Contacts of the helix formed by residues 207 - 223 (chain C) in PDB entry 1JPW
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 ASP 207 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169C ASN* 2.9 28.5 + - - +
205C THR* 2.8 12.4 + - - +
206C ASN* 1.3 80.4 - - - +
208C VAL* 1.3 63.2 + - - +
209C GLU* 3.2 26.0 + - - +
210C THR* 2.8 18.2 + - - +
211C ALA* 3.3 20.1 + - - +
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Residues in contact with VAL 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C ASN 4.9 5.2 - - - +
207C ASP* 1.3 77.0 - - - +
209C GLU* 1.3 66.2 + - + +
211C ALA* 4.0 9.3 - - - +
212C ARG* 3.5 19.2 + - - +
247C PRO* 6.1 2.9 - - + -
248C VAL* 4.0 30.3 - - + +
251C VAL* 4.6 4.0 - - - +
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Residues in contact with GLU 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C ASN* 5.0 2.9 - - - +
173C VAL* 4.6 16.3 - - + +
207C ASP* 3.2 14.4 + - - +
208C VAL* 1.3 81.2 - - + +
210C THR* 1.3 67.2 + - - +
211C ALA 3.1 1.3 - - - -
212C ARG* 3.3 31.6 + - - -
213C CYS* 2.9 49.1 + - - -
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Residues in contact with THR 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C GLN* 5.9 0.9 - - - +
168C VAL* 4.8 1.6 - - + +
169C ASN* 2.3 40.4 + - - +
172C ALA* 4.0 20.6 - - + -
173C VAL* 5.8 1.6 - - - -
201C THR* 3.9 25.6 - - + -
205C THR* 3.1 20.4 + - - +
207C ASP* 2.8 15.9 - - - +
209C GLU* 1.3 79.6 - - - +
211C ALA* 1.3 51.5 + - - +
213C CYS* 4.7 3.4 - - - -
214C THR* 2.7 42.7 + - + +
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Residues in contact with ALA 211 (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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202C MET* 4.9 4.1 - - - +
205C THR* 4.4 10.3 - - + +
207C ASP 3.3 15.4 + - - +
208C VAL* 4.0 7.2 - - - +
209C GLU 3.1 0.2 - - - -
210C THR* 1.3 76.3 - - - +
212C ARG* 1.3 71.2 + - - +
214C THR* 3.5 5.7 + - - -
215C ALA* 3.0 25.5 + - - +
243C MET* 5.0 7.4 - - - -
248C VAL* 6.5 0.2 - - + -
251C VAL* 3.6 25.6 - - + -
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Residues in contact with ARG 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C HIS* 5.9 3.4 - - + -
208C VAL 3.5 11.5 + - - +
209C GLU* 3.3 33.3 + - - +
211C ALA* 1.3 81.5 - - - +
213C CYS* 1.3 60.8 + - - +
215C ALA* 3.5 2.3 - - - +
216C GLY 3.0 21.1 + - - -
248C VAL* 5.2 6.2 - - + +
250C SER* 4.1 26.2 + - - -
251C VAL* 3.3 15.5 - - + +
254C TYR* 3.5 22.6 - - + -
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Residues in contact with CYS 213 (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 ALA 4.3 9.6 - - - +
173C VAL* 3.9 30.3 - - - +
176C HIS* 3.3 30.9 - - + -
209C GLU* 2.9 39.7 + - - +
210C THR* 3.8 4.3 - - - +
212C ARG* 1.3 78.4 - - - +
214C THR* 1.3 56.6 + - + +
215C ALA 2.7 16.6 + - - -
216C GLY 2.7 12.8 + - - -
217C THR* 2.9 16.3 + - - -
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Residues in contact with THR 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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160C LEU* 5.6 2.5 - - + -
172C ALA* 3.9 26.4 + - + +
198C ILE* 3.5 28.4 - - + +
201C THR* 4.4 9.6 - - + -
202C MET* 3.4 33.3 - - - +
210C THR* 2.7 35.0 + - + +
211C ALA* 3.5 1.6 + - - -
213C CYS* 1.3 72.6 - - - +
215C ALA* 1.3 59.3 + - - +
217C THR* 4.0 8.7 - - - -
218C LEU* 3.4 23.0 + - - +
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Residues in contact with ALA 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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202C MET* 3.5 20.0 - - + -
211C ALA 3.0 20.7 + - - +
212C ARG* 3.5 3.8 - - - +
213C CYS 2.7 5.3 + - - -
214C THR* 1.3 72.8 + - - +
216C GLY* 1.3 58.2 + - - +
217C THR 3.1 1.3 - - - -
218C LEU* 3.3 4.5 + - - +
219C HIS* 2.9 27.5 + - - +
240C LEU* 6.2 0.2 - - + -
243C MET* 5.8 0.4 - - + -
251C VAL* 4.7 12.8 - - + +
254C TYR* 3.8 24.6 - - + +
255C ALA* 5.3 1.8 - - + +
258C THR* 5.2 0.3 + - - -
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Residues in contact with GLY 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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176C HIS* 3.7 11.9 - - - -
212C ARG 3.0 7.8 + - - -
213C CYS 2.7 9.7 + - - -
215C ALA* 1.3 72.9 - - - +
217C THR* 1.3 57.1 + - - +
219C HIS* 3.1 4.2 + - - +
220C ASN* 2.9 34.4 + - - +
254C TYR* 3.4 33.1 - - - -
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Residues in contact with THR 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 ALA 4.9 1.0 + - - -
175C VAL* 4.3 10.7 - - + +
176C HIS* 3.2 25.6 + - - +
179C SER* 3.6 24.9 + - - -
188C ILE* 4.7 2.7 - - + -
198C ILE* 3.5 30.1 - - + -
213C CYS 2.9 18.1 + - - -
214C THR* 3.7 9.5 - - - -
216C GLY* 1.3 74.3 - - - +
218C LEU* 1.3 59.9 + - - +
220C ASN* 2.9 21.1 + - - +
221C LEU* 3.2 20.3 + - + +
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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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195C VAL* 6.5 0.9 - - + -
198C ILE* 4.4 9.4 - - + -
199C VAL* 4.4 24.0 - - + -
202C MET* 3.1 32.1 - - + -
214C THR 3.4 10.5 + - - +
215C ALA 3.3 3.0 + - - +
217C THR* 1.3 77.8 - - - +
219C HIS* 1.3 59.1 + - - +
221C LEU* 3.9 13.5 - - + -
222C SER 3.3 0.3 + - - -
231C ILE* 3.1 56.0 - - + +
236C GLY 5.0 2.0 - - - +
239C ALA* 6.1 0.2 - - + -
240C LEU* 3.6 16.4 - - + -
258C THR* 3.2 16.2 + - + -
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Residues in contact with HIS 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 ALA 2.9 13.4 + - - +
216C GLY* 3.3 10.1 - - - +
217C THR 3.0 0.2 - - - -
218C LEU* 1.3 77.3 - - - +
220C ASN* 1.3 60.0 + - - +
221C LEU 3.0 4.7 - - - -
222C SER* 2.4 32.8 + - - -
223C HIS* 2.7 37.7 + + - -
254C TYR* 3.3 30.6 - + + +
257C THR* 3.3 26.1 - - + +
258C THR* 3.1 14.8 - - - +
261C ASN* 4.6 0.6 + - - -
45F LYS 6.0 0.4 - - - -
46F SER* 6.1 0.2 - - - -
49F VAL* 3.5 36.1 - - + -
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Residues in contact with ASN 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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176C HIS* 4.4 5.5 + - - -
179C SER* 3.2 29.3 + - - +
180C LYS* 4.1 14.7 - - - +
185C ARG* 2.9 47.6 + - - +
216C GLY 2.9 18.2 + - - +
217C THR 2.9 7.4 + - - +
219C HIS* 1.3 83.4 + - - +
221C LEU* 1.3 59.6 + - - +
223C HIS* 3.8 21.9 + - - -
224C HIS* 4.1 5.9 + - - +
254C TYR* 5.9 0.5 - - - -
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Residues in contact with LEU 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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179C SER* 5.0 4.0 - - - -
185C ARG* 3.3 34.5 - - + +
188C ILE* 3.8 33.0 - - + -
189C MET* 4.4 14.8 - - + -
195C VAL* 4.5 14.8 - - + -
198C ILE* 4.7 7.4 - - + -
217C THR* 3.3 15.9 - - + +
218C LEU* 4.0 10.8 - - + +
219C HIS 3.0 0.6 - - - -
220C ASN* 1.3 77.7 - - - +
222C SER* 1.3 54.4 + - - +
223C HIS 3.1 2.2 - - - -
224C HIS* 2.6 38.1 + - - +
227C GLY* 3.1 15.7 - - - -
230C ALA* 5.8 0.2 - - + -
231C ILE* 3.9 17.7 - - + -
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Residues in contact with SER 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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218C LEU 3.3 5.6 + - - -
219C HIS* 2.4 28.1 + - - -
221C LEU* 1.3 78.9 - - - +
223C HIS* 1.3 62.3 + - - +
224C HIS 3.2 0.7 + - - -
228C LEU* 2.9 34.0 - - - +
231C ILE* 3.4 12.3 - - - +
258C THR* 3.1 32.0 + - - -
261C ASN* 3.5 18.8 + - - +
262C LEU* 5.7 2.5 - - - -
265C HIS* 4.0 3.3 + - - -
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Residues in contact with HIS 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C ARG* 5.9 2.7 - - - -
219C HIS* 2.7 53.8 + + - -
220C ASN* 3.8 21.9 + - - -
221C LEU 3.1 0.4 - - - -
222C SER* 1.3 79.5 - - - +
224C HIS* 1.3 67.3 + - - +
228C LEU* 5.1 1.1 - - - -
261C ASN* 4.6 12.6 - - - +
265C HIS* 5.4 1.8 - - - -
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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