Contacts of the helix formed by residues 170 - 186 (chain A) in PDB entry 1EMU
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 ASN 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A LEU* 4.6 6.9 - - + +
165A GLU 3.1 28.1 + - - +
167A CYS* 3.1 12.0 + - - +
169A SER* 1.3 87.5 + - - +
171A GLU* 1.3 59.2 + - - +
172A GLU 3.4 2.0 - - - -
173A LYS* 3.2 18.0 + - + +
174A ARG* 2.8 39.2 + - + +
506A GOL 2.8 37.5 + - - -
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Residues in contact with GLU 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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167A CYS 3.1 9.6 + - - +
168A ASP* 3.1 29.7 + - - +
169A SER 3.5 0.2 - - - -
170A ASN* 1.3 76.5 - - - +
172A GLU* 1.3 69.0 + - + +
174A ARG* 3.3 11.6 + - - +
175A LEU* 3.0 27.6 + - + +
214A ILE* 4.8 1.9 - - + +
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Residues in contact with GLU 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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168A ASP 4.6 8.0 - - - +
169A SER* 4.7 7.2 + - - +
170A ASN 3.4 0.6 - - - -
171A GLU* 1.3 82.4 - - + +
173A LYS* 1.3 63.2 + - - +
175A LEU* 3.4 7.3 + - - +
176A LYS* 3.1 34.9 + - + +
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Residues in contact with LYS 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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164A LEU* 4.7 25.2 - - + +
169A SER 5.4 1.7 + - - +
170A ASN* 3.2 21.6 + - - +
172A GLU* 1.3 76.8 - - - +
174A ARG* 1.3 60.1 + - + +
176A LYS* 3.3 7.6 + - - +
177A LEU* 2.9 29.7 + - + +
2039B LEU* 5.0 17.3 - - + +
2042B GLU* 6.1 0.9 - - - -
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Residues in contact with ARG 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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161A PHE* 3.5 18.7 + - + -
164A LEU* 3.6 33.5 + - + +
165A GLU 3.3 22.9 + - - -
166A PRO* 3.8 21.8 - - - +
170A ASN* 2.8 28.2 + - + +
171A GLU* 3.7 9.7 - - - +
173A LYS* 1.3 77.7 - - + +
175A LEU* 1.3 58.3 + - - +
177A LEU* 3.3 5.5 + - - +
178A ALA* 2.8 30.8 + - - +
214A ILE* 2.7 41.2 + - + +
215A ASP 3.8 0.2 - - - -
216A PRO* 3.4 31.1 - - - +
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Residues in contact with LEU 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 GLU* 3.0 19.6 + - + +
172A GLU* 3.9 7.0 - - - +
174A ARG* 1.3 76.0 - - - +
176A LYS* 1.3 58.6 + - + +
178A ALA* 3.3 1.1 + - + +
179A ARG* 2.9 79.5 + - + +
209A ILE* 4.7 5.2 - - - +
212A GLN* 3.5 36.8 - - + +
214A ILE* 3.4 23.7 - - + +
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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 GLU* 3.1 26.4 + - + +
173A LYS* 3.7 6.7 - - - +
175A LEU* 1.3 78.0 - - + +
177A LEU* 1.3 57.4 - - - +
179A ARG* 3.5 15.4 + - - +
180A ALA* 3.0 28.2 + - - +
2035B SER* 4.1 6.0 - - - -
2039B LEU* 3.9 16.6 - - + +
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Residues in contact with LEU 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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161A PHE* 3.8 15.9 - - + -
164A LEU* 3.5 28.7 - - + -
173A LYS* 2.9 19.7 + - + +
174A ARG* 3.7 5.2 - - - +
176A LYS* 1.3 74.9 - - - +
178A ALA* 1.3 66.0 + - - +
180A ALA* 3.1 2.1 + - + +
181A ILE* 3.0 40.4 + - + +
2039B LEU* 4.0 23.5 - - + +
2040B LEU* 4.2 10.8 - - + -
2043B CYS* 3.5 42.8 - - + -
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Residues in contact with ALA 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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161A PHE* 3.9 14.8 - - + -
174A ARG 2.8 17.5 + - - +
175A LEU* 3.7 4.0 - - + +
177A LEU* 1.3 76.4 - - - +
179A ARG* 1.3 63.1 + - - +
181A ILE 3.4 0.3 + - - -
182A TYR* 3.0 24.1 + - - +
209A ILE* 3.6 21.6 - - + +
214A ILE* 4.0 17.0 - - + -
218A MET* 4.4 0.4 - - - -
219A PHE* 3.6 20.1 - - + -
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Residues in contact with ARG 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 LEU* 2.9 47.3 + - + +
176A LYS* 3.7 11.5 - - - +
178A ALA* 1.3 76.8 - - - +
180A ALA* 1.3 52.2 + - - +
182A TYR* 3.3 8.5 + - + +
183A ARG* 2.7 60.9 + - - +
209A ILE* 4.2 23.1 + - + +
212A GLN* 2.7 34.6 - - - +
2035B SER* 3.7 13.9 - - - +
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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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176A LYS 3.0 18.6 + - - +
177A LEU* 3.1 8.5 + - - +
179A ARG* 1.3 74.5 - - - +
181A ILE* 1.3 65.0 + - - +
183A ARG* 3.9 1.0 - - - +
184A LYS* 3.0 27.4 + - - +
2035B SER* 3.6 26.7 + - - +
2036B GLU 4.3 6.1 - - - +
2039B LEU* 4.6 7.0 - - + -
2040B LEU* 3.9 24.7 - - + +
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Residues in contact with ILE 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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154A PHE* 3.6 33.7 - - + -
157A ALA* 3.8 31.6 - - + +
158A CYS* 4.7 1.1 - - - +
161A PHE* 3.9 18.8 - - + -
177A LEU* 3.0 23.6 + - + +
178A ALA 3.8 3.6 - - - +
180A ALA* 1.3 75.0 - - - +
182A TYR* 1.3 63.3 + - - +
185A TYR* 2.9 30.4 + - + +
186A ILE* 3.7 1.3 + - + +
219A PHE* 3.7 26.0 - - + -
2040B LEU* 3.7 20.9 - - + -
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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 ALA 3.0 17.3 + - - +
179A ARG* 3.5 7.6 - - + +
181A ILE* 1.3 77.0 - - - +
183A ARG* 1.3 75.2 + - + +
186A ILE* 2.8 31.1 + - + -
187A LEU* 2.7 70.8 + - + +
205A ILE* 4.6 6.7 - - + -
206A LYS* 3.6 33.5 - - + +
209A ILE* 4.0 29.6 - - + -
210A MET* 3.5 29.5 - - + +
219A PHE* 4.5 2.0 - - + -
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Residues in contact with ARG 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 ARG* 2.7 41.9 + - - +
180A ALA 3.9 3.1 - - - +
182A TYR* 1.3 90.5 - - + +
184A LYS* 1.3 61.2 + - - +
187A LEU* 3.5 31.7 + - + +
188A ASP* 4.7 2.1 + - - +
2035B SER* 2.6 49.7 + - - +
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Residues in contact with LYS 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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150A ASP* 4.3 19.4 + - - +
153A ASP* 6.0 0.2 - - - -
180A ALA 3.0 17.9 + - - +
183A ARG* 1.3 79.2 - - - +
185A TYR* 1.3 90.5 + - + +
191A GLY* 6.0 1.9 - - - -
2035B SER 5.4 1.5 - - - +
2037B ASP* 3.8 24.7 + - - +
2040B LEU* 3.8 18.2 - - + -
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Residues in contact with TYR 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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150A ASP* 3.8 37.0 + - + -
153A ASP* 3.4 22.2 + - - +
154A PHE* 3.6 42.3 + + + -
157A ALA* 4.8 4.5 - - + -
181A ILE* 2.9 20.7 + - + +
184A LYS* 1.3 109.6 - - + +
186A ILE* 1.3 63.4 + - - +
187A LEU 4.0 0.2 - - - -
188A ASP 5.3 1.1 - - - -
191A GLY* 5.8 0.7 - - - -
193A VAL* 3.6 26.9 - - + +
194A SER* 3.2 30.7 + - - -
2040B LEU* 4.4 19.4 - - + +
2044B ILE* 4.4 6.9 - - - +
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Residues in contact with ILE 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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154A PHE* 4.2 26.0 - - + -
181A ILE 4.3 2.5 - - - +
182A TYR* 2.8 44.1 + - + +
185A TYR* 1.3 81.9 - - + +
187A LEU* 1.3 69.1 + - - +
188A ASP 3.9 0.7 - - - -
189A ASN* 4.0 2.6 - - - +
193A VAL* 4.3 6.5 - - + -
194A SER* 3.5 14.8 + - - -
197A THR* 4.6 14.6 - - + +
202A LYS* 3.8 33.3 - - + +
205A ILE* 4.3 26.5 - - + -
206A LYS* 4.9 3.7 - - - -
219A PHE* 4.7 2.5 - - + -
222A ALA* 4.8 0.4 - - + -
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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