Contacts of the helix formed by residues 183 - 200 (chain A) in PDB entry 1JQO
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 ARG 183 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A SER 4.9 1.3 - - - +
182A ALA* 1.3 77.3 - - - +
184A ARG* 1.3 66.4 + - - +
185A SER* 2.8 30.9 + - - +
186A LEU* 2.8 18.1 + - + +
187A LEU* 2.9 11.6 + - - +
227A THR* 4.2 8.1 - - - +
228A ASP* 3.2 26.6 + - - +
229A GLU* 3.6 31.6 - - + +
230A ILE 4.1 4.2 + - - -
231A ARG* 3.8 34.0 - - + +
232A ARG 4.8 1.8 - - - +
960A LYS* 5.1 0.2 - - - -
971A SO4 3.0 34.5 + - - +
369B GLU* 3.6 22.4 + - - -
372B ARG* 4.2 1.0 - - - +
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Residues in contact with ARG 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ALA 4.3 0.2 + - - -
183A ARG* 1.3 70.5 - - - +
185A SER* 1.3 56.2 + - - +
187A LEU* 3.8 10.5 - - - +
188A GLN* 2.9 32.4 + - - +
231A ARG* 4.8 2.9 - - - +
239A ALA 5.5 0.6 + - - -
242A ARG* 3.6 18.5 + - - +
243A TYR* 3.4 38.8 - - + +
246A SER* 3.1 29.7 + - - -
971A SO4 3.1 23.1 + - - +
328B PHE* 3.8 24.6 - - + -
360B GLU* 2.6 41.8 + - - -
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Residues in contact with SER 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ARG* 2.8 37.4 + - - -
184A ARG* 1.3 73.7 - - - +
186A LEU* 1.3 59.3 + - - -
188A GLN* 3.1 26.8 + - - +
189A LYS* 3.1 14.0 + - - +
227A THR* 4.3 16.2 - - - -
971A SO4 3.1 9.9 + - - -
328B PHE* 4.5 4.5 - - - -
331B SER* 4.5 6.7 - - - -
372B ARG* 3.6 19.4 + - - +
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Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 5.3 9.9 - - + -
104A HIS* 4.5 13.5 - - + +
107A ASN* 3.7 19.5 - - + +
182A ALA* 4.3 19.1 - - + -
183A ARG* 2.8 17.2 + - + +
185A SER* 1.3 72.8 - - - +
187A LEU* 1.3 67.7 + - - +
188A GLN 3.0 2.2 - - - -
189A LYS* 3.3 4.8 + - - -
190A ASN* 3.0 51.0 + - - +
224A ALA* 4.2 22.4 - - + +
229A GLU* 4.7 22.9 - - + -
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Residues in contact with LEU 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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180A GLN* 3.7 28.0 - - + +
182A ALA* 3.8 25.1 - - + +
183A ARG 2.9 19.0 + - - +
184A ARG* 3.8 9.4 - - - +
186A LEU* 1.3 76.7 - - - +
188A GLN* 1.3 62.7 + - - +
190A ASN* 3.5 13.1 - - - +
191A ALA* 3.4 18.0 + - - +
194A ARG* 5.5 0.5 + - - -
243A TYR* 4.0 18.4 - - + -
247A TYR* 4.3 2.0 - - - +
678A GLU* 3.2 41.0 - - + +
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Residues in contact with GLN 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 ARG 2.9 16.5 + - - +
185A SER 3.1 4.8 + - - -
186A LEU 3.0 0.4 - - - -
187A LEU* 1.3 75.1 - - - +
189A LYS* 1.3 112.0 + - - +
190A ASN 2.9 2.8 + - - -
191A ALA* 3.0 16.8 + - - +
192A ARG* 3.2 28.8 + - + +
220A GLU* 3.7 10.0 - - - +
328B PHE* 3.1 43.7 + - + -
329B GLU* 4.0 8.1 - - - +
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Residues in contact with LYS 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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185A SER* 3.1 16.4 + - - +
186A LEU* 3.3 7.8 + - - +
188A GLN* 1.3 107.0 - - - +
190A ASN* 1.3 58.0 - - - +
192A ARG* 3.1 5.1 + - - +
193A ILE* 2.9 36.8 + - + +
220A GLU* 3.5 29.5 - - + +
223A ALA* 4.0 27.4 - - + -
224A ALA* 3.8 31.2 - - + +
227A THR* 4.1 2.9 + - - -
328B PHE 3.7 0.8 + - - -
329B GLU* 3.4 14.5 + - - -
331B SER* 3.3 23.9 + - - -
332B MET* 4.8 0.2 - - - -
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Residues in contact with ASN 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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107A ASN* 3.0 40.4 + - - +
111A LEU* 3.7 27.1 - - + +
186A LEU* 3.0 30.2 + - - +
187A LEU* 3.5 21.5 - - - +
188A GLN 2.9 0.6 + - - -
189A LYS* 1.3 73.2 - - - +
191A ALA* 1.3 62.3 + - - +
192A ARG 2.9 1.6 - - - -
193A ILE* 2.8 8.1 + - - +
194A ARG* 2.7 42.9 + - - +
678A GLU* 5.1 0.4 - - - +
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Residues in contact with ALA 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 LEU 3.4 9.0 + - - +
188A GLN* 3.0 10.5 + - - +
190A ASN* 1.3 78.5 - - - +
192A ARG* 1.3 59.2 + - + +
194A ARG* 3.8 13.3 - - - +
195A ASN* 3.3 23.7 + - - +
250A GLU* 5.4 7.6 - - - +
682A GLY 4.9 4.9 - - - +
683A GLU* 4.2 19.1 - - - +
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Residues in contact with ARG 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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188A GLN* 3.2 26.5 + - + +
189A LYS 3.1 9.8 + - - +
190A ASN 2.9 0.8 - - - -
191A ALA* 1.3 77.9 - - + +
193A ILE* 1.3 59.2 + - - +
195A ASN* 3.6 6.2 + - - +
196A CYS* 2.9 33.5 + - - +
220A GLU* 3.4 33.0 + - + +
325B GLU* 4.2 27.1 + - - +
329B GLU* 2.9 47.5 + - - +
435B SER* 3.8 9.9 + - - -
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Residues in contact with ILE 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 4.8 13.2 - - + -
107A ASN* 5.7 0.7 - - - +
108A LEU* 4.7 5.4 - - + -
111A LEU* 4.2 24.7 - - + -
189A LYS* 2.9 22.2 - - + +
190A ASN* 2.8 10.4 + - - +
192A ARG* 1.3 75.0 - - - +
194A ARG* 1.3 55.3 + - - +
196A CYS* 3.1 4.5 + - - +
197A LEU* 2.7 38.1 + - + +
217A LEU* 4.1 27.1 - - + +
220A GLU* 4.0 19.3 - - + +
221A ILE* 4.3 26.9 - - + +
224A ALA* 5.2 3.1 - - + -
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Residues in contact with ARG 194 (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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111A LEU* 3.6 26.0 - - + +
114A GLU* 3.1 29.0 + - + +
115A VAL* 4.5 17.4 - - + +
187A LEU 5.5 0.2 + - - -
190A ASN* 2.7 26.7 + - - +
191A ALA* 3.8 15.6 - - - +
193A ILE* 1.3 74.2 - - - +
195A ASN* 1.3 63.7 + - - +
197A LEU* 3.0 7.3 + - - +
198A THR* 3.0 26.7 + - - -
678A GLU* 2.8 30.5 + - - -
682A GLY* 3.2 35.8 + - - -
683A GLU* 3.2 30.4 + - + +
685A HIS* 5.6 2.5 - - - +
686A LEU* 4.2 3.2 - - - +
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Residues in contact with ASN 195 (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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191A ALA 3.3 16.0 + - - +
192A ARG* 3.7 6.5 + - - +
193A ILE 3.3 0.2 - - - -
194A ARG* 1.3 81.1 - - - +
196A CYS* 1.3 67.3 + - - +
198A THR* 3.3 8.1 + - - -
199A GLN* 2.7 54.3 + - - +
683A GLU* 4.3 12.6 + - - +
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Residues in contact with CYS 196 (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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192A ARG* 2.9 22.4 + - - +
193A ILE* 3.1 7.2 + - - +
195A ASN* 1.3 80.1 - - - +
197A LEU* 1.3 64.5 + - - +
198A THR 3.1 0.3 + - - -
199A GLN* 3.3 7.0 + - - +
200A LEU* 2.9 26.8 + - - +
213A LEU* 4.1 14.0 - - - +
216A ALA* 3.6 31.6 - - - -
217A LEU* 4.1 20.0 - - + -
220A GLU* 6.3 1.6 - - - -
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Residues in contact with LEU 197 (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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37A TYR* 3.6 29.8 - - + -
40A LEU* 3.8 24.7 - - + -
41A LEU* 3.2 44.2 - - + -
111A LEU* 5.3 1.8 - - + -
112A ALA* 4.7 1.6 - - - +
115A VAL* 4.3 21.3 - - + -
193A ILE* 2.7 22.4 + - + +
194A ARG* 3.4 5.6 - - - +
196A CYS* 1.3 73.6 - - - +
198A THR* 1.3 60.0 + - - +
200A LEU* 3.2 10.0 - - + +
201A ASN* 3.2 28.5 + - - +
217A LEU* 4.0 10.7 - - + +
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Residues in contact with THR 198 (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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115A VAL* 4.3 12.3 - - - +
119A HIS* 4.4 21.3 + - + +
194A ARG 3.0 14.0 + - - -
195A ASN* 3.6 11.5 - - - -
196A CYS 3.2 0.2 - - - -
197A LEU* 1.3 72.1 - - - +
199A GLN* 1.3 60.6 + - + +
200A LEU 2.9 4.5 - - - -
201A ASN* 2.7 31.7 + - - +
202A ALA* 3.6 2.4 + - - -
685A HIS* 5.7 2.8 + - - -
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Residues in contact with GLN 199 (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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195A ASN* 2.7 50.0 + - - +
196A CYS* 3.9 2.4 - - - +
198A THR* 1.3 84.9 - - + +
200A LEU* 1.3 57.0 + - - +
201A ASN 3.1 0.4 - - - -
202A ALA* 3.1 28.9 - - + +
205A ILE* 3.3 11.6 - - + +
213A LEU* 3.6 26.6 - - + +
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Residues in contact with LEU 200 (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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40A LEU* 4.4 20.4 - - + -
44A ARG* 5.6 0.7 - - - +
196A CYS 2.9 15.0 + - - +
197A LEU* 3.2 11.0 - - + +
198A THR 2.9 0.2 - - - -
199A GLN* 1.3 79.7 - - - +
201A ASN* 1.3 61.5 + - - +
202A ALA 3.2 2.5 + - - -
205A ILE* 4.2 1.1 - - - -
210A LYS* 3.6 39.7 - - + +
213A LEU* 3.5 29.4 - - + +
214A ASP* 4.1 21.3 - - + +
217A LEU* 3.7 29.4 - - + -
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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
------------------------------------------------------------
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