Contacts of the helix formed by residues 213 - 226 (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 ASN 213 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151B ARG* 3.8 17.7 - - - +
172C LEU* 3.9 7.0 - - - -
212C THR* 1.3 91.4 - - + +
214C ASP* 1.3 65.2 + - - +
215C GLU* 3.1 13.5 + - - +
216C GLU* 3.1 32.3 + - - +
217C GLN* 2.8 31.5 + - - +
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Residues in contact with ASP 214 (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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151B ARG* 3.1 26.2 + - - +
154B GLU* 5.6 2.8 - - - +
172C LEU* 3.5 14.9 - - + +
180C LEU* 4.3 19.7 - - + +
213C ASN* 1.3 76.2 - - - +
215C GLU* 1.3 67.0 + - - +
217C GLN* 4.1 3.8 - - - +
218C LEU* 3.4 27.5 + - - +
241C LYS* 4.7 16.1 - - - +
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Residues in contact with GLU 215 (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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70B LYS* 3.4 43.0 + - - +
71B ILE* 6.2 0.2 - - - +
213C ASN* 3.1 10.7 - - - +
214C ASP* 1.3 86.5 + - - +
216C GLU* 1.3 61.3 + - - +
218C LEU* 3.9 7.6 + - - +
219C LYS* 3.5 18.7 + - - +
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Residues in contact with GLU 216 (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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210C PRO 4.3 2.9 - - - +
211C GLY* 3.7 5.5 - - - -
212C THR* 3.4 29.1 + - - -
213C ASN* 3.1 20.4 + - - +
215C GLU* 1.3 72.6 - - - +
217C GLN* 1.3 59.3 + - - +
218C LEU 3.2 1.6 - - - -
219C LYS* 3.1 29.1 + - - +
220C LEU* 2.9 43.4 + - + +
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Residues in contact with GLN 217 (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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172C LEU* 3.5 29.2 + - + +
173C TRP* 3.4 19.2 + - - -
175C ARG 4.8 0.6 + - - -
180C LEU* 3.8 15.7 - - + -
209C PHE* 3.1 45.4 + - - +
211C GLY* 3.4 21.2 + - - +
213C ASN 2.8 24.9 + - - +
214C ASP* 4.3 5.6 - - - -
216C GLU* 1.3 72.2 - - - +
218C LEU* 1.3 60.7 + - - +
220C LEU* 3.8 3.4 + - - +
221C ILE* 3.2 38.0 + - - +
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Residues in contact with LEU 218 (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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177C PRO* 3.9 25.8 - - + -
180C LEU* 4.0 21.9 - - + +
181C MET* 3.7 33.2 - - + +
214C ASP 3.4 17.1 + - - +
215C GLU* 4.0 7.6 - - - +
216C GLU 3.2 0.2 - - - -
217C GLN* 1.3 76.7 - - - +
219C LYS* 1.3 64.7 + - - +
221C ILE* 3.2 8.6 + - + +
222C PHE* 3.1 58.8 + - + -
241C LYS* 4.7 5.6 - - + +
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Residues in contact with LYS 219 (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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215C GLU 3.5 12.5 + - - +
216C GLU* 3.1 32.7 + - + +
218C LEU* 1.3 77.8 - - - +
220C LEU* 1.3 60.7 + - - +
222C PHE* 3.0 4.2 + - - -
223C ASP* 2.9 45.5 + - - +
249C ARG* 3.3 35.3 + - - +
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Residues in contact with LEU 220 (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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208C LEU 4.6 4.3 - - - +
209C PHE* 3.6 23.6 - - + -
210C PRO* 3.3 52.0 - - + +
211C GLY* 3.8 10.3 - - - +
216C GLU* 2.9 31.4 + - + +
217C GLN* 3.9 6.5 - - - +
219C LYS* 1.3 77.5 - - - +
221C ILE* 1.3 61.7 + - - +
223C ASP* 3.6 14.2 + - + +
224C ILE* 3.6 20.4 - - + +
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Residues in contact with ILE 221 (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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175C ARG 4.0 4.7 - - - +
177C PRO* 4.4 8.5 - - + -
180C LEU* 3.9 20.0 - - + -
193C TRP* 3.6 43.1 - - + +
209C PHE* 3.7 21.5 - - + -
217C GLN* 3.2 31.1 + - - +
218C LEU* 3.2 7.5 + - - +
219C LYS 3.1 0.8 - - - -
220C LEU* 1.3 75.9 - - - +
222C PHE* 1.3 63.1 + - + +
223C ASP 3.1 0.2 - - - -
224C ILE* 3.1 3.3 + - - -
225C MET* 2.8 30.8 + - + +
280C LEU* 3.7 20.2 - - + -
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Residues in contact with PHE 222 (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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177C PRO* 4.4 6.1 - - + -
181C MET* 4.0 21.5 - - + -
218C LEU* 3.1 42.9 + - + -
219C LYS* 3.0 3.5 + - - +
221C ILE* 1.3 80.2 - - + +
223C ASP* 1.3 57.6 + - - +
224C ILE 3.3 0.2 - - - -
226C GLY* 3.0 47.1 + - - +
227C THR* 3.9 12.0 + - + -
228C PRO* 3.6 36.6 - - + -
233C TRP* 5.7 1.1 - + - -
246C ILE* 4.9 10.3 - - + -
249C ARG* 3.5 37.5 - - - +
250C PRO 5.2 0.2 - - - +
280C LEU* 4.0 17.0 - - + -
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Residues in contact with ASP 223 (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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219C LYS* 2.9 42.2 + - - +
220C LEU* 3.7 11.7 + - + +
221C ILE 3.1 0.4 - - - -
222C PHE* 1.3 77.3 - - - +
224C ILE* 1.3 60.4 + - + +
226C GLY 4.6 0.7 - - - -
249C ARG* 3.4 25.2 + - - +
250C PRO 4.8 2.6 - - - +
252C ARG* 3.2 40.0 + - - +
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Residues in contact with ILE 224 (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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208C LEU* 3.9 25.8 - - + +
209C PHE* 3.5 31.2 - - + -
220C LEU* 3.6 14.8 - - + +
221C ILE 3.1 2.4 + - - -
223C ASP* 1.3 83.9 - - + +
225C MET* 1.3 77.6 + - + +
226C GLY 3.5 0.9 - - - -
251C PRO* 4.3 1.4 - - - +
252C ARG* 3.5 41.7 + - - +
254C LEU* 4.5 15.8 - - + +
257C VAL* 4.5 24.9 - - + -
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Residues in contact with MET 225 (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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193C TRP* 4.5 2.2 - - + -
208C LEU* 4.5 2.2 - - + -
209C PHE* 3.8 20.9 - - + -
221C ILE* 2.8 25.6 + - + +
224C ILE* 1.3 85.3 - - + +
226C GLY* 1.3 62.3 + - - +
227C THR 4.6 0.9 - - - +
251C PRO* 3.7 18.0 - - - +
254C LEU* 3.6 34.1 - - + -
275C HIS* 5.6 2.5 - - - -
278C LEU* 3.7 48.0 - - + +
280C LEU* 3.8 28.2 - - + +
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Residues in contact with GLY 226 (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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222C PHE* 3.0 38.0 + - - -
223C ASP 4.6 0.2 - - - -
224C ILE 3.5 2.6 - - - +
225C MET* 1.3 84.2 - - - +
227C THR* 1.3 65.4 + - - -
249C ARG 3.3 15.7 - - - -
250C PRO 4.2 0.9 - - - -
251C PRO* 3.7 16.9 - - - +
280C LEU* 3.4 3.1 - - - +
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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
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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