Contacts of the helix formed by residues 189 - 205 (chain A) in PDB entry 2PK9
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 189 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ASP* 5.4 0.3 + - - -
186A TYR* 5.3 2.9 - - - +
187A SER* 2.8 13.9 + - - -
188A THR* 1.3 79.8 - - - +
190A ILE* 1.3 63.2 + - - +
191A ASP 3.2 2.7 - - - -
192A ILE* 3.4 18.0 + - - +
193A TRP 3.6 8.3 + - - -
282A PRO* 3.4 43.7 - - - +
285A ARG* 3.7 19.7 + - - -
286A LEU 5.9 0.2 - - - -
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Residues in contact with ILE 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LEU* 4.1 14.8 - - + -
132A ARG* 4.3 26.5 - - + +
174A TYR 4.9 0.5 - - - +
175A ARG* 4.5 9.0 - - - +
176A ALA* 4.4 14.4 + - + +
179A VAL* 3.6 34.8 - - + -
186A TYR* 4.0 25.5 - - + +
187A SER 3.4 15.5 + - - +
188A THR 4.7 0.9 - - - +
189A SER* 1.3 79.7 + - - +
191A ASP* 1.3 80.1 + - - +
192A ILE 3.5 0.3 + - - -
193A TRP* 3.6 11.8 + - - +
194A SER* 3.8 13.0 + - - +
285A ARG* 4.8 0.2 - - - +
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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
----------------------------------------------------------
121A LEU* 3.5 17.8 - - + +
125A HIS* 2.8 36.1 + - + +
130A LEU* 3.7 2.2 - - - -
131A HIS* 2.9 24.5 + - - +
132A ARG* 2.9 26.0 + - - -
134A LEU* 3.8 14.2 + - + +
188A THR 3.6 1.2 + - - -
189A SER 3.2 0.4 - - - -
190A ILE* 1.3 92.3 - - - +
192A ILE* 1.3 63.3 + - - +
193A TRP 3.4 0.2 - - - -
194A SER* 3.6 3.8 + - - +
195A CYS* 3.3 26.2 + - - -
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Residues in contact with ILE 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 4.4 9.9 - - + -
121A LEU* 4.0 14.6 - - + -
125A HIS* 4.4 2.2 - - + +
188A THR* 4.2 14.6 - - + +
189A SER* 3.4 10.2 + - - +
190A ILE 3.3 0.6 - - - -
191A ASP* 1.3 75.6 - - - +
193A TRP* 1.3 64.5 + - - +
195A CYS* 3.2 13.0 + - + +
196A GLY 3.2 9.4 + - - -
277A LEU* 3.9 29.6 - - + +
285A ARG* 3.8 16.4 - - + -
286A LEU 3.2 25.6 - - - +
287A SER* 4.2 1.8 - - - -
288A ALA* 3.6 37.9 - - + +
291A ALA* 5.7 0.9 - - + -
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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
----------------------------------------------------------
173A TRP 4.9 0.2 + - - -
174A TYR* 3.3 26.3 + - - +
175A ARG 3.1 21.1 + - - -
176A ALA* 3.7 4.7 - - + -
177A PRO* 3.7 19.7 - - + -
189A SER 3.6 4.2 + - - -
190A ILE 3.8 7.4 - - - +
191A ASP 3.4 0.2 - - - -
192A ILE* 1.3 76.4 - - - +
194A SER* 1.3 62.0 + - - +
196A GLY* 3.0 13.7 + - - -
197A CYS* 3.2 23.6 + - - -
209A PHE* 3.6 22.8 - + - -
217A GLN* 6.0 0.2 - - - +
221A ILE* 3.7 34.2 - - + +
225A MET* 4.1 11.7 - - + -
277A LEU 4.2 3.1 - - - -
278A LEU* 3.7 37.7 - - + +
279A GLN 3.5 27.6 - - - -
280A LEU* 4.6 1.3 - - + -
285A ARG* 3.6 26.5 - - - +
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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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132A ARG 5.6 1.7 + - - -
134A LEU* 3.5 39.6 + - - +
174A TYR* 2.6 31.3 + - - +
190A ILE* 3.8 9.3 + - - +
191A ASP* 3.6 10.1 + - - -
192A ILE 3.4 0.6 - - - -
193A TRP* 1.3 78.2 - - - +
195A CYS* 1.3 50.4 + - - +
197A CYS* 3.2 3.2 + - - +
198A ILE* 2.7 42.2 + - - +
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Residues in contact with CYS 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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114A GLN* 3.4 20.3 + - - +
117A LEU* 3.6 31.4 - - - -
118A LEU* 3.9 13.7 - - + -
121A LEU* 3.9 20.2 - - - -
134A LEU* 4.3 3.4 - - - -
191A ASP 3.3 19.7 + - - -
192A ILE* 3.2 13.4 + - - +
193A TRP 3.1 0.8 - - - -
194A SER* 1.3 79.6 - - - +
196A GLY* 1.3 56.8 + - - +
198A ILE* 3.5 6.8 + - - +
199A LEU* 3.0 28.1 + - - +
277A LEU* 4.5 3.8 - - + -
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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 ILE 3.2 6.5 + - - -
193A TRP 3.0 7.7 + - - -
195A CYS* 1.3 76.2 - - - +
197A CYS* 1.3 57.0 + - - +
199A LEU* 3.8 2.7 - - - -
200A ALA* 3.2 19.8 + - - +
274A LEU* 3.5 13.7 - - - +
277A LEU* 3.8 25.9 - - - +
278A LEU* 3.8 18.8 - - - +
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Residues in contact with CYS 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A TRP 3.9 8.3 - - - +
174A TYR* 3.6 21.1 - - + -
193A TRP* 3.2 38.7 + - - -
194A SER 3.6 6.5 - - - +
195A CYS 3.2 0.2 - - - -
196A GLY* 1.3 76.4 - - - +
198A ILE* 1.3 65.9 + - - +
199A LEU 3.0 1.3 - - - -
200A ALA* 3.3 5.1 + - - +
201A GLU* 3.1 25.8 + - - +
208A LEU* 5.0 9.0 + - + +
209A PHE* 3.7 28.0 - - + -
278A LEU* 4.0 4.0 - - - -
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Residues in contact with ILE 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 3.4 27.4 - - + -
114A GLN* 4.7 0.2 - - - +
117A LEU* 4.5 8.5 - - + -
134A LEU* 4.2 7.2 - - + +
135A LYS* 3.7 39.7 - - - +
136A PRO* 3.8 9.4 - - + -
139A LEU* 3.8 19.7 - - + -
174A TYR* 4.3 5.8 - - + -
194A SER* 2.7 33.2 + - - +
195A CYS* 3.7 9.6 - - - +
197A CYS* 1.3 76.3 - - - +
199A LEU* 1.3 61.8 + - - +
201A GLU* 3.3 7.4 - - - +
202A MET* 3.0 32.6 + - + +
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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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110A VAL* 3.8 23.8 - - + -
114A GLN* 3.6 21.8 - - + +
195A CYS 3.0 17.1 + - - +
196A GLY 3.7 5.6 - - - +
197A CYS 3.0 0.2 - - - -
198A ILE* 1.3 74.4 - - - +
200A ALA* 1.3 66.0 + - - +
202A MET* 3.2 6.7 + - + +
203A ILE* 3.0 40.4 + - + +
270A LEU* 4.5 6.7 - - + -
273A PHE* 3.7 36.6 - - + -
274A LEU* 3.9 18.2 - - + -
277A LEU* 4.1 4.7 - - + -
296A TRP* 4.2 13.5 - - + -
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Residues in contact with ALA 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 3.2 10.0 + - - +
197A CYS 3.3 4.0 + - - +
199A LEU* 1.3 76.8 - - - +
201A GLU* 1.3 53.5 + - - +
203A ILE* 3.1 11.8 + - - +
204A THR* 2.8 40.5 + - - +
206A LYS 4.7 0.2 - - - -
208A LEU* 3.6 37.5 - - + -
258A LEU* 3.8 18.8 - - + -
274A LEU* 4.5 6.0 - - + +
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Residues in contact with GLU 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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89A LEU* 6.4 0.9 - - + -
90A LYS* 5.3 6.4 - - - +
93A MET* 3.5 15.1 - - - +
136A PRO* 3.7 17.6 - - + +
173A TRP* 5.6 1.4 - - - -
174A TYR* 2.6 38.1 + - - -
197A CYS 3.1 9.4 + - - +
198A ILE* 3.3 11.4 - - - +
200A ALA* 1.3 76.4 - - - +
202A MET* 1.3 58.6 - - + +
203A ILE 3.2 0.2 + - - -
205A GLY* 2.6 43.5 + - - +
206A LYS 3.7 17.2 + - - +
207A PRO* 3.7 21.9 - - + +
208A LEU 4.9 1.2 + - - +
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Residues in contact with MET 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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89A LEU* 3.8 36.8 - - + -
93A MET* 3.9 9.9 - - - -
104A GLY* 3.2 1.0 - - - -
105A LEU* 2.8 39.5 + - + +
110A VAL* 3.7 37.4 - - + +
113A PHE* 3.9 23.1 - - + -
114A GLN* 3.4 33.2 - - + +
117A LEU* 5.8 0.2 - - + -
147A LEU* 5.7 0.2 - - - -
198A ILE* 3.0 23.8 + - + +
199A LEU* 3.2 8.0 + - + +
201A GLU* 1.3 78.4 - - + +
203A ILE* 1.3 58.2 + - - +
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Residues in contact with ILE 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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104A GLY* 3.8 7.7 + - - -
105A LEU 4.7 2.5 - - - +
107A LEU* 5.1 8.5 - - + +
110A VAL* 3.9 20.2 - - + -
199A LEU* 3.0 30.2 + - + +
200A ALA* 3.1 8.7 + - - +
202A MET* 1.3 77.0 - - - +
204A THR* 1.3 64.2 + - + +
258A LEU* 4.8 6.3 - - + -
261A HIS 4.1 0.5 - - - +
262A THR* 3.5 35.5 - - + -
266A LEU* 3.8 16.6 - - + -
270A LEU* 3.8 35.4 - - + -
274A LEU* 4.3 15.9 - - + -
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Residues in contact with THR 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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103A ARG* 3.9 4.5 + - - -
104A GLY 3.3 12.6 + - - -
200A ALA* 2.8 24.8 + - - +
203A ILE* 1.3 79.0 - - + +
205A GLY* 1.3 54.6 + - - +
206A LYS* 2.9 36.1 + - - +
208A LEU* 6.2 0.4 - - + +
257A VAL 5.3 0.7 - - - +
258A LEU* 3.7 48.9 - - + +
261A HIS* 3.2 28.2 - - + +
262A THR* 4.1 3.1 - - + -
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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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93A MET* 3.8 13.2 - - - +
103A ARG 3.8 14.9 + - - -
104A GLY* 3.7 13.1 - - - -
201A GLU* 2.6 26.9 + - - +
204A THR* 1.3 71.9 + - - +
206A LYS* 1.3 58.3 + - - +
207A PRO* 4.4 1.9 - - - +
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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
------------------------------------------------------------
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