Contacts of the helix formed by residues 185 - 193 (chain A) in PDB entry 2JG1
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 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A LYS* 3.8 1.8 + - - +
184A PRO* 1.3 76.8 - - - +
186A ILE* 1.3 65.5 + - + +
187A SER* 3.4 12.7 + - - +
188A GLU* 2.8 61.8 + - - +
189A LEU* 3.0 18.9 + - - +
221A VAL* 4.0 1.8 - - - -
222A SER* 3.3 24.6 + - - +
1312A ANP 2.8 34.5 + - - +
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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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185A ASN* 1.3 74.5 - - + +
187A SER* 1.3 64.4 + - - +
189A LEU* 3.3 2.6 + - + +
190A TYR* 3.3 42.3 + - + -
197A LEU* 4.5 14.1 - - + -
198A ASP 3.8 23.1 - - - +
199A GLU* 4.1 24.0 - - + +
204A LEU* 3.9 14.4 - - + -
221A VAL* 3.8 8.3 - - + +
222A SER 3.2 7.7 + - - +
223A LEU* 3.7 37.0 - - + -
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Residues in contact with SER 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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185A ASN* 3.2 13.6 - - - -
186A ILE* 1.3 83.7 - - - +
188A GLU* 1.3 62.3 + - - +
190A TYR* 4.2 1.2 - - - +
191A GLN* 3.3 38.9 + - - +
197A LEU* 4.1 17.6 - - - +
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Residues in contact with GLU 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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163A ASP* 4.7 5.6 - - - +
164A CYS 4.9 2.8 - - - +
165A SER* 3.8 34.3 + - - -
166A GLY 5.5 2.3 + - - -
169A LEU* 5.5 2.4 - - + +
183A LYS 4.3 2.9 - - - +
184A PRO* 3.5 15.3 - - + +
185A ASN* 2.8 50.0 + - - +
187A SER* 1.3 71.8 - - - +
189A LEU* 1.3 65.4 + - - +
191A GLN* 3.8 15.4 - - - +
192A LEU* 3.2 25.5 + - - +
1311A MG 4.0 11.0 - - - -
1312A ANP 4.8 2.6 + - - -
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Residues in contact with LEU 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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184A PRO* 4.0 15.5 - - + +
185A ASN 3.0 12.8 + - - +
186A ILE* 3.5 8.1 - - - +
188A GLU* 1.3 79.3 - - - +
190A TYR* 1.3 71.6 + - + +
192A LEU* 3.6 7.8 - - - +
193A LEU* 3.5 20.7 + - + +
204A LEU* 3.8 29.2 - - + -
207A ALA* 4.1 19.7 - - + -
208A VAL* 4.1 19.3 - - + -
213A PHE* 3.9 27.6 - - + -
219A ILE* 5.2 1.1 - - + -
221A VAL* 4.0 19.5 - - + -
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Residues in contact with TYR 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 ILE* 3.3 39.4 + - + +
187A SER* 4.4 2.0 - - - +
189A LEU* 1.3 87.7 - - + +
191A GLN* 1.3 60.9 + - - +
192A LEU 3.1 1.6 - - - -
193A LEU* 2.9 21.2 + - + +
194A ASN 3.0 10.0 + - - -
195A GLN* 3.2 52.4 + - + +
196A PRO 3.5 13.0 - - - -
197A LEU* 3.6 22.2 - - + +
198A ASP* 2.8 36.8 + - + -
203A SER* 3.6 16.4 + - - -
204A LEU* 3.6 19.8 + - + +
207A ALA* 4.3 11.9 - - + -
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Residues in contact with GLN 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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165A SER* 5.1 1.7 - - - -
166A GLY* 5.0 13.5 + - - +
187A SER* 3.3 32.0 + - - +
188A GLU* 3.8 22.1 - - - +
190A TYR* 1.3 77.8 - - - +
192A LEU* 1.3 61.9 + - + +
194A ASN* 3.5 23.1 + - - +
195A GLN 4.9 1.3 - - - -
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Residues in contact with LEU 192 (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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166A GLY* 3.5 31.9 - - - +
169A LEU* 3.7 21.8 - - + -
170A GLN* 3.8 44.5 - - + +
173A LEU* 3.6 22.9 - - + -
184A PRO* 6.2 1.1 - - + -
188A GLU 3.2 16.8 + - - +
189A LEU* 3.6 6.7 - - - +
190A TYR 3.1 0.2 - - - -
191A GLN* 1.3 82.9 - - + +
193A LEU* 1.3 58.9 + - - +
194A ASN* 3.3 7.1 + - - -
212A LEU* 4.2 12.0 - - + +
213A PHE* 3.8 21.1 - - + -
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Residues in contact with LEU 193 (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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189A LEU* 3.5 12.2 + - + +
190A TYR* 2.9 13.1 + - + +
192A LEU* 1.3 78.9 - - - +
194A ASN* 1.3 70.8 + - - +
195A GLN* 3.1 25.7 + - + +
207A ALA* 3.7 39.5 - - + +
210A GLN* 3.8 21.8 - - - +
212A LEU* 3.8 16.6 - - + -
213A PHE* 3.5 31.9 - - + -
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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