Contacts of the helix formed by residues 169 - 185 (chain A) in PDB entry 4J1O
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 PRO 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A ARG* 1.3 90.8 - - + +
170A VAL* 1.3 65.4 + - - +
171A GLU* 3.1 26.7 - - - +
172A ILE* 3.0 37.5 + - + +
173A ASP 3.8 1.9 + - - -
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Residues in contact with VAL 170 (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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165A ILE* 5.6 0.2 - - + -
168A ARG 3.3 2.9 + - - +
169A PRO* 1.3 71.8 - - - +
171A GLU* 1.3 60.7 + - - +
173A ASP* 3.0 24.5 + - + +
174A ILE* 2.9 38.3 + - + +
199A LEU* 4.7 9.2 - - + -
203A ASP* 3.7 53.3 + - + +
206A ARG* 3.6 33.2 - - - +
207A LEU* 4.8 5.8 - - + -
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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
----------------------------------------------------------
169A PRO* 3.4 25.1 - - - +
170A VAL* 1.3 81.4 + - - +
172A ILE* 1.3 65.7 + - + +
174A ILE* 3.5 8.3 + - - +
175A GLU* 3.0 28.9 + - - +
206A ARG* 3.8 31.9 + - - +
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Residues in contact with ILE 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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142A GLN* 5.5 3.8 - - - +
143A PRO* 4.0 20.1 - - + +
168A ARG* 3.7 33.9 - - + +
169A PRO* 3.0 34.2 + - + +
171A GLU* 1.3 84.8 - - + +
173A ASP* 1.3 59.2 + - - +
175A GLU* 3.4 11.8 + - - +
176A THR* 2.9 31.9 + - - -
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Residues in contact with ASP 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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165A ILE* 3.3 32.2 - - + +
166A GLY* 3.1 26.1 + - - -
168A ARG* 2.7 43.7 + - - +
169A PRO 4.5 1.6 - - - -
170A VAL* 3.0 29.4 + - + +
172A ILE* 1.3 76.7 - - - +
174A ILE* 1.3 57.9 + - + +
176A THR* 3.2 4.4 + - - -
177A VAL* 2.9 33.3 + - + +
199A LEU* 4.2 2.9 - - - +
207A LEU* 5.4 0.9 - - + -
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Residues in contact with ILE 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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170A VAL* 2.9 27.6 + - + +
171A GLU* 3.8 6.1 - - - +
173A ASP* 1.3 73.5 - - - +
175A GLU* 1.3 64.3 + - - +
177A VAL* 3.3 7.4 + - - +
178A ARG* 3.0 57.7 + - - +
206A ARG* 3.8 30.7 - - + +
207A LEU* 3.8 29.2 - - + -
210A GLU* 3.5 23.8 - - + +
211A CYS* 4.2 9.2 - - - -
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Residues in contact with GLU 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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143A PRO* 3.5 23.1 - - + +
171A GLU 3.0 17.2 + - - +
172A ILE* 3.7 12.1 - - - +
174A ILE* 1.3 76.4 - - - +
176A THR* 1.3 58.8 + - - +
178A ARG* 3.4 9.7 + - - +
179A LYS* 2.8 66.4 + - + +
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Residues in contact with THR 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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141A GLY 4.4 0.7 + - - -
143A PRO* 3.5 25.7 - - + +
146A ILE* 3.9 36.3 - - + -
163A ILE* 3.9 17.0 - - + -
164A LYS 5.6 0.4 - - - +
165A ILE* 5.3 1.1 - - + -
168A ARG* 3.4 18.2 + - - +
172A ILE 2.9 18.6 + - - -
173A ASP* 3.4 9.6 - - - -
175A GLU* 1.3 76.9 - - - +
177A VAL* 1.3 58.4 + - - +
179A LYS* 3.3 2.8 + - - +
180A VAL* 2.9 29.9 + - + +
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Residues in contact with VAL 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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163A ILE* 5.2 5.2 - - + -
165A ILE* 4.6 6.3 - - + -
173A ASP 2.9 20.7 + - - +
174A ILE* 3.3 8.5 + - - +
176A THR* 1.3 77.0 - - - +
178A ARG* 1.3 57.7 + - - +
180A VAL* 3.4 6.3 + - - +
181A TRP* 3.0 27.5 + - - +
191A LEU* 4.8 4.3 - - + +
193A VAL* 3.8 34.1 - - + -
207A LEU* 4.4 10.3 - - + -
211A CYS* 5.0 2.0 - - - -
214A ILE* 4.0 17.0 - - + -
216A PHE* 3.9 30.3 - - + -
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Residues in contact with ARG 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 ILE* 3.0 38.1 + - + +
175A GLU* 3.8 8.1 - - - +
177A VAL* 1.3 76.0 - - - +
179A LYS* 1.3 59.3 + - + +
181A TRP* 3.4 2.9 + - - +
182A GLU* 3.0 32.9 + - + +
210A GLU* 3.4 43.9 + - - +
211A CYS* 4.2 6.9 - - - -
213A GLU* 5.0 7.1 + - - +
214A ILE* 3.8 22.2 - - + -
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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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143A PRO* 4.0 11.0 - - + +
144A ASP* 2.8 32.9 + - - +
147A ALA* 3.7 16.1 - - + +
175A GLU* 2.8 52.8 + - + +
176A THR 3.9 2.9 - - - +
178A ARG* 1.3 74.1 - - + +
180A VAL* 1.3 66.2 + - - +
182A GLU* 3.4 10.3 + - + +
183A ARG* 3.3 25.6 + - - +
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Residues in contact with VAL 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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146A ILE* 4.0 20.9 - - + -
147A ALA* 3.9 24.5 - - - +
150A ALA* 3.9 17.3 - - + -
161A LEU* 4.8 0.2 - - + -
163A ILE* 4.0 25.6 - - + -
176A THR* 2.9 22.1 + - + +
177A VAL* 3.7 6.5 - - - +
179A LYS* 1.3 74.2 - - - +
181A TRP* 1.3 64.7 + - - +
183A ARG* 3.0 15.3 + - - +
184A ILE* 3.0 30.0 + - + +
191A LEU* 4.3 6.5 - - + -
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Residues in contact with TRP 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 VAL 3.0 18.0 + - - +
178A ARG 3.8 4.3 - - - +
179A LYS 3.3 0.2 - - - -
180A VAL* 1.3 76.8 - - - +
182A GLU* 1.3 66.6 + - - +
184A ILE* 3.9 22.7 - - + -
185A ARG* 2.9 80.2 + - + +
186A GLY 4.9 2.0 - - - -
189A THR 4.8 9.0 - - - -
191A LEU* 4.5 7.8 - - + +
213A GLU* 3.9 15.2 + - + +
214A ILE* 3.7 33.2 - - + -
215A PRO* 3.4 41.7 - - + -
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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
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178A ARG 3.0 18.7 + - - +
179A LYS* 3.6 12.8 - - + +
180A VAL 3.3 0.2 - - - -
181A TRP* 1.3 80.5 - - - +
183A ARG* 1.3 64.2 + - + +
185A ARG* 2.8 45.1 + - - +
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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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144A ASP* 4.8 3.8 + - - +
147A ALA* 3.6 31.3 - - + +
148A ARG* 3.7 50.4 - - - +
151A ALA* 4.2 24.2 - - + +
179A LYS* 3.3 11.9 + - - +
180A VAL* 3.0 9.1 + - - +
182A GLU* 1.3 81.8 - - + +
184A ILE* 1.3 63.8 + - + +
185A ARG 3.6 2.2 - - - +
187A THR* 4.4 8.1 - - - +
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Residues in contact with ILE 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 ALA* 4.2 13.7 - - + +
151A ALA* 4.5 1.6 - - - +
154A VAL* 3.8 23.3 - - + -
161A LEU* 4.0 18.2 - - + -
180A VAL* 3.0 31.9 + - + +
181A TRP* 3.9 20.1 - - + -
183A ARG* 1.3 80.8 - - + +
185A ARG* 1.3 70.1 + - - +
186A GLY 3.4 0.2 + - - -
187A THR* 2.6 34.4 + - - +
188A GLY 4.5 1.0 + - - -
189A THR* 4.3 20.2 + - + +
191A LEU* 4.2 23.3 - - + -
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Residues in contact with ARG 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 TRP* 2.9 66.6 + - + +
182A GLU* 2.8 45.6 + - - +
183A ARG 4.6 2.3 - - - +
184A ILE* 1.3 79.7 - - - +
186A GLY* 1.3 59.5 + - - +
187A THR* 3.5 4.7 + - - +
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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