Contacts of the helix formed by residues 179 - 191 (chain A) in PDB entry 3JPW
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 TYR 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A THR* 3.7 18.7 - - - +
174A THR 3.3 17.3 - - - +
175A TYR* 3.5 44.6 - + - -
176A PHE 3.1 23.6 + - - +
177A PRO* 4.8 0.7 - - + -
178A GLY* 1.3 76.1 - - - +
180A GLN* 1.3 101.7 + - + +
182A PHE* 3.2 4.6 - - - +
183A VAL* 3.2 29.7 + - + +
204A LEU* 4.0 20.0 - - + +
231A TYR* 3.2 21.9 - - + -
605A CL 4.1 5.6 - - + -
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Residues in contact with GLN 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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178A GLY 3.2 0.6 - - - -
179A TYR* 1.3 115.5 + - + +
181A ASP* 1.3 63.1 + - - +
182A PHE 3.0 1.8 - - - -
183A VAL* 3.4 0.7 + - - -
184A ASN* 2.9 43.0 + - - +
605A CL 3.4 14.5 - - + +
606A CL 3.0 29.8 - - + +
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Residues in contact with ASP 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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135A ALA* 4.4 18.5 - - - +
150A ILE* 4.3 14.1 - - + +
151A GLU* 4.3 18.5 - - + +
178A GLY* 2.9 12.6 + - - +
180A GLN* 1.3 79.7 - - - +
182A PHE* 1.3 62.9 + - - +
184A ASN* 4.2 7.9 + - - +
185A LYS* 3.4 21.5 + - - +
605A CL 4.2 0.2 - - - +
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Residues in contact with PHE 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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150A ILE* 4.0 14.6 - - + +
153A GLN* 5.0 0.9 - - + -
154A ALA* 3.8 31.6 - - + +
157A MET* 3.5 34.1 - - + -
171A ILE* 4.0 24.9 - - + -
173A THR* 4.3 2.5 - - + -
178A GLY 2.9 10.8 + - - +
179A TYR* 3.2 11.0 - - - +
180A GLN 3.0 0.2 - - - -
181A ASP* 1.3 74.4 - - - +
183A VAL* 1.3 67.7 + - - +
185A LYS* 3.1 14.6 + - - +
186A ILE* 3.1 25.5 + - + +
229A LEU* 4.5 7.9 - - + -
231A TYR* 3.7 46.4 - + + -
259A PRO* 5.0 6.3 - - + -
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Residues in contact with VAL 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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171A ILE* 4.2 20.0 - - + -
173A THR* 4.1 20.9 - - + +
179A TYR* 3.2 17.6 + - + +
180A GLN* 4.0 2.9 - - - +
182A PHE* 1.3 75.4 - - - +
184A ASN* 1.3 60.3 + - - +
186A ILE* 3.0 8.3 + - - +
187A ARG* 2.9 68.7 + - + +
202A VAL* 4.4 14.6 - - + -
606A CL 4.7 4.5 - - + -
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Residues in contact with ASN 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 GLN* 2.9 30.9 + - - +
181A ASP* 4.4 8.6 + - - +
183A VAL* 1.3 75.9 - - - +
185A LYS* 1.3 57.3 + - - +
187A ARG* 3.7 23.8 + - - +
188A SER* 3.1 26.9 + - - -
606A CL 3.8 16.2 - - - +
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Residues in contact with LYS 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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151A GLU* 3.8 48.6 + - + +
154A ALA* 3.8 21.5 - - + -
155A SER* 4.5 11.4 - - - +
181A ASP 3.4 17.7 + - - +
182A PHE 3.1 5.9 + - - +
184A ASN* 1.3 78.7 - - - +
186A ILE* 1.3 67.9 + - - +
188A SER* 3.5 9.6 + - - +
189A THR* 3.2 44.7 + - + +
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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 ALA* 3.6 35.9 - - + +
158A LEU* 3.8 21.9 - - + +
169A PHE* 3.7 30.1 - - + -
171A ILE* 3.8 25.4 - - + -
182A PHE* 3.1 21.8 + - + +
183A VAL 3.0 7.2 + - - +
185A LYS* 1.3 76.2 - - - +
187A ARG* 1.3 69.1 + - - +
189A THR* 3.1 2.3 + - - -
190A ILE* 3.0 28.9 + - + +
199A LEU* 4.9 3.4 - - + -
229A LEU* 4.4 11.9 - - + -
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Residues in contact with ARG 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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183A VAL* 2.9 42.5 + - + +
184A ASN* 3.7 23.6 + - - +
186A ILE* 1.3 71.9 - - + +
188A SER* 1.3 65.8 + - - +
190A ILE* 3.0 24.4 - - + +
191A GLU* 3.0 13.8 + - + +
199A LEU* 4.2 24.2 - - + +
202A VAL* 4.5 16.0 - - - +
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Residues in contact with SER 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 ASN 3.1 23.2 + - - -
185A LYS* 3.6 14.8 + - - +
186A ILE 3.1 0.6 + - - -
187A ARG* 1.3 80.6 - - - +
189A THR* 1.3 67.3 + - - +
190A ILE 3.1 0.2 + - - -
191A GLU* 3.4 5.3 + - - +
192A ASN* 3.3 20.2 + - - +
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Residues in contact with THR 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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155A SER* 5.6 4.3 - - - -
158A LEU* 2.9 32.6 - - + +
185A LYS* 3.2 44.9 - - + +
186A ILE 3.1 2.9 + - - -
188A SER* 1.3 76.0 - - - +
190A ILE* 1.3 57.2 + - - +
192A ASN* 3.2 17.6 + - - +
193A SER* 3.5 12.5 + - - -
197A TRP* 4.8 2.8 + - - -
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Residues in contact with ILE 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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158A LEU* 5.4 3.1 - - + -
169A PHE* 4.0 26.5 - - + -
186A ILE* 3.0 17.9 + - + +
187A ARG* 3.0 24.0 - - + +
189A THR* 1.3 79.7 + - - +
191A GLU* 1.3 71.5 + - + +
192A ASN 3.3 2.8 + - - -
193A SER* 3.5 16.5 + - - +
197A TRP* 3.2 53.2 - - + +
199A LEU* 4.2 19.1 - - + +
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Residues in contact with GLU 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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187A ARG* 3.0 16.9 + - + +
188A SER* 3.4 3.3 + - - +
190A ILE* 1.3 83.9 - - + +
192A ASN* 1.3 59.1 + - + +
193A SER 3.7 1.9 + - - +
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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