Contacts of the helix formed by residues 191 - 203 (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 ARG 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A TYR* 4.3 8.5 + - - -
151A TYR* 3.4 54.7 - - + +
154A THR* 2.9 32.7 + - - +
155A ALA* 3.4 31.6 - - + +
158A GLU* 5.0 5.8 + - - +
187A LEU* 2.9 32.1 + - + +
190A THR* 1.3 82.5 - - + +
192A TYR* 1.3 63.2 + - - +
193A GLU 3.3 1.3 - - - -
194A LYS* 3.3 4.7 + - - +
195A ALA 3.3 14.9 + - - -
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Residues in contact with TYR 192 (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* 3.8 24.0 - + - -
155A ALA* 3.4 29.4 - - + -
156A GLU* 2.9 28.0 + - - -
159A LYS* 3.5 13.3 - - + +
187A LEU* 3.4 21.4 + - + -
188A PHE* 3.1 41.6 + + + +
191A ARG* 1.3 77.6 - - - +
193A GLU* 1.3 56.7 + - - +
195A ALA* 3.0 8.8 + - - +
196A ARG* 2.9 31.0 + - - +
218A ILE* 4.0 27.3 - - + +
221A ILE* 3.2 34.7 - - + +
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Residues in contact with GLU 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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188A PHE* 2.9 15.5 + - + +
189A THR* 3.2 28.7 - - - +
191A ARG 3.3 0.2 - - - -
192A TYR* 1.3 74.9 - - - +
194A LYS* 1.3 59.6 + - + +
196A ARG* 3.6 11.9 + - - +
197A ASN* 3.0 28.6 + - - +
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Residues in contact with LYS 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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151A TYR* 3.9 40.8 + - + +
189A THR 5.4 0.9 - - - +
190A THR* 3.2 32.5 + - - +
191A ARG 3.3 7.7 + - - +
192A TYR 3.3 0.6 - - - -
193A GLU* 1.3 75.7 - - + +
195A ALA* 1.3 64.2 + - - +
197A ASN* 3.8 7.8 - - - +
198A SER* 3.2 27.2 + - - -
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Residues in contact with ALA 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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148A GLY* 3.5 26.8 - - - +
151A TYR* 3.8 8.4 - - + +
152A TYR* 3.6 26.2 - - + +
191A ARG 3.3 6.4 + - - +
192A TYR* 3.0 12.5 + - - +
194A LYS* 1.3 76.3 - - - +
196A ARG* 1.3 57.2 + - - +
198A SER 3.5 1.2 + - - -
199A LEU* 3.1 35.2 + - - +
218A ILE* 4.2 7.2 - - + -
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Residues in contact with ARG 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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188A PHE* 4.5 14.9 - - - -
192A TYR 2.9 14.7 + - - +
193A GLU* 4.1 11.2 + - - +
195A ALA* 1.3 73.0 - - - +
197A ASN* 1.3 61.0 + - - +
199A LEU* 3.9 0.3 - - - +
200A GLN* 3.0 53.7 + - - +
215A LEU* 3.8 22.2 - - + -
218A ILE* 4.1 26.0 - - + +
219A LEU* 4.9 8.1 - - - +
222A GLU* 2.9 39.8 + - - -
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Residues in contact with ASN 197 (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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193A GLU 3.0 18.9 + - - +
194A LYS* 3.8 9.5 + - - +
195A ALA 3.4 0.2 - - - -
196A ARG* 1.3 76.0 - - - +
198A SER* 1.3 61.8 + - - +
200A GLN* 3.8 9.0 + - - +
201A LYS* 3.6 44.2 + - - +
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Residues in contact with SER 198 (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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134A LEU* 5.1 4.0 - - - +
144A ASN* 3.3 45.9 + - - +
147A LEU* 4.2 10.0 - - - +
148A GLY* 3.7 18.6 + - - -
151A TYR* 5.4 0.9 - - - -
194A LYS 3.2 13.9 + - - -
196A ARG 3.3 0.4 - - - -
197A ASN* 1.3 78.9 + - - +
199A LEU* 1.3 63.3 + - - +
201A LYS* 3.4 2.8 + - - +
202A VAL* 3.2 23.7 + - - +
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Residues in contact with LEU 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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144A ASN 4.9 0.7 - - - +
145A ILE* 5.1 2.7 - - - +
148A GLY* 3.9 21.5 - - - +
149A ASN* 4.0 18.4 - - - +
195A ALA* 3.1 25.9 + - + +
196A ARG 3.4 0.6 + - - +
198A SER* 1.3 76.5 - - - +
200A GLN* 1.3 60.4 + - - +
202A VAL* 3.4 15.2 + - + +
203A ILE* 3.4 25.6 + - - +
210A GLU 5.6 0.4 - - - +
211A ALA* 4.5 23.0 - - + +
214A THR* 3.5 34.1 - - + -
215A LEU* 3.7 20.9 - - + +
218A ILE* 4.2 9.4 - - + -
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Residues in contact with GLN 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 ARG* 3.0 48.5 + - + +
197A ASN* 4.2 8.8 - - - +
198A SER 3.3 0.2 - - - -
199A LEU* 1.3 74.8 - - - +
201A LYS* 1.3 63.1 + - + +
203A ILE* 3.6 11.6 + - + +
204A LEU* 3.3 21.2 + - - +
215A LEU* 4.4 14.4 - - + +
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Residues in contact with LYS 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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134A LEU* 6.1 0.2 - - - +
138A ALA* 3.7 38.1 + - - +
139A ASP* 4.3 19.6 - - + +
141A LEU* 4.7 4.4 - - - +
144A ASN* 3.9 19.9 + - - +
197A ASN* 3.6 36.3 + - - +
198A SER 3.4 8.3 + - - +
200A GLN* 1.3 74.3 - - + +
202A VAL* 1.3 64.7 + - - +
204A LEU* 3.3 27.5 - - + +
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Residues in contact with VAL 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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141A LEU* 3.7 24.7 - - + +
144A ASN* 3.8 28.3 - - + +
145A ILE* 3.8 26.2 - - + -
198A SER 3.2 17.0 + - - +
199A LEU* 3.5 16.4 - - + +
200A GLN 3.3 0.4 - - - -
201A LYS* 1.3 78.9 - - - +
203A ILE* 1.3 59.7 + - + +
204A LEU 3.4 3.3 + - - -
205A ARG 4.6 0.3 + - - -
206A PHE* 3.2 17.4 + - - +
208A SER* 5.0 7.0 - - - -
211A ALA* 4.4 17.0 - - + -
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Residues in contact with ILE 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 LEU 3.4 10.3 + - - +
200A GLN* 3.6 9.0 - - + +
201A LYS 3.4 0.2 - - - -
202A VAL* 1.3 75.8 - - - +
204A LEU* 1.3 62.9 + - - +
205A ARG 3.5 2.0 - - - -
206A PHE 3.5 9.7 + - - +
207A PRO* 4.5 5.0 - - + +
208A SER* 3.7 23.8 - - - +
211A ALA* 3.3 28.9 - - + -
212A GLN* 3.2 37.0 - - + +
215A LEU* 3.3 24.2 - - + -
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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