Contacts of the helix formed by residues 170 - 195 (chain B) in PDB entry 3QEK
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 ASP 170 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B SER* 2.7 31.9 + - - -
169B ASP* 1.3 75.0 - - - +
171B HIS* 1.3 66.3 + - - +
172B GLU* 4.1 8.4 - - - +
173B GLY 3.0 11.1 + - - -
174B ARG* 2.9 36.2 + - - +
220B PRO* 3.8 19.1 - - + +
248B ASP* 5.4 0.5 - - - +
273B ARG* 5.8 1.6 + - - -
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Residues in contact with HIS 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 4.3 22.0 - - + -
73A GLN* 4.4 6.4 + - - +
76A LEU* 4.2 14.4 - - + +
126B SER* 4.1 11.3 + - - -
127B ILE* 3.5 56.7 + - + +
130B ASP* 4.0 17.9 + - - +
170B ASP* 1.3 76.8 - - - +
172B GLU* 1.3 60.1 + - - +
174B ARG* 3.8 11.5 + - - +
175B ALA* 2.9 29.7 + - + +
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Residues in contact with GLU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B MSE 3.1 28.4 - - + +
126B SER* 2.7 45.9 + - - -
127B ILE 4.6 0.9 + - - -
144B TYR* 3.2 28.5 - - + +
145B SER* 3.8 2.1 + - - -
168B SER* 5.2 0.4 - - - +
170B ASP* 3.3 8.8 + - - +
171B HIS* 1.3 82.5 - - - +
173B GLY* 1.3 62.1 + - - +
175B ALA* 3.2 6.1 + - - +
176B ALA* 3.1 21.1 + - - +
243B SER* 4.5 4.9 - - - +
273B ARG* 3.6 26.9 - - - +
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Residues in contact with GLY 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B VAL* 3.5 17.0 - - - +
168B SER* 3.3 26.6 + - - -
170B ASP* 3.0 10.1 + - - -
172B GLU* 1.3 76.3 - - - +
174B ARG* 1.3 62.6 + - - +
176B ALA* 3.2 4.2 + - - +
177B GLN 3.1 17.5 + - - -
243B SER* 3.7 14.1 - - - -
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Residues in contact with ARG 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLN* 3.5 30.3 + - - +
167B VAL* 5.2 1.1 - - + -
168B SER 3.7 3.1 + - - +
169B ASP* 2.8 55.1 + - - +
170B ASP* 2.9 29.5 + - - +
171B HIS* 3.8 6.9 + - - +
173B GLY* 1.3 75.3 - - - +
175B ALA* 1.3 57.5 + - - +
177B GLN* 3.6 8.6 - - - +
178B LYS* 2.9 60.1 + - - +
217B GLN* 4.4 18.4 - - - +
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Residues in contact with ALA 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B SER* 3.8 26.0 - - - -
145B SER* 3.7 10.4 - - - +
171B HIS* 2.9 25.0 + - + +
172B GLU 3.5 5.4 - - - +
173B GLY 3.2 0.2 - - - -
174B ARG* 1.3 73.8 - - - +
176B ALA* 1.3 66.1 + - - +
178B LYS* 3.5 8.3 + - - +
179B LYS* 3.0 25.3 + - - +
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Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B TYR 5.4 1.3 - - - +
145B SER* 4.0 20.1 - - - +
148B ALA* 4.2 3.1 - - - +
151B TRP* 4.3 18.1 - - + -
165B LEU* 5.1 1.1 - - - -
167B VAL* 4.9 0.9 - - + -
172B GLU* 3.1 8.7 + - - +
173B GLY 3.2 4.4 + - - +
175B ALA* 1.3 76.9 - - - +
177B GLN* 1.3 63.6 + - - +
179B LYS* 3.4 2.1 + - - +
180B LEU* 3.1 24.8 + - - +
243B SER* 3.5 33.0 - - - +
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Residues in contact with GLN 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LEU* 3.7 19.5 - - + -
167B VAL* 3.9 11.4 - - + +
173B GLY 3.1 11.9 + - - +
174B ARG* 3.6 14.0 - - - +
175B ALA 3.3 0.2 - - - -
176B ALA* 1.3 77.5 - - - +
178B LYS* 1.3 61.8 + - + +
180B LEU* 3.3 1.9 + - - +
181B GLU* 2.9 64.6 + - - +
215B VAL* 3.6 27.0 - - + +
217B GLN* 2.9 28.6 + - - +
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Residues in contact with LYS 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B HIS* 6.4 0.2 - - - -
174B ARG* 2.9 46.2 + - - +
175B ALA* 4.0 7.0 - - - +
177B GLN* 1.3 79.5 - - + +
179B LYS* 1.3 57.2 + - - +
181B GLU* 3.8 12.1 - - - +
182B THR* 2.8 37.2 + - - +
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Residues in contact with LYS 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B SER* 3.5 27.4 - - - +
146B HIS* 3.9 29.9 + - + +
148B ALA* 3.7 9.0 - - + -
149B LEU* 4.1 28.7 - - - +
175B ALA 3.0 18.1 + - - +
176B ALA 3.8 2.2 - - - +
177B GLN 3.3 0.2 - - - -
178B LYS* 1.3 77.9 - - - +
180B LEU* 1.3 60.4 + - - +
182B THR* 3.5 11.6 - - + +
183B LEU* 3.2 36.4 + - + +
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Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ALA* 3.8 29.3 - - + +
151B TRP* 4.5 12.3 - - + -
152B PHE* 4.3 18.4 - - + +
155B MSE 4.3 12.1 - - + -
163B VAL* 5.0 4.0 - - + -
165B LEU* 4.1 22.7 - - + -
176B ALA 3.1 16.7 + - - +
177B GLN 4.0 2.7 - - - +
179B LYS* 1.3 74.1 - - - +
181B GLU* 1.3 61.9 + - + +
183B LEU* 3.2 3.5 + - + +
184B LEU* 2.9 47.2 + - + +
212B ALA* 5.5 1.1 - - + -
241B ILE* 4.2 23.1 - - + -
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Residues in contact with GLU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LEU* 5.3 3.6 - - + -
177B GLN* 2.9 52.4 + - + +
178B LYS* 3.8 11.8 - - - +
180B LEU* 1.3 75.8 - - + +
182B THR* 1.3 52.3 + - - +
184B LEU* 3.3 8.1 + - + +
185B GLU* 2.6 55.1 + - + +
212B ALA* 5.6 7.6 - - + -
215B VAL* 3.6 18.1 - - + +
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Residues in contact with THR 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B LYS* 2.8 25.1 + - - +
179B LYS* 3.5 15.1 - - + +
180B LEU 3.2 0.2 - - - -
181B GLU* 1.3 77.1 - - - +
183B LEU* 1.3 68.4 + - + +
185B GLU* 3.9 5.4 - - - +
186B GLY* 3.0 21.0 + - - -
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Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ALA* 3.4 36.3 - - + +
149B LEU* 3.8 28.0 - - + +
152B PHE* 3.8 33.7 - - + -
179B LYS* 3.2 26.9 + - + +
180B LEU* 3.2 7.9 + - - +
182B THR* 1.3 80.1 - - + +
184B LEU* 1.3 62.3 + - - +
186B GLY* 3.4 2.1 + - - -
187B LYS* 3.1 22.7 + - - +
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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
----------------------------------------------------------
152B PHE* 3.8 27.8 - - + -
155B MSE 4.4 11.9 - - - -
163B VAL* 5.1 3.4 - - + -
180B LEU* 2.9 37.4 + - + +
181B GLU* 3.7 7.6 - - + +
183B LEU* 1.3 73.3 - - - +
185B GLU* 1.3 62.3 + - + +
187B LYS* 3.3 4.0 + - - +
188B GLU* 2.9 27.9 + - - +
210B PRO* 3.6 33.6 - - + +
211B LYS* 4.1 3.6 - - - -
212B ALA* 3.7 35.9 - - + +
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Residues in contact with GLU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B GLU* 2.6 42.9 + - - +
182B THR* 4.0 5.4 - - - +
184B LEU* 1.3 71.0 - - - +
186B GLY* 1.3 59.8 + - - +
188B GLU* 3.7 7.0 - - - +
189B SER* 2.8 33.4 + - - -
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Residues in contact with GLY 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B THR 3.0 14.4 + - - -
183B LEU* 3.4 5.1 + - - -
184B LEU 3.2 0.2 - - - -
185B GLU* 1.3 78.5 - - - +
187B LYS* 1.3 60.4 + - - +
189B SER* 3.4 6.5 + - - -
190B LYS* 3.1 30.2 + - - +
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Residues in contact with LYS 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B PHE* 3.8 20.6 - - + -
156B ARG* 3.8 35.2 - - - +
183B LEU 3.1 12.9 + - - +
184B LEU* 3.6 7.2 - - - +
185B GLU 3.3 0.2 - - - -
186B GLY* 1.3 74.2 - - - +
188B GLU* 1.3 65.6 + - - +
190B LYS* 3.3 23.2 + - + +
191B SER* 2.9 35.5 + - - +
210B PRO* 4.5 22.4 - - + +
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Residues in contact with GLU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LEU 2.9 16.5 + - - +
185B GLU* 3.3 9.4 + - - +
187B LYS* 1.3 74.9 - - - +
189B SER* 1.3 53.5 + - - +
191B SER* 3.1 7.1 + - - -
192B LYS* 2.7 36.3 + - - +
210B PRO* 5.7 5.8 - - - +
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Residues in contact with SER 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B GLU 2.8 19.0 + - - -
186B GLY* 3.6 7.2 - - - -
187B LYS 3.2 0.2 - - - -
188B GLU* 1.3 73.0 - - - +
190B LYS* 1.3 65.2 + - - +
192B LYS* 3.4 5.9 + - - +
193B LYS* 3.0 33.9 + - - +
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Residues in contact with LYS 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ARG* 5.9 2.6 - - - +
186B GLY 3.1 19.5 + - - +
187B LYS* 3.6 25.8 - - + +
189B SER* 1.3 75.4 - - - +
191B SER* 1.3 52.9 + - - +
193B LYS* 3.2 11.9 + - + +
194B ARG* 2.8 35.8 + - - +
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Residues in contact with SER 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LYS* 2.9 28.3 + - - +
188B GLU* 3.4 8.7 - - - -
190B LYS* 1.3 75.1 - - - +
192B LYS* 1.3 65.6 + - - +
194B ARG* 3.3 5.6 + - - +
195B ASN* 3.1 37.6 + - - +
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Residues in contact with LYS 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B GLU 2.7 19.5 + - - +
189B SER* 3.7 7.2 - - - +
191B SER* 1.3 72.1 - - - +
193B LYS* 1.3 64.5 + - - +
195B ASN* 3.3 4.4 + - - -
196B TYR* 3.1 24.7 + - - +
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Residues in contact with LYS 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B SER* 3.0 24.1 + - - +
190B LYS* 3.4 11.7 - - - +
192B LYS* 1.3 78.2 - - + +
194B ARG* 1.3 62.5 + - - +
195B ASN 3.2 1.2 + - - -
196B TYR* 3.3 16.2 + - - +
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Residues in contact with ARG 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B LYS 2.8 19.6 + - - +
191B SER* 3.7 7.6 - - - +
192B LYS 3.3 0.2 - - - -
193B LYS* 1.3 74.9 - - - +
195B ASN* 1.3 76.5 + - - +
196B TYR 3.8 0.9 + - - -
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Residues in contact with ASN 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B SER* 3.1 29.6 + - - +
192B LYS* 3.6 3.8 - - - +
194B ARG* 1.3 100.4 + - - +
196B TYR* 1.3 66.5 + - - +
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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