Contacts of the helix formed by residues 188 - 205 (chain C) 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 THR 188 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C HIS* 3.2 57.9 + - + +
130C LEU* 3.8 11.0 - - - +
187C SER* 1.3 81.6 + - - +
189C SER* 1.3 67.1 + - - +
190C ILE* 3.0 2.9 + - - +
191C ASP* 3.2 11.1 + - - +
192C ILE* 4.1 10.3 + - + -
287C SER* 5.1 14.8 - - - -
288C ALA 5.2 0.4 - - - +
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Residues in contact with SER 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C ASP* 4.8 1.0 + - - -
186C TYR* 4.6 3.8 - - - +
187C SER* 2.7 24.2 + - - -
188C THR* 1.3 77.4 - - - +
190C ILE* 1.3 63.1 + - - -
192C ILE* 3.0 22.4 + - - +
193C TRP* 3.5 11.8 + - - +
282C PRO* 3.7 41.1 - - - +
285C ARG* 4.4 15.3 + - - -
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Residues in contact with ILE 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C LEU* 4.0 11.2 - - + -
132C ARG* 4.2 32.5 - - + +
174C TYR 5.0 0.3 - - - +
175C ARG* 4.9 9.9 - - - +
176C ALA* 4.5 18.0 - - + +
178C ASP* 5.8 1.5 + - - -
179C VAL* 3.7 26.9 - - + -
186C TYR* 3.4 40.8 - - + +
187C SER 3.1 15.6 + - - +
188C THR 3.0 2.6 + - - +
189C SER* 1.3 77.6 + - - +
191C ASP* 1.3 68.5 + - - +
193C TRP* 4.1 4.9 + - - +
194C SER* 3.4 18.1 + - - +
285C ARG* 5.2 0.2 - - - +
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Residues in contact with ASP 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C LEU* 3.4 20.6 - - + +
125C HIS* 3.3 34.0 - - - +
130C LEU* 3.5 1.7 - - - -
131C HIS* 2.7 30.3 + - - +
132C ARG* 3.0 25.2 + - - -
134C LEU* 3.5 12.4 - - + +
188C THR 3.2 2.6 + - - +
189C SER 3.1 0.8 - - - -
190C ILE* 1.3 79.8 - - - +
192C ILE* 1.3 66.1 + - - +
194C SER* 3.1 17.5 + - - -
195C CYS* 3.2 15.5 + - - -
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Residues in contact with ILE 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LEU* 4.3 9.2 - - + -
121C LEU* 4.2 12.8 - - + -
125C HIS* 4.6 2.9 - - + +
188C THR* 4.6 10.3 - - + +
189C SER* 3.0 20.2 + - - +
191C ASP* 1.3 75.6 - - - +
193C TRP* 1.3 63.0 + - - +
195C CYS* 3.0 10.1 + - - +
196C GLY* 3.0 17.7 + - - -
277C LEU* 3.8 33.2 - - + +
285C ARG* 4.2 8.3 - - + -
286C LEU* 3.2 26.0 - - + +
287C SER 4.1 0.4 - - - -
288C ALA* 3.6 38.1 - - + +
291C ALA* 5.7 1.6 - - + -
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Residues in contact with TRP 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C TRP 5.0 1.0 + - - -
174C TYR* 3.7 10.6 + - - +
175C ARG 3.4 13.3 + - - +
176C ALA* 3.5 20.9 - - + -
177C PRO* 3.6 22.0 - - + -
189C SER 3.5 3.2 + - - +
190C ILE 4.2 3.6 - - - +
191C ASP 3.3 0.4 - - - -
192C ILE* 1.3 77.7 - - - +
194C SER* 1.3 64.4 + - - +
196C GLY* 3.0 11.4 + - - -
197C CYS* 3.0 25.2 + - - -
209C PHE* 3.8 12.3 - + - -
221C ILE* 3.6 42.1 - - + +
225C MET* 4.5 3.4 - - + -
277C LEU 3.6 10.1 + - - -
278C LEU* 3.2 46.0 - - + +
279C GLN 3.4 22.4 - - - -
280C LEU* 4.3 3.4 - - + -
285C ARG* 3.2 29.6 - - - +
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Residues in contact with SER 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C ARG 6.1 0.9 - - - -
134C LEU* 3.8 35.4 + - - +
174C TYR* 2.8 30.1 + - - -
190C ILE 3.4 14.0 + - - -
191C ASP* 3.1 10.9 + - - -
193C TRP* 1.3 75.5 - - - +
195C CYS* 1.3 60.0 + - - +
197C CYS* 3.1 4.3 + - - +
198C ILE* 2.8 34.3 + - - +
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Residues in contact with CYS 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C GLN* 3.1 19.4 + - - +
117C LEU* 4.0 14.1 - - + -
118C LEU* 4.1 12.8 - - + -
121C LEU* 3.3 29.8 - - - -
134C LEU* 4.1 8.7 - - - +
191C ASP 3.2 19.3 + - - -
192C ILE* 3.0 15.1 + - - +
194C SER* 1.3 75.6 - - - +
196C GLY* 1.3 55.6 + - - +
198C ILE* 3.5 9.1 - - - +
199C LEU* 3.0 23.2 + - - +
277C LEU* 3.7 12.6 - - + -
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Residues in contact with GLY 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C ILE 3.0 10.1 + - - -
193C TRP 3.0 6.0 + - - -
195C CYS* 1.3 77.2 - - - +
197C CYS* 1.3 60.4 + - - +
199C LEU* 3.3 5.2 - - - +
200C ALA* 3.1 23.6 + - - +
274C LEU* 3.9 5.5 - - - +
277C LEU* 3.5 24.8 - - - +
278C LEU* 4.1 15.8 - - - +
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Residues in contact with CYS 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C TRP 4.1 8.5 - - - +
174C TYR* 3.5 27.5 - - + -
193C TRP* 3.0 47.6 + - - -
194C SER 3.1 3.3 + - - +
196C GLY* 1.3 73.0 - - - +
198C ILE* 1.3 66.4 + - - +
200C ALA* 3.4 6.7 + - - +
201C GLU* 3.0 24.3 + - - +
208C LEU* 4.9 10.2 + - + +
209C PHE* 4.1 20.4 - - + -
278C LEU* 4.1 6.5 - - - -
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Residues in contact with ILE 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C LEU* 3.9 15.7 - - + -
117C LEU* 3.8 18.2 - - + -
134C LEU* 4.3 5.2 - - + +
135C LYS* 3.8 16.8 - - - +
136C PRO* 3.6 31.6 - - + +
139C LEU* 3.8 23.1 - - + -
174C TYR* 3.8 10.1 - - + -
194C SER* 2.8 31.7 + - - +
195C CYS* 3.5 9.0 - - - +
197C CYS* 1.3 71.6 - - - +
199C LEU* 1.3 64.3 + - - +
201C GLU* 3.0 9.5 + - - +
202C MET* 2.8 31.6 + - + +
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Residues in contact with LEU 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C VAL* 4.2 11.7 - - + -
114C GLN* 3.4 34.3 + - + +
195C CYS 3.0 8.0 + - - +
196C GLY 3.3 9.6 - - - +
198C ILE* 1.3 77.6 - - - +
200C ALA* 1.3 63.2 + - - +
202C MET* 2.9 19.7 + - - +
203C ILE* 3.1 39.6 + - + +
270C LEU* 3.9 13.0 - - + -
273C PHE* 3.5 30.7 - - + -
274C LEU* 3.6 19.3 - - + -
277C LEU* 4.2 5.6 - - + -
296C TRP* 4.7 3.8 - - + -
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Residues in contact with ALA 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C GLY 3.1 11.5 + - - +
197C CYS 3.8 3.1 - - - +
198C ILE 3.4 0.2 - - - -
199C LEU* 1.3 78.5 - - - +
201C GLU* 1.3 56.2 + - - +
203C ILE* 3.5 13.6 + - - +
204C THR* 3.1 34.7 + - - +
206C LYS 4.9 0.4 - - - -
208C LEU* 3.7 33.9 - - + -
258C LEU* 3.9 16.2 - - + -
274C LEU* 4.2 8.7 - - + +
278C LEU* 4.9 0.7 - - + -
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Residues in contact with GLU 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C LYS* 5.6 6.1 - - - +
93C MET* 3.6 18.1 - - + +
136C PRO* 3.6 15.8 - - + +
174C TYR* 2.5 40.5 + - - -
197C CYS 3.0 11.3 + - - +
198C ILE* 3.0 9.9 + - - +
200C ALA* 1.3 74.2 - - - +
202C MET* 1.3 64.2 + - - +
203C ILE 3.1 1.6 - - - -
205C GLY* 3.0 27.0 + - - +
206C LYS 3.7 22.4 - - - +
207C PRO* 3.5 26.6 - - + +
208C LEU 5.1 0.8 - - - +
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Residues in contact with MET 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C LEU* 3.7 35.7 - - + -
93C MET* 4.2 8.9 - - - +
104C GLY* 3.7 1.0 - - - -
105C LEU* 2.8 41.2 + - + +
110C VAL* 3.4 43.5 - - + +
113C PHE* 3.8 24.5 - - + -
114C GLN* 3.2 35.2 - - - +
117C LEU* 5.6 0.2 - - + -
139C LEU* 6.1 0.2 - - + -
198C ILE* 2.8 21.4 + - + +
199C LEU* 3.3 9.9 - - - +
201C GLU* 1.3 76.3 - - + +
203C ILE* 1.3 53.8 + - - +
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Residues in contact with ILE 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C GLY* 3.4 9.5 - - - -
105C LEU 3.9 8.0 + - - +
107C LEU* 4.7 6.5 - - + -
110C VAL* 4.4 11.0 - - + -
199C LEU* 3.1 38.8 + - + +
200C ALA* 3.6 13.7 - - - +
201C GLU 3.1 0.2 - - - -
202C MET* 1.3 80.0 - - - +
204C THR* 1.3 67.1 + - + +
258C LEU* 5.0 5.6 - - + +
261C HIS 3.8 0.2 - - - +
262C THR* 3.5 40.9 - - + +
266C LEU* 3.8 24.5 - - + -
270C LEU* 4.5 9.2 - - + -
271C MET* 5.1 0.7 - - + -
274C LEU* 4.2 15.5 - - + -
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Residues in contact with THR 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C GLY 3.0 9.5 + - - -
200C ALA 3.1 15.4 + - - +
203C ILE* 1.3 76.9 - - + +
205C GLY* 1.3 60.3 + - - +
206C LYS* 2.7 35.7 + - - +
258C LEU* 3.6 37.0 - - + +
261C HIS* 3.0 56.0 - - - +
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Residues in contact with GLY 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C MET* 3.6 18.6 - - - +
104C GLY* 3.7 16.1 - - - -
201C GLU* 3.0 16.2 + - - +
203C ILE 3.6 0.4 - - - -
204C THR* 1.3 78.1 + - - +
206C LYS* 1.3 58.6 + - - +
207C PRO* 4.3 2.1 - - - +
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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