
71A ILE* 5.1 6.7 - - + -
75A LEU* 4.3 20.6 - - + -
91A LEU* 4.7 9.6 - - + -
95A LEU* 4.0 29.4 - - + -
194A ALA* 3.1 27.1 + - + +
195A ASP* 4.2 4.7 - - - +
197A ILE* 1.3 76.3 - - - +
199A TYR* 1.3 55.9 + - - +
201A ALA* 3.3 6.4 + - - +
202A ARG* 2.9 43.7 + - - +
213A LEU* 5.1 7.6 - - + -
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Residues in contact with TYR 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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145A GLY* 3.5 12.3 + - - -
146A ARG* 2.5 52.1 + - + -
147A GLY 4.0 3.1 - - - -
148A LEU* 3.4 37.6 - - + +
187A GLN* 4.1 7.2 - - - -
195A ASP* 2.7 29.5 + - - +
196A GLY* 3.7 7.0 - - - +
198A LEU* 1.3 74.0 - - - +
200A ALA* 1.3 67.0 + - - +
202A ARG* 3.5 12.1 + - - +
203A ASP* 3.3 17.9 + - + +
217A SER* 3.8 17.0 - - - -
221A LYS* 4.4 1.1 - - - -
1481A CMU 3.5 44.0 + + - -
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Residues in contact with ALA 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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196A GLY 3.2 14.7 + - - +
197A ILE* 3.3 5.8 + - - +
199A TYR* 1.3 83.2 - - - +
201A ALA* 1.3 60.5 + - - +
203A ASP* 3.5 17.7 - - - +
204A VAL* 4.0 12.0 + - - +
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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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71A ILE* 4.1 14.8 - - + -
72A GLY* 5.7 1.6 - - - +
75A LEU* 3.7 16.8 - - + -
197A ILE* 3.1 17.2 + - + +
198A LEU 3.7 4.5 - - - +
199A TYR 3.2 0.2 - - - -
200A ALA* 1.3 74.9 - - - +
202A ARG* 1.3 58.3 + - - +
203A ASP 3.2 1.8 - - - -
204A VAL* 3.3 11.1 + - - +
205A THR* 2.7 35.2 + - + +
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Residues in contact with ARG 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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75A LEU* 3.8 15.3 - - + -
148A LEU* 4.3 10.3 - - + +
195A ASP* 4.7 0.8 + - - -
198A LEU* 2.9 32.4 + - - +
199A TYR* 3.8 14.2 - - - +
201A ALA* 1.3 74.8 - - - +
203A ASP* 1.3 64.5 + - - +
204A VAL 3.1 1.0 + - - -
205A THR* 3.3 8.9 + - - -
206A ALA 3.6 8.0 + - - -
207A THR* 3.1 37.9 + - - +
208A VAL* 3.1 44.1 + - + +
213A LEU* 3.6 22.8 + - - +
214A ILE* 3.6 12.9 - - - +
217A SER* 3.6 19.6 + - - -
1481A CMU 3.0 31.3 + - - -
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Residues in contact with ASP 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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147A GLY 3.9 16.8 - - - +
148A LEU* 3.7 11.6 - - + +
149A GLY* 3.0 31.1 + - - +
199A TYR* 3.3 10.9 + - + +
200A ALA* 3.5 16.1 - - - +
201A ALA 3.2 0.2 - - - -
202A ARG* 1.3 80.2 - - - +
204A VAL* 1.3 66.2 + - + +
205A THR 4.0 0.2 + - - -
206A ALA 4.9 1.2 + - - -
208A VAL* 4.0 5.1 - - - +
402A HIS* 5.1 7.7 - - - -
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Residues in contact with VAL 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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200A ALA 4.1 12.8 - - - +
201A ALA* 3.5 14.1 - - - +
202A ARG 3.1 0.2 - - - -
203A ASP* 1.3 93.1 - - - +
205A THR* 1.3 63.4 + - + +
206A ALA 3.7 1.5 + - - -
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Residues in contact with THR 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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72A GLY* 4.7 20.0 - - - -
75A LEU* 4.4 3.6 - - - +
76A MET* 3.7 9.5 - - - +
201A ALA* 2.7 27.0 + - + +
202A ARG* 3.3 1.3 + - - -
204A VAL* 1.3 90.4 - - + +
206A ALA* 1.3 70.4 + - - +
207A THR* 3.1 28.0 + - - +
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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