Contacts of the helix formed by residues 171 - 190 (chain B) in PDB entry 6QPA
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 HIS 171 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B VAL* 3.7 5.2 - - + -
168B MET* 2.9 47.3 + - + +
169B ASP 3.4 16.8 + - - -
170B GLY* 1.3 80.9 - - - +
172B GLU* 1.3 57.8 + - - +
173B LYS 3.3 2.2 - - - -
174B ALA* 3.2 8.4 + - - +
175B PHE* 2.8 29.5 + - - +
288B ALA 4.5 3.6 - - - -
289B HIS* 2.9 45.5 + + + +
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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
----------------------------------------------------------
167B VAL* 4.0 9.3 - - + +
168B MET 4.2 6.0 - - - +
169B ASP* 4.4 7.9 - - - +
170B GLY* 3.0 29.5 + - - -
171B HIS* 1.3 77.5 - - - +
173B LYS* 1.3 58.0 + - - +
175B PHE* 3.3 2.4 + - - +
176B GLU* 2.9 35.0 + - - +
200B LYS* 4.5 10.8 - - - +
251B THR* 2.7 33.4 + - + +
253B TYR* 3.3 28.4 + - + +
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Residues in contact with LYS 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B GLY 5.2 1.0 + - - +
171B HIS 3.3 0.2 - - - -
172B GLU* 1.3 77.9 - - - +
174B ALA* 1.3 63.8 + - - +
176B GLU* 3.2 13.5 + - + +
177B GLN* 3.0 54.1 + - + +
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Residues in contact with ALA 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B HIS* 3.2 11.0 + - - +
173B LYS* 1.3 77.5 - - - +
175B PHE* 1.3 58.6 + - - +
177B GLN* 3.3 13.9 + - - +
178B GLY* 2.9 25.3 + - - -
285B GLY* 3.6 4.0 - - - +
289B HIS* 3.4 32.7 + - + +
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Residues in contact with PHE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B HIS* 3.9 25.1 - + + -
167B VAL* 3.5 22.4 - - + -
171B HIS 2.8 21.7 + - - +
172B GLU 3.6 2.9 - - - +
174B ALA* 1.3 73.2 - - - +
176B GLU* 1.3 60.9 + - - +
178B GLY 3.2 0.2 + - - -
179B ALA* 2.7 47.0 + - + +
198B ILE* 4.6 6.3 - - + -
253B TYR* 3.4 51.8 - + + -
255B VAL* 4.3 7.6 - - + -
285B GLY 3.8 6.7 - - - -
286B VAL* 3.8 32.5 - - + -
289B HIS* 3.9 6.2 - - + -
290B LEU* 4.0 7.6 - - + -
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Residues in contact with GLU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B VAL* 3.4 32.0 - - + +
172B GLU* 2.9 22.6 + - - +
173B LYS* 3.2 10.4 + - + +
175B PHE* 1.3 79.0 - - + +
177B GLN* 1.3 58.9 + - + +
179B ALA* 4.0 2.3 - - - +
180B THR* 2.8 34.8 + - - +
198B ILE* 4.1 4.7 - - + +
200B LYS* 3.8 13.7 + - - +
253B TYR* 2.5 40.5 + - + -
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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
----------------------------------------------------------
173B LYS* 3.0 56.1 + - + +
174B ALA* 3.6 10.0 - - - +
176B GLU* 1.3 76.8 - - + +
178B GLY* 1.3 58.4 + - - +
180B THR* 3.3 6.7 + - - -
181B GLU* 2.9 31.4 + - - +
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Residues in contact with GLY 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ALA 2.9 11.1 + - - -
177B GLN* 1.3 75.0 - - - +
179B ALA* 1.3 60.2 + - - +
181B GLU* 3.3 9.4 + - - +
182B THR* 2.9 32.9 + - - -
281B ILE* 4.4 1.9 - - - +
285B GLY* 3.3 29.2 - - - -
286B VAL* 3.7 6.3 - - - -
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Residues in contact with ALA 179 (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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175B PHE* 2.7 44.2 + - + +
176B GLU 4.0 0.2 - - - +
178B GLY* 1.3 71.0 - - - -
180B THR* 1.3 63.0 + - - +
182B THR* 3.2 3.6 + - - -
183B LEU* 2.9 32.5 + - + +
198B ILE* 3.6 22.0 - - + -
255B VAL* 4.8 4.9 - - + -
286B VAL* 3.5 14.1 - - + +
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Residues in contact with THR 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B VAL* 5.8 1.0 - - - +
123B LYS* 4.1 30.9 - - + +
176B GLU* 2.8 22.7 + - - +
177B GLN* 3.5 6.1 - - - -
179B ALA* 1.3 77.1 - - - +
181B GLU* 1.3 62.4 + - - +
183B LEU* 3.8 0.7 - - - +
184B GLU* 2.9 50.2 + - + +
196B TRP* 4.3 7.4 - - + -
198B ILE* 3.4 16.6 - - - +
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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
----------------------------------------------------------
177B GLN 2.9 16.7 + - - +
178B GLY* 3.8 8.1 - - - +
179B ALA 3.3 0.2 - - - -
180B THR* 1.3 77.8 - - - +
182B THR* 1.3 62.8 + - - +
184B GLU* 4.1 7.5 - - - +
185B TRP* 3.1 23.3 + - + +
281B ILE* 3.7 35.3 - - + +
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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 GLY 2.9 18.6 + - - -
179B ALA* 3.5 7.2 - - - -
181B GLU* 1.3 75.7 - - - +
183B LEU* 1.3 62.5 + - + +
185B TRP* 3.4 4.0 + - - +
186B MET* 3.0 42.6 + - - +
272B VAL* 4.3 3.4 - - + -
278B LEU* 3.7 17.2 - - + +
281B ILE* 3.6 18.0 - - - +
282B HIS* 3.7 35.6 - - + -
286B VAL* 3.9 4.2 - - - +
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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
----------------------------------------------------------
179B ALA* 2.9 23.5 + - + +
180B THR 4.0 1.6 - - - +
182B THR* 1.3 76.2 - - + +
184B GLU* 1.3 61.3 + - - +
186B MET* 3.2 15.1 + - - +
187B LYS* 2.8 30.8 + - - +
193B MET* 4.5 2.5 - - + +
196B TRP* 3.5 50.4 + - + -
197B MET 5.0 0.2 - - - +
198B ILE* 3.6 20.2 - - + -
255B VAL* 3.8 16.6 - - + -
257B ILE* 3.6 37.2 - - + -
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Residues in contact with GLU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LYS* 3.2 25.5 + - - -
125B ASP* 6.0 0.9 - - - +
180B THR* 2.9 31.8 + - - +
181B GLU* 4.1 5.9 - - - +
183B LEU* 1.3 76.5 - - - +
185B TRP* 1.3 63.3 + - - +
187B LYS* 3.3 4.4 + - - +
188B ALA* 3.0 24.4 + - - +
196B TRP* 3.9 18.5 - - + +
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Residues in contact with TRP 185 (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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181B GLU 3.1 17.9 + - - +
182B THR 3.5 4.3 - - - +
184B GLU* 1.3 76.3 - - - +
186B MET* 1.3 66.8 + - - +
188B ALA* 3.2 2.6 + - - -
189B ASN* 3.0 59.0 + - + +
190B VAL* 3.8 18.8 - - + -
271B HIS* 4.5 8.1 - + - -
275B ASP* 3.5 39.0 - - + -
277B GLU* 3.2 33.9 + - - +
278B LEU* 3.6 39.0 - - + -
281B ILE* 3.8 16.4 - - + -
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Residues in contact with MET 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 34.1 + - - +
183B LEU* 3.2 15.7 + - - +
185B TRP* 1.3 78.0 - - - +
187B LYS* 1.3 61.9 + - - +
190B VAL* 3.0 38.1 + - + +
193B MET* 3.3 18.3 - - + +
257B ILE* 4.6 4.0 - - + -
259B TRP* 3.3 37.7 - - + -
268B GLY 3.9 14.4 - - - +
269B LEU* 4.3 14.1 - - + -
272B VAL* 4.5 6.5 - - - -
278B LEU* 3.6 23.8 - - + -
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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
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125B ASP* 3.1 41.2 + - - +
127B PRO* 5.4 1.8 - - - -
148B ARG* 5.3 9.3 - - - +
150B PRO* 6.2 0.2 - - - +
151B LYS* 3.9 39.7 + - - +
183B LEU 2.8 20.0 + - - +
184B GLU* 3.3 4.9 + - - +
186B MET* 1.3 73.1 - - - +
188B ALA* 1.3 61.1 + - - +
189B ASN 3.5 0.2 + - - -
190B VAL 4.7 1.4 + - - +
193B MET* 3.3 20.2 - - + +
194B VAL 3.4 23.6 - - - -
195B GLY* 4.1 6.5 - - - -
196B TRP* 4.0 17.3 - - + +
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Residues in contact with ALA 188 (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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148B ARG* 6.4 0.4 - - - +
184B GLU 3.0 17.0 + - - +
185B TRP* 3.8 4.7 - - - +
186B MET 3.2 0.2 - - - -
187B LYS* 1.3 79.4 - - - +
189B ASN* 1.3 71.3 + - - +
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Residues in contact with ASN 189 (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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185B TRP* 3.0 69.4 + - + +
186B MET 3.3 0.2 + - - -
188B ALA* 1.3 92.5 - - - +
190B VAL* 1.3 62.3 + - - +
191B PRO* 3.9 5.9 - - - +
271B HIS* 5.4 2.4 + - - -
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Residues in contact with VAL 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LYS* 4.4 5.9 + - - -
185B TRP* 3.8 17.0 - - + -
186B MET* 3.0 36.4 + - + +
187B LYS 4.8 1.0 - - - +
188B ALA 4.0 0.2 - - - -
189B ASN* 1.3 80.5 - - - +
191B PRO* 1.3 76.2 - - + +
192B GLY 3.5 1.6 + - - -
193B MET* 3.6 13.5 + - - +
259B TRP* 3.7 15.3 - - + -
268B GLY* 3.6 31.4 - - - +
271B HIS* 3.9 22.9 - - + -
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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
------------------------------------------------------------
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