Contacts of the helix formed by residues 170 - 184 (chain A) in PDB entry 3D8U
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A GLU* 4.5 4.7 - - - -
168A GLY 4.3 0.2 + - - -
169A VAL* 1.3 73.2 - - - +
171A HIS* 1.3 59.8 + - - +
172A PHE* 3.2 14.6 + - - +
173A GLU* 2.6 43.2 + - + +
174A VAL* 3.2 24.3 + - - +
204A ARG* 5.0 6.4 + - - -
329A MSE 4.8 4.2 + - - -
331A PHE* 5.1 0.7 - - - -
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Residues in contact with HIS 171 (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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157A GLU* 4.2 11.8 + - - -
169A VAL* 3.2 40.5 + - + +
170A ASP* 1.3 69.9 - - - +
172A PHE* 1.3 58.0 + - - +
173A GLU 3.2 0.2 - - - -
174A VAL* 3.0 12.3 + - - +
175A GLY* 2.6 34.3 + - - -
201A THR* 3.8 41.7 + - + +
204A ARG* 4.2 9.0 - - + +
205A GLN* 4.0 26.2 + - + +
283A LEU 5.7 1.2 + - - -
284A GLU* 6.5 1.3 - - + -
301A PHE* 5.0 9.1 - + - -
303A TYR* 5.5 4.5 - - - -
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Residues in contact with PHE 172 (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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170A ASP* 3.3 10.1 - - - +
171A HIS* 1.3 78.4 - - - +
173A GLU* 1.3 62.7 + - + +
175A GLY* 3.1 1.2 + - - -
176A LYS* 2.8 53.7 + - + +
204A ARG* 3.2 60.0 + - - +
207A HIS* 3.7 13.2 - - + -
208A GLY* 3.4 28.2 - - - -
211A SER* 3.7 24.9 - - - -
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Residues in contact with GLU 173 (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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170A ASP* 2.6 33.0 + - + +
172A PHE* 1.3 77.3 - - + +
174A VAL* 1.3 54.9 + - - +
176A LYS* 3.1 20.8 + - - +
177A ALA* 2.7 43.2 + - + +
180A ARG* 4.3 6.7 + - - -
331A PHE* 4.5 14.1 - - + -
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Residues in contact with VAL 174 (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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169A VAL* 4.6 1.6 - - + -
170A ASP 3.2 14.5 + - - +
171A HIS* 3.0 15.6 + - - +
173A GLU* 1.3 75.9 - - - +
175A GLY* 1.3 64.7 + - - +
177A ALA* 4.2 0.3 - - - +
178A CYS* 3.2 25.6 + - - +
205A GLN* 5.0 3.4 - - - +
283A LEU* 3.7 36.1 - - + +
299A ALA* 4.1 12.8 - - + -
301A PHE* 3.5 27.1 - - + -
331A PHE* 3.6 26.2 - - + -
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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
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171A HIS 2.6 18.0 + - - -
172A PHE 3.5 3.1 - - - -
174A VAL* 1.3 75.1 - - - +
176A LYS* 1.3 54.7 + - - +
178A CYS* 3.8 1.4 - - - +
179A THR* 2.6 39.3 + - - +
205A GLN* 3.9 17.3 - - - -
208A GLY 4.0 4.5 - - - -
209A TRP* 5.4 0.2 - - - -
283A LEU* 4.5 15.9 - - - -
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Residues in contact with LYS 176 (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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172A PHE* 2.8 41.1 + - + +
173A GLU* 3.5 17.3 - - - +
175A GLY* 1.3 69.1 - - - +
177A ALA* 1.3 68.5 + - - +
178A CYS 2.9 1.7 + - - -
179A THR 3.1 0.9 + - - -
180A ARG* 2.7 37.1 + - - +
208A GLY* 3.5 22.0 - - - +
211A SER* 4.6 13.0 + - - -
212A ALA* 3.8 12.4 - - + +
215A GLU* 3.7 31.1 + - - -
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Residues in contact with ALA 177 (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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173A GLU* 2.7 24.4 + - - +
176A LYS* 1.3 73.7 - - - +
178A CYS* 1.3 57.2 + - - +
180A ARG* 3.0 29.1 + - - +
181A HIS* 2.8 29.6 + - - +
331A PHE* 4.0 24.0 - - + -
333A LEU* 5.4 6.1 - - + +
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Residues in contact with CYS 178 (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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174A VAL* 3.2 20.2 + - - +
175A GLY 3.8 2.2 - - - +
176A LYS 3.0 0.8 - - - -
177A ALA* 1.3 76.3 - - - +
179A THR* 1.3 65.3 + - + +
181A HIS* 3.2 10.2 + - - +
182A LEU* 3.4 11.4 + - - +
253A VAL* 5.3 0.2 - - + -
281A ILE* 3.4 40.7 - - + +
282A CYS 4.3 0.4 - - - -
283A LEU* 3.5 27.1 - - + -
299A ALA* 3.8 16.4 - - - -
331A PHE* 5.0 2.5 - - - -
333A LEU* 3.7 20.0 - - - -
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Residues in contact with THR 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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175A GLY* 2.6 27.8 + - - +
176A LYS 4.3 1.6 - - - +
178A CYS* 1.3 72.9 - - - +
180A ARG* 1.3 65.9 + - - +
182A LEU* 3.1 9.7 + - - +
183A ILE* 3.0 33.2 + - - +
190A VAL* 4.5 4.7 - - - +
209A TRP* 3.4 48.7 + - + -
212A ALA* 3.4 14.8 - - + +
213A MSE 4.3 4.9 - - - -
253A VAL* 3.9 17.9 - - + -
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Residues in contact with ARG 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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173A GLU* 4.3 9.9 + - - -
176A LYS* 2.7 32.5 + - - +
177A ALA* 3.0 43.2 - - - +
179A THR* 1.3 73.1 + - - +
181A HIS* 1.3 63.1 + - - +
183A ILE* 2.9 18.2 + - - +
184A GLU* 2.9 35.8 + - - +
212A ALA* 3.8 9.3 - - + +
215A GLU* 4.0 21.3 - - - +
216A ASN* 4.9 7.0 - - - +
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Residues in contact with HIS 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 ALA 2.8 16.5 + - - +
178A CYS* 3.5 10.5 - - - +
179A THR 3.1 0.6 - - - -
180A ARG* 1.3 74.5 - - - +
182A LEU* 1.3 64.1 + - - +
183A ILE 3.3 0.7 + - - -
184A GLU* 3.4 13.4 + - + +
185A GLN* 3.2 35.7 + - - +
281A ILE* 4.5 6.0 - - + +
297A THR* 4.2 13.2 - - + +
333A LEU* 4.1 17.6 - - + +
335A ARG* 4.1 39.2 + - + +
339A THR* 3.2 33.6 + - + +
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Residues in contact with LEU 182 (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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178A CYS 3.4 8.8 + - - +
179A THR* 3.1 8.6 + - - +
181A HIS* 1.3 77.1 - - - +
183A ILE* 1.3 64.2 + - - +
185A GLN* 3.0 18.4 + - - +
187A PHE* 3.1 27.0 + - + +
190A VAL* 3.7 31.2 - - + -
251A ALA* 3.7 11.7 - - + -
252A LEU 4.3 3.4 - - - +
253A VAL* 3.8 6.1 - - + -
279A ALA* 3.5 35.7 - - + -
280A ILE 4.6 0.2 - - - +
281A ILE* 3.7 28.5 - - + -
339A THR* 4.0 15.9 - - + -
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Residues in contact with ILE 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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179A THR* 3.0 16.8 + - - +
180A ARG* 2.9 10.5 + - + +
182A LEU* 1.3 72.7 - - - +
184A GLU* 1.3 56.9 + - - +
185A GLN 2.7 14.9 + - - -
186A GLY* 3.1 11.6 + - - -
187A PHE 3.8 11.4 + - - +
188A LYS* 3.7 22.8 + - + +
190A VAL* 4.6 6.7 - - + -
212A ALA* 3.5 31.9 - - + +
213A MSE 4.1 9.4 - - - -
216A ASN* 3.8 29.4 - - + +
218A LEU* 3.8 27.8 - - + -
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Residues in contact with GLU 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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180A ARG* 2.9 49.6 + - - +
181A HIS* 3.6 14.9 - - + +
183A ILE* 1.3 76.5 - - + +
185A GLN* 1.3 71.6 + - - +
186A GLY 3.5 0.4 - - - -
335A ARG* 5.9 1.2 + - - -
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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