Contacts of the helix formed by residues 173 - 190 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ALA* 5.4 0.9 - - - +
100A PRO 4.6 9.5 - - - +
102A VAL* 4.8 1.9 - - - +
170A SER* 3.0 21.8 + - - +
171A VAL 3.3 1.0 - - - -
172A THR* 1.3 80.7 - - - +
174A LYS* 1.3 61.4 + - - +
175A GLY* 3.1 8.0 + - - -
176A SER* 2.9 48.7 + - - +
177A PHE* 3.4 4.2 + - - +
212A GLU* 3.7 2.4 - - - +
213A VAL* 4.6 1.3 - - - -
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Residues in contact with LYS 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ASP* 1.3 72.9 + - - +
175A GLY* 1.3 63.8 + - - +
177A PHE* 3.2 11.5 + - + +
178A GLU* 3.1 35.5 + - + +
212A GLU* 2.8 35.9 + - + +
213A VAL* 3.9 19.5 - - + -
217A GLU* 5.0 7.0 - - - +
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Residues in contact with GLY 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ASP* 3.1 7.6 + - - -
174A LYS* 1.3 78.9 - - - +
176A SER* 1.3 56.7 + - - +
178A GLU* 3.0 21.4 - - - +
179A LYS* 2.9 29.0 + - - +
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Residues in contact with SER 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ALA* 3.4 32.4 + - - +
102A VAL* 3.5 14.1 - - - +
168A VAL 4.7 1.4 - - - +
169A TYR* 3.4 5.7 - - - +
170A SER 3.0 22.4 + - - -
173A ASP* 2.9 33.4 + - - -
175A GLY* 1.3 73.6 - - - +
177A PHE* 1.3 56.4 + - - +
178A GLU 3.5 0.2 - - - -
179A LYS* 3.8 3.7 - - - +
180A ALA* 2.9 28.6 + - - +
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Residues in contact with PHE 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A TYR* 3.6 46.9 - + + -
173A ASP 3.4 1.3 + - - +
174A LYS* 3.2 15.2 + - + +
175A GLY 3.1 0.4 - - - -
176A SER* 1.3 79.1 + - - +
178A GLU* 1.3 66.1 + - + +
180A ALA* 3.2 5.5 - - + +
181A SER* 3.1 24.0 + - - -
200A LEU* 4.5 4.7 - - + -
213A VAL* 3.7 37.5 - - + -
217A GLU* 3.5 38.1 - - + -
218A GLY* 4.0 7.6 - - - -
221A CYS* 3.9 23.6 - - + -
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Residues in contact with GLU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LYS* 3.1 24.0 + - + +
175A GLY* 3.0 29.8 - - - +
177A PHE* 1.3 78.3 - - + +
179A LYS* 1.3 59.6 + - + +
181A SER* 3.1 9.0 + - - +
182A GLU* 2.9 28.3 + - - +
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Residues in contact with LYS 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLY* 5.4 1.8 - - - -
99A ALA* 4.3 25.5 - - + +
100A PRO* 5.7 3.2 - - - +
175A GLY 2.9 18.0 + - - +
176A SER* 3.8 8.7 - - - +
178A GLU* 1.3 79.2 - - + +
180A ALA* 1.3 51.9 + - - +
182A GLU* 2.9 42.5 + - - +
183A LEU* 2.8 38.6 + - + +
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Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLY* 6.4 1.1 - - - -
167A ILE* 3.7 29.5 - - + +
168A VAL 5.0 0.9 - - - +
169A TYR* 4.1 9.4 - - + -
176A SER 2.9 19.8 + - - +
177A PHE* 3.2 12.1 - - + +
179A LYS* 1.3 74.7 - - - +
181A SER* 1.3 58.2 + - - +
183A LEU* 3.4 4.8 + - - +
184A ARG* 3.0 26.9 + - - +
200A LEU* 3.9 19.0 - - + +
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Residues in contact with SER 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A PHE* 3.1 13.6 + - - -
178A GLU* 3.1 11.3 + - - -
180A ALA* 1.3 76.0 - - - +
182A GLU* 1.3 64.8 + - - +
184A ARG* 3.2 9.1 + - - +
185A VAL* 3.2 27.4 + - - +
200A LEU* 5.8 1.3 - - - +
221A CYS* 3.2 30.2 - - - -
225A PHE* 5.6 9.1 - - - -
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Residues in contact with GLU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A GLU 2.9 13.1 + - - +
179A LYS* 2.9 45.0 - - - +
181A SER* 1.3 78.2 - - - +
183A LEU* 1.3 61.3 + - - +
185A VAL* 3.5 5.0 + - - +
186A GLN* 3.1 39.0 + - + +
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Residues in contact with LEU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 3.6 39.3 - - + -
98A GLY* 4.5 7.9 - - - +
167A ILE* 4.0 20.0 - - + -
179A LYS* 2.8 22.4 + - + +
180A ALA* 3.7 6.1 - - - +
182A GLU* 1.3 75.3 - - - +
184A ARG* 1.3 64.9 + - - +
186A GLN* 3.2 26.4 + - + +
187A LEU* 2.9 35.2 + - + +
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Residues in contact with ARG 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ILE* 3.9 9.4 - - + +
180A ALA 3.0 15.3 + - - +
181A SER* 3.2 12.3 + - - +
183A LEU* 1.3 76.2 - - - +
185A VAL* 1.3 57.7 + - - +
187A LEU* 3.4 3.4 + - - +
188A ARG* 3.0 47.8 + - - +
198A ILE* 3.4 35.0 - - - +
200A LEU* 6.3 1.3 - - + -
225A PHE* 2.9 36.6 + - + +
226A ASP* 2.9 40.2 + - - +
227A CYS* 3.5 21.6 - - - -
254A ARG* 5.2 3.0 - - - +
146B TRP* 3.6 10.3 - - + -
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Residues in contact with VAL 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A SER 3.2 14.7 + - - +
182A GLU* 3.5 5.1 + - - +
184A ARG* 1.3 74.7 - - + +
186A GLN* 1.3 65.4 + - - +
188A ARG* 3.4 7.6 + - + +
189A ARG* 3.1 61.3 + - + +
225A PHE* 3.8 36.1 - - + -
145B ILE 5.7 1.1 - - - +
146B TRP* 4.1 12.1 - - + +
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Residues in contact with GLN 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A GLU* 3.1 32.1 + - + +
183A LEU* 3.3 32.7 - - + +
185A VAL* 1.3 76.9 - - - +
187A LEU* 1.3 57.9 + - + +
189A ARG* 3.0 8.6 + - - +
190A ALA* 2.9 31.4 + - + +
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Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 4.2 9.9 - - + -
165A TYR* 3.9 43.5 - - + -
167A ILE* 3.9 22.9 - - + -
183A LEU* 2.9 26.4 + - + +
184A ARG* 3.4 7.6 + - - +
186A GLN* 1.3 76.1 - - + +
188A ARG* 1.3 59.3 + - - +
190A ALA* 2.8 28.7 - - + +
191A ARG* 4.6 15.0 - - - +
196A VAL* 5.9 1.1 - - + -
198A ILE* 3.9 20.6 - - + -
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Residues in contact with ARG 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ARG* 3.0 34.0 + - - +
185A VAL* 3.5 7.0 - - + +
187A LEU* 1.3 75.2 - - - +
189A ARG* 1.3 63.4 + - + +
190A ALA 4.8 0.2 - - - -
226A ASP* 4.8 7.9 + - - +
98B GLY 2.7 29.5 + - - -
99B ALA* 3.5 2.2 - - - +
100B PRO* 3.4 44.8 - - - +
104B LYS* 3.6 9.5 - - - +
146B TRP* 3.3 67.9 - - + +
179B LYS* 5.8 1.8 - - - +
256B GNP 3.9 3.8 + - - -
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Residues in contact with ARG 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A VAL* 3.1 37.9 + - - +
186A GLN* 3.0 8.9 + - - +
188A ARG* 1.3 83.4 - - + +
190A ALA* 1.3 60.2 + - - +
191A ARG 4.1 1.6 + - - +
146B TRP 2.7 29.9 + - - -
147B GLU* 3.5 22.0 + - - +
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Residues in contact with ALA 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A GLN 2.9 15.5 + - - +
187A LEU* 2.8 23.1 + - + +
188A ARG 4.8 0.3 - - - -
189A ARG* 1.3 80.4 - - - +
191A ARG* 1.3 92.8 + - - +
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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