Contacts of the helix formed by residues 177 - 187 (chain A) in PDB entry 1JQE
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 SER 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A VAL* 3.8 4.7 - - - +
174A SER* 2.7 22.7 + - - -
175A GLY 3.4 0.2 - - - -
176A SER* 1.3 85.4 + - - +
178A GLY* 1.3 63.3 + - - +
179A TRP* 3.3 26.7 + - - +
180A ASP* 3.3 10.4 + - - +
181A LYS* 3.5 14.7 + - - +
270A GLU 5.0 0.7 - - - -
282A ASN* 3.4 18.6 - - - -
284A THR* 3.6 23.8 - - - -
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Residues in contact with GLY 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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177A SER* 1.3 70.6 - - - +
179A TRP* 1.3 59.7 + - - +
180A ASP 3.2 0.2 - - - -
181A LYS* 3.2 3.7 + - - +
182A LEU* 2.9 29.1 + - - +
270A GLU 4.0 11.7 - - - -
271A PHE* 4.0 15.6 - - - -
281A PHE* 3.3 17.8 - - - -
282A ASN* 2.7 23.4 + - - +
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Residues in contact with TRP 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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22A PHE* 4.4 6.1 - + - -
173A VAL* 3.4 25.2 - - + +
177A SER* 3.1 12.1 - - - +
178A GLY* 1.3 78.2 - - - +
180A ASP* 1.3 57.3 + - - +
182A LEU* 3.1 11.8 + - + +
183A TRP* 2.8 74.1 + + + -
224A MET* 4.1 11.7 - - - -
243A PHE* 3.7 33.4 - + - -
244A LEU* 3.8 35.4 - - + -
246A GLU* 5.4 1.8 - - - -
281A PHE* 3.5 20.7 - + - -
282A ASN 4.0 5.6 - - - -
283A ASN* 2.8 23.5 + - - -
500A QUN 3.7 22.7 - - + -
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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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174A SER 4.1 0.7 - - - +
175A GLY* 3.0 32.6 - - - +
177A SER* 3.3 9.6 + - - +
178A GLY 3.2 0.4 - - - -
179A TRP* 1.3 79.2 - - - +
181A LYS* 1.3 81.4 + - - +
183A TRP* 4.2 3.6 - - - +
184A LYS* 3.0 68.8 + - - +
200A THR* 4.1 24.8 + - + +
202A ASP* 4.5 2.9 - - - +
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Residues in contact with LYS 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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175A GLY 3.4 14.5 + - - -
176A SER* 3.9 10.9 + - - +
177A SER 3.5 15.0 + - - +
178A GLY 3.2 6.2 + - - +
180A ASP* 1.3 96.9 + - - +
182A LEU* 1.3 66.0 + - - +
184A LYS* 4.1 7.1 - - + +
185A LYS* 3.2 26.2 + - - +
270A GLU* 3.5 33.0 - - + +
271A PHE* 3.7 21.6 - - + -
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Residues in contact with LEU 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 GLY 2.9 16.5 + - - +
179A TRP* 3.1 25.8 + - + +
181A LYS* 1.3 77.1 - - - +
183A TRP* 1.3 61.8 + - + +
186A TYR* 2.8 38.3 + - + +
187A GLY 3.5 0.2 + - - -
190A PHE* 4.0 15.0 - - + -
244A LEU* 3.5 31.6 - - + +
262A LEU* 3.7 29.6 - - + -
266A LEU* 4.4 9.0 - - + -
271A PHE* 3.4 17.6 - - + -
281A PHE* 4.4 8.3 - - + -
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Residues in contact with TRP 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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146A TYR* 4.2 1.6 - + - -
173A VAL* 3.8 19.5 - - + -
179A TRP* 2.8 56.0 + + + +
180A ASP* 4.2 2.5 - - - +
182A LEU* 1.3 83.9 - - + +
184A LYS* 1.3 62.1 + - + +
187A GLY* 2.7 30.7 + - - +
190A PHE* 5.0 3.8 - + - -
198A TYR* 3.6 63.4 - + + +
199A ILE 3.3 23.8 - - - -
200A THR* 3.8 18.4 - - + -
244A LEU 5.1 1.8 + - - -
246A GLU* 4.4 2.0 + - - -
500A QUN 3.5 36.3 - - + -
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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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175A GLY 5.2 0.6 + - - -
180A ASP* 3.0 53.0 + - - +
181A LYS* 4.1 9.5 - - + +
182A LEU 3.4 0.2 - - - -
183A TRP* 1.3 77.8 - - + +
185A LYS* 1.3 61.2 + - - +
187A GLY 4.7 0.2 + - - -
188A SER 5.7 0.5 + - - -
202A ASP* 5.3 3.4 + - - -
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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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181A LYS 3.2 15.1 + - - +
184A LYS* 1.3 81.9 - - + +
186A TYR* 1.3 78.6 + - + +
187A GLY 3.6 0.2 - - - -
188A SER* 5.0 4.2 + - - -
189A ARG* 3.7 24.7 + - - +
261A GLU* 3.8 20.3 + - - +
265A ASP* 2.7 34.6 + - - +
271A PHE* 4.7 6.5 - - + -
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Residues in contact with TYR 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 LEU* 2.8 24.9 + - + +
185A LYS* 1.3 94.7 - - + +
187A GLY* 1.3 69.0 + - - +
188A SER 3.3 2.7 - - - -
189A ARG* 2.8 51.5 + - - +
190A PHE* 3.2 28.6 + - + -
258A LEU* 3.6 19.7 - - + -
261A GLU* 3.1 27.4 + - + +
262A LEU* 3.5 34.1 - - + -
265A ASP* 2.3 36.4 + - + +
271A PHE* 4.4 5.4 - + - -
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Residues in contact with GLY 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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182A LEU 3.5 3.0 + - - -
183A TRP* 2.7 32.7 + - - -
185A LYS 3.6 0.8 - - - -
186A TYR* 1.3 69.5 - - - +
188A SER* 1.3 62.5 + - - +
190A PHE* 3.0 24.6 + - - +
192A GLN* 5.8 0.9 - - - -
198A TYR* 3.9 25.4 - - - -
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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