Contacts of the helix formed by residues 173 - 189 (chain B) in PDB entry 3Q72
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 173 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ALA* 5.8 0.3 - - - +
100B PRO 4.9 7.6 - - - +
102B VAL* 5.7 0.5 - - - +
170B SER* 2.9 20.4 + - - +
171B VAL 3.4 1.0 - - - -
172B THR* 1.3 81.3 - - - +
174B LYS* 1.3 64.2 + - - +
175B GLY* 2.9 16.3 + - - -
176B SER* 2.7 44.5 + - - +
177B PHE* 3.3 3.5 + - - +
212B GLU* 3.8 3.4 - - - +
213B VAL* 4.8 0.7 - - - -
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Residues in contact with LYS 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ASP* 1.3 72.5 - - - +
175B GLY* 1.3 62.5 + - - +
177B PHE* 3.1 10.7 + - + +
178B GLU* 3.0 24.6 + - + +
212B GLU* 3.1 41.2 + - + +
213B VAL* 3.7 17.7 - - + -
217B GLU* 4.8 6.3 - - - +
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Residues in contact with GLY 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ASP* 2.9 10.8 + - - -
174B LYS* 1.3 81.1 - - - +
176B SER* 1.3 56.2 + - - +
178B GLU* 3.3 8.1 + - - +
179B LYS* 3.0 24.8 + - - +
212B GLU* 4.8 0.2 + - - -
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Residues in contact with SER 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ALA* 3.4 32.3 + - - +
102B VAL* 3.7 13.7 - - - -
168B VAL 4.7 1.4 - - - +
169B TYR* 3.5 5.5 - - - +
170B SER 3.1 20.7 + - - -
173B ASP* 2.7 36.0 + - - +
175B GLY* 1.3 74.1 - - - +
177B PHE* 1.3 60.6 + - - +
179B LYS* 3.6 4.1 - - - +
180B ALA* 2.9 28.2 + - - +
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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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169B TYR* 3.7 46.0 - + + -
173B ASP 3.3 1.1 + - - +
174B LYS* 3.2 16.2 - - + +
176B SER* 1.3 82.5 + - - +
178B GLU* 1.3 59.3 + - + +
180B ALA* 3.6 3.0 - - + +
181B SER* 3.3 22.6 + - - -
200B LEU* 4.5 5.2 - - + -
213B VAL* 3.6 31.6 - - + -
217B GLU* 3.3 34.8 - - + -
218B GLY* 4.1 6.1 - - - -
221B CYS* 3.7 37.9 - - + -
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Residues in contact with GLU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU 5.8 3.8 - - - +
174B LYS* 3.0 13.9 + - + +
175B GLY* 3.3 9.8 + - - +
176B SER 3.2 0.2 - - - -
177B PHE* 1.3 75.1 - - + +
179B LYS* 1.3 67.6 + - - +
180B ALA 3.2 1.3 - - - -
181B SER* 3.4 7.8 + - - +
182B GLU* 3.1 23.5 + - + +
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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
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188A ARG* 5.8 2.0 - - - +
226A ASP* 2.9 38.5 + - - +
254A ARG* 3.3 22.9 - - - +
98B GLY 5.6 0.4 - - - -
99B ALA* 4.3 22.2 - - + +
100B PRO* 5.8 2.2 - - + -
175B GLY 3.0 14.5 + - - +
176B SER* 3.6 12.1 - - - +
178B GLU* 1.3 78.0 - - - +
180B ALA* 1.3 55.1 + - - +
182B GLU* 2.5 38.0 + - - +
183B LEU* 2.9 53.9 + - + +
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Residues in contact with ALA 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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167B ILE* 3.7 30.4 - - + +
168B VAL 4.9 1.6 - - - +
169B TYR* 4.3 7.0 - - + -
176B SER 2.9 18.6 + - - +
177B PHE* 3.6 11.4 - - + +
178B GLU 3.2 0.2 - - - -
179B LYS* 1.3 74.4 - - - +
181B SER* 1.3 65.9 + - - +
183B LEU* 3.3 5.9 + - - +
184B ARG* 3.0 23.3 + - - +
200B LEU* 4.0 19.2 - - + +
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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
----------------------------------------------------------
177B PHE* 3.3 12.8 + - - -
178B GLU* 3.4 11.7 + - - -
179B LYS 3.4 0.2 - - - -
180B ALA* 1.3 77.4 - - - +
182B GLU* 1.3 63.5 + - - +
184B ARG* 3.0 18.4 + - - +
185B VAL* 3.0 19.0 + - - +
221B CYS* 3.4 27.3 - - - -
225B PHE* 5.5 11.3 - - - -
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Residues in contact with GLU 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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226A ASP* 3.8 2.6 - - - +
250A GLN* 3.7 12.9 - - - +
253A LEU* 4.6 18.4 - - + +
254A ARG* 3.3 17.1 + - - -
178B GLU* 3.1 11.7 + - + +
179B LYS* 2.5 43.3 + - - +
181B SER* 1.3 78.3 - - - +
183B LEU* 1.3 55.9 + - - +
185B VAL* 3.3 8.3 + - - +
186B GLN* 3.0 50.8 + - + +
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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
----------------------------------------------------------
223A VAL 5.5 6.1 - - - +
226A ASP* 3.7 19.3 - - + +
97B LEU* 4.7 9.2 - - + -
98B GLY* 4.0 28.7 - - - +
167B ILE* 4.3 19.3 - - + -
179B LYS* 2.9 62.8 + - + +
180B ALA* 3.5 5.2 - - - +
182B GLU* 1.3 75.3 - - - +
184B ARG* 1.3 62.6 + - - +
186B GLN* 3.4 11.8 + - - +
187B LEU* 3.0 34.7 + - + +
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Residues in contact with ARG 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ILE* 4.0 10.7 - - + +
180B ALA 3.0 12.9 + - - +
181B SER* 3.3 13.2 - - - +
183B LEU* 1.3 77.0 - - - +
185B VAL* 1.3 59.9 + - + +
187B LEU* 3.4 2.7 + - - +
188B ARG* 3.0 25.3 + - - +
194B ASP* 2.7 42.8 + - - -
198B ILE* 3.4 28.1 - - - +
225B PHE* 2.8 39.7 + - + +
226B ASP* 3.2 18.8 + - - +
227B CYS* 3.3 28.5 - - - -
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Residues in contact with VAL 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B SER* 3.0 14.5 + - - +
182B GLU* 3.7 9.2 - - - +
184B ARG* 1.3 76.2 - - + +
186B GLN* 1.3 58.8 - - + +
188B ARG* 3.3 8.9 + - + +
189B ARG* 2.9 76.5 + - + +
225B PHE* 5.0 25.4 - - + -
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Residues in contact with GLN 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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223A VAL* 3.4 26.4 - - + +
226A ASP* 3.8 11.0 + - - +
227A CYS 3.2 30.5 + - - +
228A LYS* 4.8 2.6 - - - +
182B GLU* 3.0 49.2 + - + +
183B LEU* 3.6 12.4 - - - +
185B VAL* 1.3 77.1 - - + +
187B LEU* 1.3 57.2 + - + +
189B ARG* 3.4 11.0 + - - +
190B ALA* 2.9 27.5 + - - +
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Residues in contact with LEU 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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223A VAL* 3.5 33.9 - - + +
224A VAL* 5.1 0.4 - - - +
97B LEU* 4.1 19.7 - - + -
165B TYR* 4.0 30.1 - - + -
167B ILE* 4.1 12.1 - - + -
183B LEU* 3.0 24.9 + - + +
184B ARG* 3.6 4.3 - - - +
186B GLN* 1.3 74.7 - - + +
188B ARG* 1.3 61.2 + - - +
189B ARG 3.0 1.1 - - - -
190B ALA* 2.8 21.9 + - + +
191B ARG* 3.3 32.5 + - - +
194B ASP* 4.5 2.6 + - - +
198B ILE* 4.0 20.6 - - + -
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Residues in contact with ARG 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 ARG* 3.0 26.8 + - - +
185B VAL* 3.5 13.2 - - + +
187B LEU* 1.3 75.8 - - - +
189B ARG* 1.3 65.2 + - + +
190B ALA 3.6 3.5 + - - +
194B ASP* 3.0 48.8 + - - +
226B ASP* 4.4 11.9 + - - +
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Residues in contact with ARG 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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219A ARG* 5.5 3.3 - - - -
185B VAL* 2.9 51.3 + - + +
186B GLN* 3.6 10.4 - - - +
188B ARG* 1.3 81.7 - - + +
190B ALA* 1.3 62.5 + - - +
191B ARG 5.1 0.7 - - - +
192B GLN 4.7 5.5 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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