Contacts of the helix formed by residues 189 - 207 (chain A) in PDB entry 3MIZ
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 189 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A TYR* 3.4 49.6 - - + -
185A LEU* 3.7 33.2 - - + -
186A ASN* 3.0 19.1 + - + +
187A PRO 3.7 5.5 - - - +
188A ILE* 1.3 85.6 - - + +
190A LEU* 1.3 67.0 + - - +
191A GLY* 4.4 2.0 - - - +
192A ALA* 3.2 19.1 + - + +
193A GLU 3.3 9.0 + - - -
223A VAL* 3.8 22.7 - - + -
226A GLU* 5.3 1.3 - - - +
201B ARG* 3.9 2.5 + - - -
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Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ARG* 3.8 36.0 + - + +
128A ARG* 4.9 2.2 - - - -
129A ILE* 4.0 20.0 - - + +
147A ARG* 3.6 26.7 - - - +
188A ILE 3.5 4.0 + - - -
189A LEU* 1.3 71.4 - - - +
191A GLY* 1.3 64.0 + - - +
193A GLU* 3.2 4.0 + - + +
194A LEU* 3.0 42.2 + - + +
162B TYR* 4.0 26.2 - - + +
201B ARG* 3.5 27.3 - - + +
205B GLU* 5.4 1.1 - - - +
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Residues in contact with GLY 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ARG* 4.6 12.0 + - - +
161A ASP* 3.8 24.0 - - - -
189A LEU* 3.2 2.2 - - - +
190A LEU* 1.3 81.6 - - - +
192A ALA* 1.3 61.1 + - - +
194A LEU* 3.3 4.0 + - - +
195A ARG* 3.0 38.0 + - - +
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Residues in contact with ALA 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A TYR* 4.2 4.3 + - - -
184A ARG* 6.2 0.5 - - - +
185A LEU* 3.6 43.0 + - + +
186A ASN 3.3 27.1 - - - +
187A PRO* 4.7 2.0 - - + -
189A LEU* 3.2 8.8 + - + +
191A GLY* 1.3 75.6 - - - +
193A GLU* 1.3 64.3 + - - +
195A ARG* 3.4 8.1 + - - +
196A LEU* 3.2 21.9 + - - +
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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
----------------------------------------------------------
184A ARG* 3.4 27.1 + - - -
187A PRO* 3.8 18.6 - - - +
189A LEU 3.3 6.3 + - - +
190A LEU* 3.2 10.3 + - + +
192A ALA* 1.3 78.1 - - - +
194A LEU* 1.3 61.6 + - + +
196A LEU* 3.2 15.6 + - - +
197A ASP* 2.8 46.7 + - - +
162B TYR* 6.0 0.7 - - - +
201B ARG* 4.2 31.2 - - + +
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Residues in contact with LEU 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ARG* 3.5 35.7 - - - +
147A ARG* 5.3 2.0 - - - +
161A ASP* 4.2 9.9 - - + -
162A TYR* 3.6 26.2 - - + +
190A LEU* 3.0 38.7 + - + +
191A GLY* 3.3 4.5 + - - +
193A GLU* 1.3 76.3 - - + +
195A ARG* 1.3 62.7 + - - +
197A ASP* 3.3 18.6 + - - +
198A ALA* 3.1 18.2 + - - +
162B TYR* 4.1 32.3 - - + +
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Residues in contact with ARG 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ASP* 2.7 41.7 + - + +
165A ALA* 3.4 22.7 - - + +
182A TYR* 3.4 17.6 + - - +
185A LEU* 4.0 19.0 - - - +
191A GLY* 3.0 19.4 + - - +
192A ALA* 3.7 4.9 - - - +
193A GLU 3.3 0.2 - - - -
194A LEU* 1.3 76.5 - - - +
196A LEU* 1.3 58.6 + - - +
198A ALA 3.4 0.9 + - - -
199A PHE* 3.1 25.3 + - - +
250A GLY 3.2 24.7 + - - -
251A ASN* 4.1 3.0 - - - +
278A PHE* 3.5 31.3 - - + +
279A ASP* 3.2 26.3 + - - -
297A LEU* 3.9 13.3 - - - +
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Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A TYR* 3.9 30.9 + - + -
184A ARG* 3.4 36.8 - - + +
192A ALA 3.2 14.0 + - - +
193A GLU* 3.5 22.7 - - - +
195A ARG* 1.3 76.2 - - - +
197A ASP* 1.3 67.2 + - - +
199A PHE* 3.2 7.3 + - + -
200A ARG* 2.9 56.5 + - + +
215A ILE* 4.1 18.4 - - + -
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Residues in contact with ASP 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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162A TYR* 3.9 8.9 - - + -
193A GLU* 2.8 32.0 + - - +
194A LEU* 3.5 24.5 - - - +
196A LEU* 1.3 77.5 - - - +
198A ALA* 1.3 62.7 + - - +
200A ARG* 3.4 12.0 + - - +
201A ARG* 3.1 24.1 + - - +
162B TYR* 4.6 2.6 + - - -
197B ASP* 3.6 46.5 - - - +
201B ARG* 6.0 0.7 - - - +
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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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162A TYR* 3.3 45.1 - - + +
165A ALA* 3.6 11.0 - - + -
166A ARG* 3.7 6.7 - - + +
169A THR* 4.9 0.4 - - - -
194A LEU 3.1 11.5 + - - +
195A ARG 3.5 9.0 - - - +
197A ASP* 1.3 76.1 - - - +
199A PHE* 1.3 54.7 + - - +
202A THR* 2.7 43.5 + - - +
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Residues in contact with PHE 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ALA* 5.6 0.4 - - + -
169A THR* 3.5 30.2 + - + +
180A ILE* 3.6 37.7 - - + -
182A TYR* 3.5 41.3 - + + -
195A ARG 3.1 13.6 + - - +
196A LEU* 3.2 11.4 + - + +
198A ALA* 1.3 75.8 - - - +
200A ARG* 1.3 55.7 + - - +
202A THR* 3.1 13.5 + - - -
203A THR* 2.8 32.1 - - - +
213A LEU* 3.9 33.0 - - + -
215A ILE* 4.1 19.5 - - + -
248A MSE 3.6 13.9 - - - -
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Residues in contact with ARG 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ARG* 5.2 5.5 - - - +
196A LEU* 2.9 48.4 + - + +
197A ASP* 3.7 11.4 + - - +
199A PHE* 1.3 77.6 - - - +
201A ARG* 1.3 59.7 + - - +
203A THR* 2.8 24.9 - - - +
204A SER* 3.2 13.7 + - - -
210A GLU* 2.6 38.1 + - - +
215A ILE* 3.7 28.8 - - + +
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Residues in contact with ARG 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A TYR* 3.6 22.0 - - - +
197A ASP 3.1 14.2 + - - +
200A ARG* 1.3 76.2 - - - +
202A THR* 1.3 58.6 + - + +
204A SER* 3.1 6.7 + - - -
205A GLU* 2.7 60.6 + - + +
187B PRO 3.2 21.8 + - - -
188B ILE* 2.9 26.3 + - - +
190B LEU* 3.5 35.0 - - - +
193B GLU* 3.5 22.9 - - + +
194B LEU* 6.1 0.2 - - - -
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Residues in contact with THR 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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162A TYR* 5.5 2.5 - - - +
166A ARG* 3.4 47.1 - - + +
169A THR* 3.0 28.6 - - - +
170A ARG* 4.9 8.0 - - + +
173A LEU* 4.0 5.5 - - - +
198A ALA* 2.7 33.7 + - - +
199A PHE 3.1 2.3 + - - -
201A ARG* 1.3 74.2 - - + +
203A THR* 1.3 65.4 + - - +
205A GLU* 3.4 13.6 + - - +
206A PHE* 3.1 23.4 + - - +
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Residues in contact with THR 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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169A THR* 4.7 7.2 - - - -
173A LEU* 4.4 10.5 - - - -
199A PHE* 2.8 27.6 - - + +
200A ARG* 2.8 23.1 - - - +
202A THR* 1.3 81.5 + - - +
204A SER* 1.3 59.2 + - - +
206A PHE* 3.4 2.1 + - - +
207A GLY 3.1 7.4 + - - -
208A LEU* 3.0 59.9 + - - +
210A GLU* 5.7 0.4 - - - +
213A LEU* 3.6 29.9 - - + +
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Residues in contact with SER 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 ARG 3.2 17.9 + - - -
201A ARG* 3.1 9.3 + - - -
203A THR* 1.3 74.9 - - - +
205A GLU* 1.3 64.3 + - - +
206A PHE 3.1 2.0 - - - -
207A GLY* 3.1 14.2 + - - -
208A LEU 3.7 13.0 + - - -
209A THR* 5.6 0.9 - - - -
210A GLU 5.7 1.2 + - - -
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Residues in contact with GLU 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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166A ARG* 5.6 4.7 - - - +
170A ARG* 4.7 13.3 + - - +
201A ARG* 2.7 48.7 + - + +
202A THR* 3.7 13.7 - - - +
204A SER* 1.3 72.9 - - - +
206A PHE* 1.3 59.9 + - - +
129B ILE* 6.1 1.2 - - - +
149B GLN* 5.7 1.0 + - - -
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Residues in contact with PHE 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A LEU* 3.5 43.3 - - + -
174A GLU* 5.9 2.9 - - + -
178A ARG* 3.8 48.5 - - - -
202A THR 3.1 17.3 + - - +
203A THR 3.7 3.6 - - - +
204A SER 3.1 0.8 - - - -
205A GLU* 1.3 79.5 - - - +
207A GLY* 1.3 58.5 + - - +
208A LEU* 4.2 11.4 - - + -
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Residues in contact with GLY 207 (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 THR 3.1 0.4 + - - -
204A SER 3.1 11.0 + - - -
206A PHE* 1.3 82.1 - - - +
208A LEU* 1.3 70.0 + - - +
209A THR* 3.7 9.4 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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