Contacts of the helix formed by residues 170 - 188 (chain B) in PDB entry 2QUH
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 170 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B MET* 1.3 75.7 - - - +
171B VAL* 1.3 65.6 + - - +
172B GLY* 2.9 32.1 - - - -
173B HIS* 3.1 66.7 + + - +
174B LEU* 3.7 3.1 + - - +
350B MET* 3.3 41.9 + - - +
351B SER* 4.1 0.4 - - - -
352B ALA* 3.5 22.0 + - - +
358B SER* 3.5 19.4 + - - -
359B ILE 3.5 16.4 - - - +
360B PHE* 3.9 4.3 - - + +
361B LEU* 3.6 10.6 - - - +
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Residues in contact with VAL 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B HIS* 1.3 74.8 - - - +
172B GLY* 1.3 61.8 + - - +
174B LEU* 3.1 19.4 + - + +
175B ILE* 3.9 6.9 + - - +
340B PHE* 3.5 18.4 - - + -
350B MET* 4.7 2.2 - - - -
359B ILE* 3.0 26.0 + - + +
361B LEU* 3.6 13.7 - - + +
406B PHE* 3.1 37.7 - - + -
438B LEU* 4.8 4.9 - - + -
441B LEU* 4.3 8.7 - - + -
442B ILE* 3.8 27.6 - - + -
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Residues in contact with GLY 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B HIS* 2.9 18.0 - - - -
171B VAL* 1.3 78.4 - - - +
173B HIS* 1.3 63.5 + - - +
174B LEU 3.2 0.7 + - - -
175B ILE* 3.4 18.0 + - - +
176B PRO* 4.0 3.3 - - - +
340B PHE* 3.6 32.6 - - - +
350B MET* 3.9 4.5 - - - -
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Residues in contact with HIS 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ARG* 3.4 31.1 + - - +
168B ALA 4.2 5.6 - - - -
169B MET* 3.4 26.0 - - + +
170B HIS* 3.1 62.1 + + - +
172B GLY* 1.3 76.7 - - - +
174B LEU* 1.3 62.6 + - + +
176B PRO* 3.5 10.9 - - - +
177B PHE* 3.3 23.4 - - + -
349B LYS* 6.1 3.1 - - - -
352B ALA* 4.4 7.5 - - + +
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B MET* 6.1 2.0 - - - -
170B HIS 4.2 0.9 - - - +
171B VAL* 3.1 17.1 + - + +
172B GLY 3.1 1.4 - - - -
173B HIS* 1.3 78.4 - - + +
175B ILE* 1.3 66.9 + - + +
177B PHE* 3.1 9.3 + - + +
178B ILE* 2.8 43.2 + - + +
221B ASP* 5.1 3.1 - - + +
225B CYS* 4.1 18.4 - - - -
361B LEU* 3.5 45.1 - - + -
406B PHE* 5.3 1.8 - - + -
441B LEU* 4.8 17.7 - - + -
445B HIS* 4.0 20.9 - - + +
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Residues in contact with ILE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B PHE* 3.5 32.3 - - + -
136B ILE* 4.2 8.7 - - + -
137B PHE* 4.5 7.4 - - + -
171B VAL 4.2 2.0 - - - +
172B GLY 3.5 13.2 - - - +
174B LEU* 1.3 75.1 - - - +
176B PRO* 1.3 75.0 - - + +
178B ILE* 3.0 11.2 + - + +
179B PHE* 3.1 10.2 + - - +
337B SER* 4.5 7.9 - - - +
338B THR 5.2 2.9 - - - +
340B PHE* 3.9 17.3 - - + +
405B PHE* 3.4 38.6 - - + -
406B PHE* 3.9 27.6 - - + -
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Residues in contact with PRO 176 (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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137B PHE* 4.2 16.0 - - + -
160B THR* 4.8 5.8 - - - +
161B GLY 6.1 0.2 - - - +
172B GLY 4.0 4.9 - - - +
173B HIS* 3.5 15.3 - - - +
175B ILE* 1.3 94.9 - - + +
177B PHE* 1.3 66.3 + - + +
179B PHE* 3.3 2.8 + - - +
180B THR* 2.8 34.2 + - - -
308B PRO* 4.7 5.3 - - - +
309B CYS* 4.5 21.8 - - - -
310B ALA* 4.6 11.4 - - + +
337B SER* 4.9 4.7 - - - +
818B TRP* 6.4 0.2 - - + -
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Residues in contact with PHE 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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160B THR* 3.9 24.0 - - + -
161B GLY 3.5 24.9 - - - -
162B ARG* 3.7 14.8 - - + -
169B MET* 6.1 1.8 - - - -
173B HIS* 3.3 28.0 - - + -
174B LEU* 3.1 9.7 + - + +
176B PRO* 1.3 85.0 - - + +
178B ILE* 1.3 62.7 + - - +
180B THR* 3.2 3.0 + - - -
181B LYS* 2.9 22.7 + - - +
193B ILE* 4.1 5.8 - - + -
222B ILE* 3.5 52.0 - - + -
225B CYS* 4.1 18.8 - - - -
227B PHE* 3.4 17.7 - + + -
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Residues in contact with ILE 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B HIS* 4.1 13.7 - - - +
130B HIS* 5.8 1.3 - - + -
131B PHE* 3.9 19.1 - - + -
174B LEU* 2.8 41.2 + - + +
175B ILE* 3.4 10.3 - - - +
177B PHE* 1.3 72.7 - - - +
179B PHE* 1.3 61.9 + - - +
181B LYS* 3.5 7.8 + - - +
182B TRP* 3.3 18.9 + - - +
225B CYS* 5.1 10.1 - - + -
406B PHE* 3.8 31.2 - - + -
441B LEU* 5.4 3.4 - - + -
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Residues in contact with PHE 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B HIS* 4.0 13.9 - + + -
131B PHE* 3.6 25.8 - + + -
132B LEU* 3.8 38.4 - - + -
137B PHE* 3.3 51.4 - + + -
175B ILE 3.1 5.3 + - - +
176B PRO 3.7 4.3 - - - +
178B ILE* 1.3 76.6 - - - +
180B THR* 1.3 59.0 + - - +
182B TRP* 2.9 24.5 + + - +
183B LEU* 2.8 57.9 + - + +
308B PRO* 4.4 3.1 - - + -
335B LEU* 3.9 11.4 - - + -
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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
----------------------------------------------------------
158B LEU* 4.0 7.4 - - + +
160B THR* 4.1 13.7 + - + +
176B PRO 2.8 20.5 + - - -
177B PHE* 3.2 6.0 + - - -
179B PHE* 1.3 76.4 - - - +
181B LYS* 1.3 58.8 + - - +
183B LEU* 3.3 10.5 + - - +
184B GLN* 2.9 27.4 + - - +
191B LEU* 3.5 42.8 - - + -
227B PHE* 3.7 5.2 - - + -
308B PRO* 3.0 26.7 - - + +
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Residues in contact with LYS 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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177B PHE 2.9 14.1 + - - +
178B ILE* 3.7 7.6 - - - +
180B THR* 1.3 77.3 - - - +
182B TRP* 1.3 65.1 + - - +
184B GLN* 3.5 3.1 + - - +
185B ASP* 2.9 49.6 + - - +
225B CYS 3.2 27.6 - - - +
226B GLY* 2.9 33.3 + - - -
227B PHE* 3.3 24.4 - - + +
228B ASP 5.2 1.0 - - - +
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Residues in contact with TRP 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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120B ILE* 4.5 12.8 - - + -
124B THR* 6.3 0.2 - - - -
126B GLN* 5.0 4.1 + - + +
127B ARG 3.8 13.6 + - - -
128B PRO* 4.0 7.2 - - + -
129B HIS* 3.4 53.7 - + + +
132B LEU* 4.0 12.6 - - + -
178B ILE 3.3 7.3 + - - +
179B PHE* 2.9 34.8 + + - +
181B LYS* 1.3 82.8 - - - +
183B LEU* 1.3 87.0 + - + +
185B ASP* 3.0 7.4 + - + +
186B VAL* 2.8 63.7 + - + +
187B PHE* 5.2 0.2 - + - -
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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
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120B ILE* 6.3 1.1 - - + -
132B LEU* 5.9 0.4 - - + -
143B MET* 5.3 1.3 - - + -
158B LEU* 3.8 26.1 - - + +
179B PHE* 2.8 38.2 + - + +
180B THR* 3.6 7.4 - - - +
182B TRP* 1.3 98.9 - - + +
184B GLN* 1.3 56.2 + - - +
186B VAL* 4.6 0.2 - - - -
187B PHE* 3.0 63.0 + - + +
306B LEU* 4.4 1.3 - - + -
308B PRO* 4.0 15.7 - - + -
335B LEU* 3.7 29.4 - - + -
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Residues in contact with GLN 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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158B LEU* 3.6 15.6 - - + +
180B THR 2.9 16.8 + - - +
181B LYS* 3.9 5.1 + - - +
183B LEU* 1.3 77.5 - - - +
185B ASP* 1.3 68.2 + - - +
188B ASN* 2.9 30.1 + - - +
189B VAL 3.7 14.3 - - - +
191B LEU* 3.3 24.5 - - + +
226B GLY 5.0 0.4 + - - -
227B PHE* 3.5 22.6 - - + +
228B ASP* 3.2 30.6 - - + +
231B LYS* 3.6 20.6 + - + +
232B THR* 3.4 11.1 - - - +
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Residues in contact with ASP 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 LYS* 2.9 49.5 + - - +
182B TRP* 3.0 8.4 + - + +
184B GLN* 1.3 88.7 + - - +
186B VAL* 1.3 65.6 + - + +
188B ASN* 3.6 10.4 + - - +
228B ASP* 5.7 3.1 - - - +
231B LYS* 5.9 1.4 + - - +
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Residues in contact with VAL 186 (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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124B THR* 3.2 44.1 - - + +
126B GLN* 4.3 15.5 - - + -
150B TYR* 4.1 5.0 + - - -
182B TRP* 2.8 64.5 + - + +
183B LEU 4.1 1.3 - - - +
185B ASP* 1.3 76.8 - - + +
187B PHE* 1.3 81.0 + - + +
188B ASN* 4.7 1.2 - - - +
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Residues in contact with PHE 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ILE* 4.4 10.3 - - + -
123B ALA* 5.3 0.2 - - + -
124B THR* 3.9 19.3 - - - -
143B MET* 4.2 23.3 - - + -
146B VAL* 5.7 0.9 - - + -
147B LEU* 4.2 16.2 - - + -
150B TYR* 3.6 56.5 + + + -
156B PHE* 3.7 29.8 - + + -
182B TRP* 5.2 0.2 - + - -
183B LEU* 3.0 54.0 + - + +
186B VAL* 1.3 84.4 - - + +
188B ASN* 1.3 71.4 + - - +
189B VAL* 3.6 9.5 - - + +
306B LEU* 5.3 1.1 - - + -
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Residues in contact with ASN 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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184B GLN 2.9 18.8 + - - +
185B ASP* 4.1 8.2 - - - +
186B VAL 3.4 2.5 - - - +
187B PHE* 1.3 83.0 - - - +
189B VAL* 1.3 58.5 + - - +
231B LYS* 2.7 37.1 + - - +
468B PHE* 3.3 19.1 - - - -
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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