Contacts of the helix formed by residues 167 - 185 (chain B) in PDB entry 3MI9
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 SER 167 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B ARG 3.7 0.6 + - - -
166B ALA* 1.3 77.2 - - - +
168B LYS* 1.3 65.0 + - - +
169B ASP* 3.5 9.6 + - - +
170B LEU* 3.0 27.6 + - - +
171B ALA* 2.9 20.4 + - - +
210B TRP* 5.9 0.2 - - - -
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Residues in contact with LYS 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ALA 3.7 0.8 + - - -
167B SER* 1.3 73.6 - - - +
169B ASP* 1.3 57.5 + - - +
171B ALA* 3.3 8.0 + - - +
172B GLN* 3.0 29.6 + - - +
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Residues in contact with ASP 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B SER* 3.0 8.0 - - - +
168B LYS* 1.3 78.6 - - - +
170B LEU* 1.3 59.2 + - - +
172B GLN* 3.8 13.5 - - - +
173B THR* 2.8 39.7 + - - -
208B SER* 6.0 1.6 - - - -
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Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B THR* 5.3 2.2 - - + -
166B ALA* 3.3 16.6 - - + -
167B SER* 3.0 21.2 + - - +
169B ASP* 1.3 74.3 - - - +
171B ALA* 1.3 65.1 + - - +
173B THR* 3.8 4.7 - - - -
174B SER* 2.9 36.2 + - - +
201B ILE* 4.9 2.9 - - + +
204B ALA* 3.6 31.4 - - + +
205B CYS* 3.8 10.1 - - - +
208B SER* 3.4 26.9 - - - +
210B TRP* 3.1 41.5 - - + -
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Residues in contact with ALA 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B VAL* 4.8 1.2 - - - +
161B THR* 4.1 31.7 + - - +
166B ALA* 4.4 2.9 - - + +
167B SER 2.9 13.1 + - - +
168B LYS* 3.4 13.7 - - - +
170B LEU* 1.3 79.1 - - - +
172B GLN* 1.3 61.6 + - - +
174B SER* 3.6 2.6 + - - -
175B TYR* 3.2 22.5 + - - +
3C PRO* 4.0 8.2 - - + +
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Residues in contact with GLN 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LYS* 3.0 17.2 + - - +
169B ASP* 3.8 15.0 - - - +
171B ALA* 1.3 74.5 - - - +
173B THR* 1.3 72.7 + - - +
175B TYR* 3.3 2.6 + - - +
176B PHE* 2.8 45.6 + - - +
1C MET* 3.0 36.3 + - - +
2C GLU* 4.9 0.9 - - + -
3C PRO* 3.6 21.5 - - + +
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Residues in contact with THR 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ASP* 2.8 29.5 + - - -
170B LEU* 3.8 6.5 - - - -
172B GLN* 1.3 85.0 + - - +
174B SER* 1.3 58.2 + - - +
176B PHE* 3.2 11.0 + - + +
177B MET* 2.9 33.1 + - + +
204B ALA* 3.9 19.7 - - + +
207B TRP* 4.1 23.8 - - + -
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Residues in contact with SER 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B VAL* 3.6 20.3 - - - +
161B THR* 4.3 4.5 - - - +
170B LEU* 2.9 23.3 + - - +
171B ALA 3.8 2.9 - - - -
173B THR* 1.3 75.7 - - - +
175B TYR* 1.3 66.5 + - - +
177B MET* 3.2 4.2 + - - +
178B ALA* 3.0 19.8 + - - +
200B CYS* 3.7 18.7 - - - +
201B ILE* 3.7 21.4 - - - +
204B ALA* 3.2 16.2 - - - +
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Residues in contact with TYR 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B GLN* 4.1 16.8 - - + +
60B ASN* 5.2 0.3 + - - -
154B HIS* 3.5 39.8 + + + +
157B VAL* 3.8 9.3 - - + +
158B VAL* 4.0 17.7 - - + -
171B ALA 3.2 14.3 + - - +
172B GLN 3.3 4.0 + - - +
174B SER* 1.3 79.2 - - - +
176B PHE* 1.3 65.0 + - - +
178B ALA* 3.1 15.0 + - - +
179B THR* 3.3 12.1 + - - -
1C MET 3.9 10.5 - - - -
2C GLU 2.8 39.5 - - - -
3C PRO* 3.5 15.3 - - + -
4C VAL* 3.3 40.3 - - + +
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Residues in contact with PHE 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B GLN* 2.8 33.1 + - - +
173B THR* 3.4 10.3 - - + +
174B SER 3.2 0.2 - - - -
175B TYR* 1.3 78.2 - - - +
177B MET* 1.3 68.5 + - - +
179B THR* 3.3 4.4 + - - -
180B ASN* 2.9 47.3 + - - -
1C MET* 3.4 44.6 - - + +
32C PHE* 4.6 11.7 - + - -
35C GLN* 3.1 26.7 - - - -
38C PHE* 3.4 34.1 - + - -
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Residues in contact with MET 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B THR* 2.9 24.6 + - + +
174B SER 3.2 4.5 + - - +
176B PHE* 1.3 82.2 - - - +
178B ALA* 1.3 60.8 + - - +
180B ASN* 3.2 19.6 + - + +
181B SER* 2.8 28.9 + - - -
200B CYS* 3.6 26.3 - - + +
203B LEU* 4.0 8.7 - - + -
204B ALA* 5.2 0.7 - - + -
207B TRP* 3.4 42.4 - - + -
241B PHE* 3.5 36.9 - - + -
245B LEU* 4.5 7.9 - - + -
38C PHE* 6.4 0.4 - - - -
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Residues in contact with ALA 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B PRO* 4.0 16.2 - - + +
154B HIS* 3.6 31.3 - - + +
157B VAL* 4.2 7.4 - - + -
174B SER 3.0 12.8 + - - +
175B TYR 3.1 11.2 + - - +
177B MET* 1.3 75.3 - - - +
179B THR* 1.3 61.2 + - - +
181B SER* 2.5 22.9 + - - -
182B LEU* 3.3 5.0 + - - +
200B CYS* 3.4 15.7 - - - -
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Residues in contact with THR 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLN* 4.0 21.7 + - - +
60B ASN* 4.5 1.8 - - - +
154B HIS* 2.9 23.5 + - - -
175B TYR* 3.3 9.3 + - - -
176B PHE* 3.4 9.9 - - - -
178B ALA* 1.3 78.7 - - - +
180B ASN* 1.3 62.1 + - - +
182B LEU* 3.0 7.7 + - - +
183B HIS* 3.0 46.7 + - + +
1C MET 4.0 13.6 + - - +
35C GLN* 3.6 21.8 - - + +
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Residues in contact with ASN 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B PHE* 2.9 43.6 + - - -
177B MET* 3.2 20.9 + - + +
179B THR* 1.3 73.3 - - - +
181B SER* 1.3 58.6 + - - +
183B HIS* 4.1 6.1 - - - -
184B LEU* 2.7 46.0 + - + +
241B PHE* 3.9 13.2 - - + -
245B LEU* 6.0 0.7 - - + -
35C GLN* 2.9 24.3 + - - -
38C PHE* 3.5 19.9 - - - -
39C ILE* 4.0 2.4 - - - +
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Residues in contact with SER 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B PRO* 4.4 1.6 - - - +
177B MET 2.8 13.6 + - - -
178B ALA 2.5 21.0 + - - -
180B ASN* 1.3 77.4 - - - +
182B LEU* 1.3 63.8 + - - +
185B THR* 2.7 39.2 + - - +
187B PHE* 4.6 6.1 + - - +
188B SER 5.4 1.3 + - - -
196B VAL* 3.5 29.2 - - - +
200B CYS* 4.2 2.2 - - - -
241B PHE* 3.6 19.2 - - - -
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Residues in contact with LEU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ALA* 4.7 0.2 - - - +
60B ASN* 3.6 46.2 - - + +
63B ILE* 3.5 23.3 - - + +
64B VAL* 4.1 14.8 - - + -
67B HIS* 3.0 28.0 + - - -
152B HIS* 4.1 9.0 - - - +
153B PRO* 4.8 11.0 - - + -
154B HIS* 3.8 15.0 - - + +
178B ALA 3.8 6.7 - - - +
179B THR 3.0 8.9 + - - +
181B SER* 1.3 87.7 + - - +
183B HIS* 1.3 60.8 + - - +
185B THR 3.5 1.4 - - - +
188B SER* 3.9 28.7 - - - +
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Residues in contact with HIS 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ARG 4.5 1.0 - - - +
39B GLN* 3.4 29.0 + - - +
42B ALA* 3.4 32.0 + - + +
43B ASN* 4.1 4.2 + - - -
46B GLN* 2.7 50.9 + - + -
63B ILE* 4.0 12.2 - - + +
67B HIS* 4.9 2.1 + - - -
179B THR* 3.0 36.8 + - + +
180B ASN* 3.7 7.9 - - - +
182B LEU* 1.3 80.1 - - - +
184B LEU* 1.3 72.5 + - + +
185B THR 4.8 0.3 - - - +
35C GLN* 3.5 17.4 - - + +
39C ILE* 4.0 15.6 - - + +
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Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LEU* 5.8 3.3 - - - +
39B GLN* 2.7 32.3 + - + +
67B HIS* 6.1 0.4 - - - -
180B ASN* 2.7 36.6 + - + +
183B HIS* 1.3 82.4 - - + +
185B THR* 1.3 62.8 + - + +
241B PHE* 4.6 3.8 - - + -
244B ILE* 3.4 17.3 - - + +
245B LEU* 3.8 22.0 - - + -
248B THR* 4.7 4.0 - - + -
39C ILE* 3.9 11.4 - - + -
43C LEU* 3.4 25.8 - - + -
45C ILE* 3.4 33.2 - - + -
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Residues in contact with THR 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B HIS* 3.4 21.3 + - - -
181B SER* 2.7 28.5 + - - +
182B LEU* 3.5 1.2 - - - +
184B LEU* 1.3 82.3 - - + +
186B THR* 1.3 63.2 + - - +
187B PHE* 2.7 38.2 + - + +
188B SER* 5.1 0.5 + - - -
241B PHE* 3.9 33.7 - - + -
244B ILE* 4.0 23.1 - - + -
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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