Contacts of the helix formed by residues 186 - 205 (chain A) in PDB entry 5IHC
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 LEU 186 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A GLU* 4.9 0.3 - - - +
185A TYR* 1.3 82.6 - - - +
187A GLY* 1.3 67.2 + - - +
188A SER* 4.2 9.6 - - - +
189A GLU* 3.2 50.4 + - + +
190A ALA* 3.2 9.2 + - - +
249A LYS* 3.9 15.9 - - - +
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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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129A ALA* 3.5 24.6 - - - +
131A ARG* 4.1 21.6 - - - +
185A TYR* 3.9 11.6 + - - -
186A LEU* 1.3 72.6 - - - +
188A SER* 1.3 55.9 + - - +
190A ALA* 3.4 2.8 + - - +
191A ASP* 2.9 34.7 + - - +
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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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124A HIS* 3.6 33.2 - - - -
129A ALA* 4.1 2.6 - - - +
186A LEU* 3.1 11.2 - - - +
187A GLY* 1.3 76.4 - - - +
189A GLU* 1.3 67.9 + - - +
191A ASP* 3.4 3.8 + - - +
192A VAL* 3.1 32.5 + - - +
254A MET* 6.3 0.7 - - - -
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Residues in contact with GLU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A GLU* 4.5 1.5 - - - +
185A TYR* 5.5 0.2 - - - -
186A LEU* 3.2 39.0 + - + +
188A SER* 1.3 80.8 + - - +
190A ALA* 1.4 60.9 + - - +
192A VAL* 3.5 6.5 + - - +
193A TRP 3.2 13.3 + - - -
248A PRO* 3.6 33.6 - - + +
249A LYS* 3.4 33.5 + - - +
251A ARG* 2.8 33.6 + - + +
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Residues in contact with ALA 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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131A ARG* 5.4 5.2 - - + -
176A ALA* 4.1 10.2 - - + +
178A GLU* 4.3 2.0 + - - +
179A LEU* 3.9 28.7 - - + -
185A TYR* 3.9 13.0 - - + -
186A LEU 3.2 12.2 + - - +
187A GLY* 3.7 7.9 - - - +
188A SER 3.4 0.2 - - - -
189A GLU* 1.4 74.0 - - - +
191A ASP* 1.4 58.9 + - - +
193A TRP* 3.4 4.7 + - - +
194A SER* 3.0 32.3 + - - +
251A ARG* 4.0 7.6 - - - +
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Residues in contact with ASP 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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120A VAL* 4.0 4.6 - - + +
124A HIS* 2.7 32.2 + - + +
129A ALA* 3.6 1.6 - - - -
130A HIS* 2.9 22.5 + - - +
131A ARG* 2.9 28.1 + - - -
133A LEU* 3.6 25.8 - - + +
187A GLY 2.9 17.3 + - - +
188A SER 3.5 6.1 - - - +
190A ALA* 1.4 73.2 - - - +
192A VAL* 1.4 58.5 + - - +
194A SER* 3.3 3.0 + - - -
195A MET* 2.9 34.0 + - - +
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Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A HIS* 5.1 0.2 - - + -
188A SER* 3.1 19.0 + - - +
189A GLU* 3.8 7.9 - - - +
190A ALA 3.4 0.4 - - - -
191A ASP* 1.4 70.8 - - - +
193A TRP* 1.4 64.6 + - - +
195A MET* 3.2 9.6 + - - +
196A GLY* 3.0 18.5 + - - -
243A MET* 3.6 15.6 - - + +
251A ARG* 4.2 13.0 - - + -
252A ILE* 3.5 43.5 - - + +
253A SER* 4.9 0.4 - - - -
254A MET* 3.7 33.7 - - + +
257A LEU* 5.1 3.1 - - + -
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Residues in contact with TRP 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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173A ALA 5.0 0.6 + - - -
174A TYR 3.5 12.1 - - - -
175A ALA 3.4 12.1 + - - -
176A ALA* 3.4 26.2 - - + -
177A PRO* 3.7 30.5 - - + -
189A GLU 3.2 6.1 + - - -
190A ALA 3.5 7.4 - - - +
192A VAL* 1.4 75.9 - - - +
194A SER* 1.4 65.8 + - - +
196A GLY* 2.9 13.9 + - - -
197A ILE* 3.0 27.5 + - + +
209A PHE* 3.5 36.8 - + - -
221A ILE* 4.1 15.2 - - + +
224A GLY* 4.8 0.7 - - - -
243A MET 3.9 9.4 - - - -
244A LEU* 3.6 33.5 - - + +
245A GLN 3.6 28.7 - - - -
246A VAL* 3.9 7.2 - - + -
251A ARG* 3.8 13.6 - - - +
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Residues in contact with SER 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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131A ARG* 5.3 5.0 + - - -
132A ASP* 5.7 0.2 - - - -
133A LEU* 3.8 33.4 + - - +
174A TYR* 2.8 28.3 + - - +
175A ALA* 4.8 1.9 - - - -
176A ALA 5.0 0.5 + - - -
179A LEU* 6.1 1.0 - - - +
190A ALA 3.0 15.9 + - - -
191A ASP* 3.7 9.6 + - - -
193A TRP* 1.4 75.0 - - - +
195A MET* 1.3 56.1 + - - +
197A ILE* 3.2 7.0 + - - +
198A LEU* 2.9 31.5 + - - +
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Residues in contact with MET 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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113A PHE* 3.3 17.0 - - + -
116A ILE* 4.1 15.5 - - + -
117A VAL* 3.4 46.7 - - + +
120A VAL* 3.8 29.4 - - + -
133A LEU* 3.9 12.1 - - + -
191A ASP 2.9 18.9 + - - +
192A VAL* 3.5 6.1 - - - +
193A TRP 3.1 0.2 - - - -
194A SER* 1.3 73.7 - - - +
196A GLY* 1.3 53.2 + - - +
198A LEU* 3.2 7.4 + - + +
199A LEU* 2.8 29.6 + - - +
243A MET* 3.6 9.9 - - + -
254A MET* 4.1 10.8 - - + -
257A LEU* 3.8 15.3 - - + -
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Residues in contact with GLY 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 VAL 3.0 6.9 + - - -
193A TRP 2.9 8.4 + - - -
195A MET* 1.3 73.0 - - - +
197A ILE* 1.4 62.3 + - - +
199A LEU* 3.4 2.4 + - - -
200A TYR* 3.1 19.6 + - - +
240A LEU* 3.4 13.2 - - - +
243A MET* 3.7 29.7 - - - +
244A LEU* 3.8 13.4 - - - +
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Residues in contact with ILE 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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173A ALA 3.8 18.6 - - - +
174A TYR* 3.5 31.6 - - + +
193A TRP* 3.0 44.1 + - + +
194A SER 3.2 6.3 + - - +
196A GLY* 1.4 75.3 - - - +
198A LEU* 1.4 61.2 + - - +
200A TYR* 3.2 7.5 + - - +
201A VAL* 3.1 21.8 + - - +
207A LEU* 4.2 6.1 - - + -
208A PRO* 3.8 18.6 - - + -
209A PHE* 3.6 34.5 - - + -
244A LEU* 3.6 9.2 - - + +
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Residues in contact with LEU 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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94A LEU* 4.8 3.8 - - + -
98A ILE* 5.6 0.2 - - - +
113A PHE* 4.6 5.4 - - + -
116A ILE* 4.3 22.4 - - + -
133A LEU* 4.1 23.6 - - + -
134A LYS* 3.8 2.9 - - - +
135A PRO* 3.6 42.4 - - + -
138A LEU* 4.1 21.1 - - + -
174A TYR* 3.9 9.9 - - + +
194A SER 2.9 16.3 + - - +
195A MET* 3.2 14.8 + - + +
197A ILE* 1.4 70.6 - - - +
199A LEU* 1.3 60.5 + - - +
201A VAL* 3.3 5.3 + - + +
202A LEU* 2.8 38.1 + - + +
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Residues in contact with LEU 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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109A THR* 3.8 12.1 - - + -
113A PHE* 3.8 22.6 - - + -
195A MET 2.8 19.3 + - - +
196A GLY* 3.5 6.3 - - - +
197A ILE 3.4 0.2 - - - -
198A LEU* 1.3 73.8 - - - +
200A TYR* 1.3 61.9 + - - +
202A LEU* 3.5 4.7 + - - +
203A MET* 3.3 36.5 + - + +
236A SER 4.7 0.9 - - - +
239A LEU* 3.7 33.2 - - + -
240A LEU* 3.8 20.9 - - + +
243A MET* 4.1 10.1 - - - -
262A TRP* 3.7 29.4 - - + -
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Residues in contact with TYR 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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196A GLY 3.1 13.8 + - - +
197A ILE 3.2 8.3 + - - +
199A LEU* 1.3 77.5 - - - +
201A VAL* 1.3 50.5 + - - +
203A MET* 3.4 1.8 + - - -
204A CYS* 2.8 62.3 + - + +
206A PHE* 3.3 40.6 - + - -
207A LEU 3.8 1.6 - - - -
208A PRO* 3.5 41.6 - - + +
226A TYR* 3.7 19.1 - + - -
227A ASP* 2.6 35.1 + - - +
228A VAL* 5.2 0.2 - - - -
229A PRO* 3.8 5.6 - - + +
232A LEU* 4.9 2.7 - - + -
240A LEU* 3.7 27.8 - - + +
244A LEU* 5.0 1.8 - - + -
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Residues in contact with VAL 201 (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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95A PHE* 6.4 0.7 - - + -
98A ILE* 3.9 27.4 - - + +
135A PRO* 5.0 2.9 - - + -
174A TYR* 3.4 25.4 - - - +
197A ILE* 3.1 17.8 + - + +
198A LEU* 3.8 4.7 - - + +
200A TYR* 1.3 71.1 - - - +
202A LEU* 1.3 61.7 + - - +
205A GLY* 2.7 28.6 + - - -
206A PHE* 3.7 27.8 - - - +
207A LEU* 3.7 23.6 - - + -
208A PRO* 4.3 0.9 - - + -
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Residues in contact with LEU 202 (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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94A LEU* 3.9 15.0 - - + -
98A ILE* 3.8 24.1 - - + +
103A ARG* 3.8 1.7 - - - -
104A LEU* 2.8 55.5 + - + +
109A THR* 3.7 20.2 - - + +
112A VAL* 3.7 22.0 - - + -
113A PHE* 4.1 25.4 - - + -
116A ILE* 4.1 11.7 - - + -
198A LEU* 2.8 24.3 + - + +
199A LEU* 3.7 4.0 - - - +
200A TYR 3.3 0.2 - - - -
201A VAL* 1.3 78.2 - - - +
203A MET* 1.3 58.0 + - - +
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Residues in contact with MET 203 (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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103A ARG* 3.5 10.5 - - - +
104A LEU 3.8 10.3 - - - +
106A GLU* 4.3 14.8 - - - +
109A THR* 3.2 27.6 - - + +
199A LEU* 3.3 40.3 + - + +
200A TYR* 4.1 2.0 - - - +
202A LEU* 1.3 75.9 - - - +
204A CYS* 1.3 58.0 + - - +
231A TRP* 2.9 23.3 + - + -
232A LEU* 3.7 20.9 - - + -
236A SER* 3.3 37.2 - - - +
240A LEU* 4.5 9.0 - - + -
262A TRP* 4.2 7.6 - - + -
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Residues in contact with CYS 204 (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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102A ASP 4.5 0.3 - - - +
103A ARG* 3.7 15.3 + - - +
200A TYR* 2.8 53.1 + - + +
203A MET* 1.3 80.0 - - - +
205A GLY* 1.3 57.1 + - - +
206A PHE* 3.3 31.8 - - + +
229A PRO* 3.7 27.1 - - - -
231A TRP* 3.9 10.1 - - + +
232A LEU* 4.1 13.9 - - - -
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Residues in contact with GLY 205 (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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98A ILE* 4.0 10.9 - - - +
99A ILE* 6.2 0.2 - - - +
102A ASP 3.1 25.8 - - - +
103A ARG* 3.8 2.0 - - - +
201A VAL* 2.7 26.9 + - - -
204A CYS* 1.3 72.1 - - - +
206A PHE* 1.3 59.4 + - - +
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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