Contacts of the helix formed by residues 178 - 191 (chain A) in PDB entry 3DUF
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 GLN 178 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ILE* 3.7 28.5 - - + +
145A GLY* 4.6 3.8 - - - -
175A GLY 3.1 14.6 + - - +
177A SER* 1.3 80.6 - - - +
179A GLY* 1.3 68.8 + - - +
180A ASP* 4.2 7.4 + - + +
181A PHE* 3.2 20.3 + - + +
182A TYR 3.6 2.9 + - - -
1370A R1T 3.4 14.1 - - - +
182C TYR* 3.9 5.2 - - - -
183C GLU* 4.5 2.6 - - - +
57D LEU* 3.4 30.6 + - + +
58D ALA* 3.7 11.9 - - - +
59D GLU* 3.2 26.0 + - - +
60D SER 5.5 0.7 + - - -
88D GLU* 4.6 9.5 - - - +
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Residues in contact with GLY 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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177A SER 3.7 0.8 + - - -
178A GLN* 1.3 74.9 + - - +
180A ASP* 1.3 58.6 + - - +
182A TYR* 3.2 4.3 + - - +
183A GLU* 3.0 31.4 + - - +
179C GLY* 3.9 23.1 - - - -
182C TYR* 4.5 4.9 - - - -
183C GLU* 3.3 26.4 + - - -
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Residues in contact with ASP 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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144A ILE 5.2 1.6 - - - +
145A GLY* 3.3 25.3 - - - +
146A ALA* 4.3 9.0 + - - -
148A TYR* 4.0 2.8 - - - +
149A ILE* 3.5 29.9 - - + +
178A GLN* 3.2 4.0 + - + +
179A GLY* 1.3 73.7 - - - +
181A PHE* 1.3 67.2 + - - +
183A GLU* 4.2 3.1 - - - +
184A GLY* 2.9 21.0 + - - -
60B SER* 2.5 31.8 + - - -
91B ASP* 4.7 5.5 - - - +
88D GLU* 4.5 14.0 - - - +
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Residues in contact with PHE 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLY* 4.4 4.6 + - - -
148A TYR* 3.4 44.8 - + + -
171A THR* 4.4 3.8 - - + +
175A GLY 3.5 14.8 - - - +
176A THR* 3.4 42.2 - - + -
178A GLN* 3.2 14.5 + - + +
180A ASP* 1.3 80.2 - - - +
182A TYR* 1.3 70.1 + + + +
185A ILE* 3.4 39.2 + - + +
199A VAL* 3.9 18.8 - - + -
219A LEU 5.3 0.4 - - - -
222A LYS* 4.1 21.1 - - + -
260A LEU* 4.4 22.0 - - + -
182C TYR* 4.5 3.4 - + - -
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Residues in contact with TYR 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 GLN 3.6 1.0 + - - -
179A GLY 3.2 8.2 + - - +
180A ASP 3.2 0.4 - - - -
181A PHE* 1.3 85.8 - + + +
183A GLU* 1.3 67.3 + - - +
185A ILE* 3.6 10.4 - - + +
186A ASN* 3.1 34.9 + - + +
222A LYS 5.7 0.4 - - - -
225A ALA* 3.7 35.0 - - + -
226A ALA* 5.3 0.2 - - - -
176C THR 2.7 30.1 + - - -
177C SER* 3.8 11.3 - - - -
178C GLN 3.7 20.6 - - - -
181C PHE* 4.6 4.7 - + - -
182C TYR* 3.6 44.9 - + + -
222C LYS* 3.0 26.9 + - + +
225C ALA* 5.7 0.2 - - + -
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Residues in contact with GLU 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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149A ILE* 4.1 10.1 - - + -
179A GLY 3.0 18.2 + - - +
180A ASP* 3.4 7.4 + - - +
182A TYR* 1.3 78.3 - - + +
184A GLY* 1.3 58.6 + - - +
186A ASN* 4.5 3.4 - - - +
187A PHE* 2.9 42.4 + - + +
58B ALA* 2.8 31.3 - - + +
60B SER* 3.3 22.9 + - - -
61B GLY* 2.9 18.8 + - - -
177C SER 3.5 17.0 - - - +
178C GLN* 4.1 3.9 - - - +
179C GLY* 3.2 25.2 + - - +
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Residues in contact with GLY 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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148A TYR* 4.0 18.6 - - - -
149A ILE* 3.8 9.8 - - - +
152A ALA* 3.8 5.5 - - - +
180A ASP 2.9 17.2 + - - -
181A PHE 3.9 1.8 - - - -
182A TYR 3.2 0.2 - - - -
183A GLU* 1.3 74.7 - - - +
185A ILE* 1.3 64.6 + - - +
187A PHE* 3.8 4.0 - - - +
188A ALA* 3.0 23.7 + - - +
197A PHE* 3.8 6.2 - - - -
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Residues in contact with ILE 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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148A TYR* 3.9 13.7 - - + -
181A PHE* 3.4 34.0 + - + +
182A TYR* 3.6 16.2 - - + +
184A GLY* 1.3 74.3 - - - +
186A ASN* 1.3 59.5 - - - +
188A ALA* 3.8 1.9 - - - +
189A GLY* 3.2 19.4 + - - -
197A PHE* 3.9 37.5 - - + -
222A LYS 4.1 17.5 - - - +
223A ALA* 4.3 8.3 - - - -
226A ALA* 3.6 26.9 - - + +
228A ILE* 4.3 14.1 - - + +
260A LEU* 4.8 6.7 - - + -
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Residues in contact with ASN 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 TYR* 3.1 32.5 + - + +
183A GLU* 3.9 4.0 - - - +
185A ILE* 1.3 80.9 - - - +
187A PHE* 1.3 61.5 + - - +
189A GLY* 3.2 2.5 + - - -
190A ALA* 3.0 27.4 + - - +
226A ALA* 3.8 17.0 - - + +
56B PRO* 4.7 5.1 - - - +
177C SER* 3.8 25.1 + - - +
213C GLN 3.3 20.7 + - - -
214C THR* 3.2 28.5 + - - -
222C LYS* 3.6 5.7 + - - +
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Residues in contact with PHE 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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149A ILE* 6.3 0.4 - - + -
152A ALA* 4.3 11.7 - - + -
183A GLU* 2.9 30.7 + - + +
184A GLY* 3.8 4.3 - - - +
186A ASN* 1.3 76.8 - - - +
188A ALA* 1.3 65.7 + - - +
190A ALA* 3.5 5.8 + - - +
191A PHE* 3.2 39.6 + + - -
55B THR* 4.3 9.2 - - - -
56B PRO* 3.7 44.2 - - + -
58B ALA* 3.6 37.2 - - + -
61B GLY* 3.7 24.5 - - - -
62B ILE* 3.9 3.8 - - + -
65B LEU* 3.9 26.5 - - + -
177C SER 5.3 1.3 - - - -
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Residues in contact with ALA 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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152A ALA* 4.2 12.1 - - + +
184A GLY 3.0 17.4 + - - +
185A ILE 3.8 2.5 - - - +
187A PHE* 1.3 77.4 - - - +
189A GLY* 1.3 58.6 + - - +
191A PHE 3.6 0.2 + - - -
192A LYS* 3.0 22.0 + - - -
193A ALA* 3.0 21.4 + - + -
195A ALA* 4.5 6.1 - - + -
197A PHE* 3.6 28.9 - - + -
258A PRO* 3.8 13.4 - - + +
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Residues in contact with GLY 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 ILE 3.2 15.2 + - - -
186A ASN 3.2 3.5 + - - -
188A ALA* 1.3 75.4 - - - +
190A ALA* 1.3 63.0 + - - +
192A LYS* 3.1 14.1 + - - +
226A ALA 4.9 0.4 - - - -
228A ILE* 4.0 13.5 - - - -
258A PRO* 4.0 4.5 - - - +
215C VAL* 3.5 34.4 - - - +
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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 ASN 3.0 16.3 + - - +
187A PHE 3.5 4.2 + - - +
189A GLY* 1.3 76.1 - - - +
191A PHE* 1.3 64.1 + - + +
192A LYS* 3.7 0.7 + - - +
56B PRO* 3.9 13.7 - - + -
211C GLU 6.1 0.2 - - - -
212C LYS* 3.7 25.3 - - - +
213C GLN 3.8 15.0 - - - +
214C THR* 4.5 2.9 - - - +
215C VAL* 4.4 11.6 - - - +
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Residues in contact with PHE 191 (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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152A ALA 6.0 0.4 - - - -
156A LEU* 4.1 29.8 - - + +
159A LYS* 3.8 17.0 - - - +
187A PHE* 3.2 31.7 + + - +
188A ALA 4.3 1.6 - - - +
189A GLY 3.2 0.2 - - - -
190A ALA* 1.3 81.0 - - + +
192A LYS* 1.3 72.5 + - - +
193A ALA* 3.3 7.4 + - + +
53B PHE* 3.7 39.5 - + + -
54B ASP 4.0 12.3 - - - -
55B THR* 4.0 6.7 - - + -
56B PRO* 4.0 21.1 - - + -
65B LEU* 4.1 20.0 - - + -
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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