Contacts of the helix formed by residues 173 - 191 (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 THR 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A SER* 5.2 3.5 - - - -
172A PRO* 1.3 75.8 - - - +
174A LYS* 1.3 66.5 + - + +
175A MSE 3.7 20.0 - - + +
176A GLN* 3.2 30.0 + - + +
177A TYR* 3.1 24.4 + - - +
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Residues in contact with LYS 174 (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 PRO 3.9 1.8 + - - -
173A THR* 1.3 73.9 - - + +
175A MSE 1.3 62.1 + - - +
177A TYR* 3.8 13.8 - - + +
178A ALA* 3.1 24.8 + - - +
178B ALA* 4.7 5.8 - - + +
181B ARG* 5.4 18.1 + - - +
182B ASP* 6.1 4.5 - - - +
185B SER* 6.1 2.8 - - - -
225B VAL 5.2 7.1 + - - -
226B ASN* 5.3 9.5 - - - +
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Residues in contact with MSE 175 (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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173A THR* 3.2 13.7 - - + +
174A LYS* 1.3 78.6 - - + +
176A GLN* 1.3 68.2 + - + +
178A ALA* 3.3 4.5 + - - +
179A ARG* 3.2 20.4 + - - +
175B MSE 3.3 38.5 - - + +
178B ALA* 3.8 27.8 - - + -
179B ARG* 4.3 22.0 - - + +
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Residues in contact with GLN 176 (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 TYR* 5.6 1.8 - - - +
171A SER* 5.7 0.3 + - - -
172A PRO* 4.8 7.9 - - + +
173A THR* 3.2 33.4 + - - +
175A MSE 1.3 79.4 - - + +
177A TYR* 1.3 57.7 + - - +
179A ARG* 3.4 9.4 + - - +
180A TYR* 3.0 27.6 + - - +
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Residues in contact with TYR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A TYR* 6.2 1.8 - - + -
172A PRO* 5.8 10.7 - - + +
173A THR 3.1 16.1 + - - +
174A LYS* 3.8 12.3 - - + +
175A MSE 3.3 0.2 - - - -
176A GLN* 1.3 75.3 - - - +
178A ALA* 1.3 64.2 - - - +
180A TYR* 3.5 30.6 - + - +
181A ARG* 3.1 62.7 + - + +
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Residues in contact with ALA 178 (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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174A LYS 3.1 15.2 + - - +
175A MSE 3.4 10.1 - - - +
176A GLN 3.3 0.4 - - - -
177A TYR* 1.3 78.5 - - - +
179A ARG* 1.3 57.2 + - - +
181A ARG* 3.5 4.0 + - - +
182A ASP* 3.0 36.2 + - - +
174B LYS* 3.6 31.4 - - + +
175B MSE 4.3 4.3 - - - -
178B ALA* 4.0 12.8 - - + -
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Residues in contact with ARG 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LEU* 4.6 2.6 - - - +
175A MSE 3.2 6.8 + - - +
176A GLN* 3.7 11.4 - - - +
177A TYR 3.4 0.2 - - - -
178A ALA* 1.3 76.9 - - - +
180A TYR* 1.3 60.5 + - - +
182A ASP* 3.9 5.0 - - - +
183A GLY* 3.2 19.1 + - - -
175B MSE 3.6 30.8 - - + -
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Residues in contact with TYR 180 (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 LEU* 3.5 44.9 - - + +
163A GLU* 3.6 38.5 + - + +
166A TYR* 3.8 21.8 - - + -
167A LYS* 5.2 9.2 - - + +
176A GLN 3.0 17.2 + - - +
177A TYR* 3.5 37.2 - + - +
178A ALA 3.2 0.4 - - - -
179A ARG* 1.3 74.7 - - - +
181A ARG* 1.3 88.5 + - + +
183A GLY 3.3 9.4 + - - -
184A LEU* 3.3 26.1 + - + +
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Residues in contact with ARG 181 (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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177A TYR* 3.1 48.2 + - + +
178A ALA* 4.2 1.1 - - - +
180A TYR* 1.3 89.2 - - + +
182A ASP* 1.3 59.8 + - - +
184A LEU* 3.4 27.3 + - - +
185A SER* 3.1 25.3 + - - -
224A GLU 3.7 18.4 + - - -
225A VAL* 4.2 12.0 + - - +
226A ASN* 3.7 24.4 - - - +
174B LYS* 3.4 29.1 + - + +
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Residues in contact with ASP 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ALA 3.0 21.2 + - - +
179A ARG* 3.9 7.0 - - - +
180A TYR 3.3 0.2 - - - -
181A ARG* 1.3 72.8 - - - +
183A GLY* 1.3 60.9 + - - +
185A SER* 3.4 5.0 + - - -
186A LYS* 2.9 30.5 + - - +
173B THR* 3.2 26.0 - - + +
174B LYS* 3.2 25.1 + - - +
175B MSE 2.8 32.9 + - + +
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Residues in contact with GLY 183 (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 LEU* 3.4 17.3 - - - +
179A ARG 3.2 14.1 + - - -
180A TYR 3.3 4.6 + - - -
182A ASP* 1.3 74.8 - - - +
184A LEU* 1.3 57.6 + - - +
186A LYS* 4.0 5.0 - - - +
187A LEU* 3.0 33.8 + - - +
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Residues in contact with LEU 184 (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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159A LYS* 4.0 28.9 - - + -
162A LEU* 3.2 27.0 - - + +
163A GLU* 4.6 7.0 - - - +
180A TYR* 3.3 27.9 + - + +
181A ARG* 3.5 32.3 - - - +
183A GLY* 1.3 76.1 - - - +
185A SER* 1.3 58.9 + - - +
187A LEU* 4.3 3.9 - - - +
188A PHE* 3.2 23.7 + - - +
224A GLU 6.1 0.2 - - - -
225A VAL* 3.5 35.5 - - + +
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Residues in contact with SER 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ARG 3.1 15.1 + - - -
182A ASP* 3.7 9.6 - - - -
184A LEU* 1.3 75.1 - - - +
186A LYS* 1.3 63.1 + - - +
188A PHE* 3.3 5.0 + - - +
189A THR* 3.1 32.2 + - - +
225A VAL* 3.6 12.1 - - - +
226A ASN 6.2 0.8 - - - -
174B LYS* 4.0 16.3 + - - -
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Residues in contact with LYS 186 (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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182A ASP 2.9 18.1 + - - +
183A GLY* 4.0 5.2 - - - +
185A SER* 1.3 72.3 - - - +
187A LEU* 1.3 64.7 + - - +
189A THR* 3.4 7.4 + - - +
190A THR* 2.7 46.6 + - - +
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Residues in contact with LEU 187 (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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155A ALA* 3.4 33.4 - - + +
158A GLU* 3.9 25.8 - - + -
159A LYS* 5.0 7.2 - - + +
162A LEU* 5.7 2.9 - - + -
183A GLY 3.0 20.2 + - - +
184A LEU* 4.3 4.3 - - - +
186A LYS* 1.3 76.4 - - - +
188A PHE* 1.3 57.0 + - - +
190A THR* 4.7 3.1 - - - -
191A ARG* 2.9 52.3 + - + +
192A TYR* 3.4 16.0 + - + -
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Residues in contact with PHE 188 (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 LEU 3.2 20.8 + - - +
185A SER* 3.6 6.3 - - - +
186A LYS 3.2 0.4 - - - -
187A LEU* 1.3 76.2 - - - +
189A THR* 1.3 70.0 + - + +
192A TYR* 3.1 42.5 + + + +
193A GLU* 2.9 33.7 + - + -
196A ARG* 4.5 10.5 - - - -
218A ILE* 3.9 22.4 - - + -
221A ILE* 4.7 8.5 - - + -
222A GLU* 3.5 57.0 - - + -
225A VAL* 5.2 7.0 - - + -
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Residues in contact with THR 189 (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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185A SER* 3.1 20.1 + - - +
186A LYS* 3.4 11.6 + - - +
188A PHE* 1.3 87.1 - - + +
190A THR* 1.3 61.0 + - - +
193A GLU* 3.2 23.0 - - - +
194A LYS* 5.4 1.4 - - - +
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Residues in contact with THR 190 (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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186A LYS* 2.7 40.7 + - - +
187A LEU* 4.3 3.6 - - - -
189A THR* 1.3 80.2 + - - +
191A ARG* 1.3 65.5 + - + +
193A GLU 4.9 0.2 - - - -
194A LYS* 3.2 45.0 - - - +
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Residues in contact with ARG 191 (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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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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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