Contacts of the helix formed by residues 163 - 183 (chain A) in PDB entry 1JNK
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 HIS 163 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ASP* 1.3 73.2 - - - +
164A GLU* 1.3 52.2 + - - +
166A MET* 4.1 5.4 - - + +
167A SER* 2.6 36.2 + - - -
318A PHE* 3.9 21.3 - + - -
319A PRO* 3.1 50.8 + - + +
324A HIS* 5.2 5.2 - - + -
325A ASN* 3.6 27.3 + - - +
328A LYS* 3.6 30.7 - - + +
329A ALA* 3.9 13.0 - - - -
332A ALA* 4.7 0.7 - - + -
358A TYR* 3.0 30.0 + - + +
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Residues in contact with GLU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ASP* 3.1 16.1 + - + +
163A HIS* 1.3 79.6 - - - +
165A ARG* 1.3 72.9 + - + +
167A SER* 3.2 15.5 + - - -
168A TYR* 3.2 8.3 + - - +
324A HIS* 6.2 1.9 - - + -
362A TRP* 3.2 37.5 - - + -
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Residues in contact with ARG 165 (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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159A MET* 6.2 2.7 - - - -
161A LEU* 4.0 18.4 - - + -
162A ASP* 3.2 31.2 + - - +
164A GLU* 1.3 87.1 + - + +
166A MET* 1.3 60.9 + - - +
168A TYR* 3.2 3.2 + - - +
169A LEU* 2.9 37.0 + - - +
199A SER 5.3 6.3 + - - -
200A ASP* 5.8 2.6 - - - +
201A CYS* 3.7 33.1 - - + +
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Residues in contact with MET 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 3.7 45.2 - - + +
162A ASP 3.0 14.2 + - - +
163A HIS* 5.2 6.5 - - + +
165A ARG* 1.3 76.8 - - - +
167A SER* 1.3 56.8 + - - +
169A LEU* 3.8 3.9 - - - +
170A LEU* 3.0 38.6 + - + +
253A MET* 5.2 6.5 - - + -
256A MET* 4.2 34.3 - - + +
257A VAL* 4.0 25.6 - - + -
317A LEU 6.0 1.3 - - - +
318A PHE* 5.4 6.3 - - + -
319A PRO* 5.8 2.7 - - + -
358A TYR* 3.7 22.9 - - + +
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Residues in contact with SER 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A HIS 2.6 23.6 + - - -
164A GLU* 3.2 9.5 + - - -
166A MET* 1.3 79.6 - - - +
168A TYR* 1.3 56.4 + - - +
170A LEU* 3.9 4.5 - - - +
171A TYR* 2.9 28.5 + - - +
358A TYR* 3.1 47.4 + - - -
359A ILE* 4.0 3.8 - - - +
361A VAL* 4.8 2.8 - - - +
362A TRP* 3.3 13.7 + - - -
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Residues in contact with TYR 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LYS* 5.4 6.4 + - - -
164A GLU 3.2 17.5 + - - +
165A ARG* 3.2 7.0 + - - +
167A SER* 1.3 74.3 + - - +
169A LEU* 1.3 66.8 + - - +
171A TYR* 3.2 14.3 + + - +
172A GLN* 3.0 55.9 + - + +
200A ASP 4.7 3.8 - - - -
201A CYS* 3.3 42.2 - - + -
202A THR* 4.3 10.5 - - + +
362A TRP* 3.7 44.9 - + + +
367A GLU* 5.4 5.9 + - - -
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Residues in contact with LEU 169 (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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153A LEU* 4.4 5.6 - - + -
156A VAL* 3.8 21.8 - - + -
161A LEU* 4.1 9.4 - - + -
165A ARG 2.9 18.9 + - - +
166A MET 3.8 3.1 - - - +
168A TYR* 1.3 76.1 - - - +
170A LEU* 1.3 54.5 + - - +
172A GLN* 2.8 29.1 + - - +
173A MET* 3.0 15.7 + - + +
197A VAL* 4.0 15.7 - - + -
201A CYS* 3.7 33.9 - - - +
203A LEU* 3.8 24.7 - - + +
256A MET* 3.4 30.3 - - + -
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Residues in contact with LEU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A MET* 3.0 31.3 + - + +
167A SER* 3.9 1.3 - - - +
169A LEU* 1.3 76.1 - - - +
171A TYR* 1.3 61.7 + - - +
173A MET* 3.4 15.3 + - + +
174A LEU* 3.2 30.6 + - + +
249A VAL* 3.5 34.3 - - + +
253A MET* 4.2 32.3 - - + -
256A MET* 3.4 33.9 - - + -
335A LEU* 5.4 0.4 - - + -
339A MET* 5.2 1.6 - - + -
359A ILE* 3.8 20.4 - - + -
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Residues in contact with TYR 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 SER 2.9 21.0 + - - +
168A TYR* 3.6 19.7 - + - +
169A LEU 3.2 0.2 - - - -
170A LEU* 1.3 77.1 - - - +
172A GLN* 1.3 61.9 + - + +
174A LEU* 3.9 4.4 - - - +
175A CYS* 3.1 45.8 + - - -
354A LEU* 3.5 20.6 - - + -
359A ILE* 3.6 27.4 - - + -
362A TRP* 3.1 28.4 + - + -
363A TYR* 3.8 17.0 - + - -
364A ASP* 3.1 20.6 + - - +
367A GLU* 3.0 28.8 + - - +
368A VAL* 3.5 12.4 - - + +
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Residues in contact with GLN 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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121A LYS* 5.8 2.4 - - - -
122A ASN* 3.2 30.3 + - - +
168A TYR* 3.0 47.5 + - + +
169A LEU* 2.8 10.8 + - - +
171A TYR* 1.3 81.8 - - + +
173A MET* 1.3 65.5 - - - +
175A CYS* 2.9 16.7 + - - +
176A GLY* 2.9 11.8 + - - -
201A CYS 2.9 24.4 + - - -
202A THR* 3.4 9.0 - - - +
203A LEU* 2.8 39.0 + - + +
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Residues in contact with MET 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LEU* 3.4 29.2 - - + -
169A LEU 3.0 17.5 + - - +
170A LEU* 3.7 28.0 - - + +
172A GLN* 1.3 76.2 - - - +
174A LEU* 1.3 57.2 + - + +
176A GLY* 3.3 1.2 + - - -
177A ILE* 2.9 44.9 + - + +
195A ILE* 4.2 20.0 - - + -
203A LEU* 3.8 27.8 - - + +
205A ILE* 4.0 6.7 - - + +
249A VAL* 4.9 11.9 - - + -
252A ILE* 4.1 20.6 - - + -
256A MET* 4.4 5.4 - - + -
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Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LEU* 3.2 20.0 + - + +
171A TYR 4.1 0.4 - - - +
173A MET* 1.3 80.4 - - - +
175A CYS* 1.3 56.5 + - - +
177A ILE* 4.3 5.4 - - + -
178A LYS* 3.1 29.5 + - - +
246A ILE* 3.5 32.3 - - + -
249A VAL* 4.4 15.5 - - + -
339A MET* 4.1 14.6 - - + -
350A VAL* 3.6 16.3 - - + +
353A ALA* 4.2 20.2 - - + +
354A LEU* 3.8 20.1 - - + +
359A ILE* 4.2 26.0 - - + -
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Residues in contact with CYS 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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120A HIS* 3.7 14.3 + - - +
122A ASN* 3.5 14.8 - - - +
171A TYR* 3.1 56.1 + - - +
172A GLN* 2.9 11.3 + - - +
174A LEU* 1.3 77.3 - - - +
176A GLY* 1.3 63.9 + - - +
178A LYS* 3.5 6.6 + - - +
179A HIS* 3.2 16.5 + - - +
354A LEU* 4.7 2.5 - - - -
367A GLU* 4.0 17.2 - - - +
368A VAL* 3.8 14.5 - - - +
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Residues in contact with GLY 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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120A HIS* 3.9 17.3 - - - -
122A ASN* 3.9 7.7 - - - +
123A ILE* 4.1 19.9 - - - +
172A GLN 2.9 12.1 + - - -
173A MET 3.8 1.8 - - - -
175A CYS* 1.3 75.1 - - - +
177A ILE* 1.3 58.1 + - - +
179A HIS* 2.9 5.9 + - - +
180A LEU* 2.8 27.5 + - - +
205A ILE* 4.5 2.5 - - - -
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Residues in contact with ILE 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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173A MET* 2.9 33.7 + - + +
174A LEU* 4.2 6.1 - - + +
176A GLY* 1.3 73.5 - - - +
178A LYS* 1.3 57.8 + - - +
180A LEU* 3.4 11.5 + - + +
181A HIS* 2.9 55.9 + - + +
187A HIS* 5.8 1.1 - - + -
190A LEU* 3.4 32.3 - - + -
205A ILE* 3.9 12.0 - - + +
245A ASP* 3.9 12.3 - - + +
246A ILE* 6.0 0.4 - - + -
249A VAL* 3.7 23.3 - - + -
350A VAL* 4.2 11.7 - - + -
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Residues in contact with LYS 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 LEU 3.1 21.4 + - - +
175A CYS* 3.5 5.4 - - - +
176A GLY 3.1 0.2 - - - -
177A ILE* 1.3 75.3 - - - +
179A HIS* 1.3 63.7 + - - +
181A HIS* 3.2 8.7 + - + +
182A SER* 3.1 26.0 + - - -
350A VAL* 3.8 13.9 - - + -
351A ASP* 3.0 41.3 + - - +
354A LEU* 4.5 2.2 - - + -
368A VAL* 3.5 42.6 - - + +
369A GLU* 5.0 10.5 + - - +
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Residues in contact with HIS 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A VAL* 3.8 18.4 - - + +
119A ASN 3.9 19.8 + - - -
120A HIS* 3.5 38.0 + - + +
123A ILE* 5.3 1.1 - - + -
175A CYS 3.2 10.3 + - - +
176A GLY 2.9 9.7 + - - +
178A LYS* 1.3 80.9 - - - +
180A LEU* 1.3 61.3 + - + +
182A SER* 2.5 23.2 + - - -
183A ALA* 3.2 9.0 + - + +
368A VAL 5.6 2.4 + - - +
370A ALA* 3.7 23.9 + - + +
371A PRO 3.2 33.7 + - - -
372A PRO* 4.2 8.9 - - + +
373A PRO* 4.8 4.7 - - + +
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Residues in contact with LEU 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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118A VAL* 4.3 10.8 - - + -
123A ILE* 3.7 36.6 - - + -
176A GLY 2.8 7.3 + - - +
177A ILE* 3.5 15.3 - - + +
179A HIS* 1.3 77.3 - - - +
181A HIS* 1.3 60.8 + - + +
183A ALA* 3.0 11.4 + - - +
184A GLY 3.2 0.2 + - - -
185A ILE* 2.8 58.2 + - + +
187A HIS* 4.1 30.5 - - + -
205A ILE* 5.2 3.4 - - + -
207A ASP 4.9 1.6 - - - +
208A PHE* 4.1 24.0 - - + -
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Residues in contact with HIS 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 ILE* 2.9 38.6 + - + +
178A LYS* 3.5 8.9 - - + +
179A HIS 3.2 0.2 - - - -
180A LEU* 1.3 76.7 - - + +
182A SER* 1.3 61.7 + - - +
184A GLY* 3.3 12.6 + - - -
185A ILE 3.2 20.4 - - - -
186A ILE* 3.9 11.5 - - + +
187A HIS 5.0 0.2 - - - -
242A GLU* 3.0 62.2 + - + +
245A ASP* 2.8 25.6 + - + -
350A VAL* 3.9 16.5 - - + +
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Residues in contact with SER 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LYS* 3.1 14.7 + - - -
179A HIS* 2.5 30.3 + - - -
181A HIS* 1.3 76.7 - - - +
183A ALA* 1.3 57.4 + - - +
184A GLY 3.3 1.4 + - - -
370A ALA 4.7 2.9 + - - -
372A PRO* 3.5 34.9 - - - +
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Residues in contact with ALA 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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118A VAL* 5.0 5.6 - - + -
179A HIS* 3.2 11.4 + - + +
180A LEU* 3.0 11.1 + - - +
182A SER* 1.3 76.6 + - - +
184A GLY* 1.3 60.5 + - - +
185A ILE* 3.4 19.3 - - + +
372A PRO* 4.2 4.7 - - + -
373A PRO* 4.0 30.5 - - + +
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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