Contacts of the helix formed by residues 209 - 222 (chain D) in PDB entry 1P4A
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 GLY 209 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206D MET* 4.2 22.4 - - - +
207D LYS 3.8 0.6 - - - -
208D ALA* 1.3 79.8 - - - +
210D GLY* 1.3 64.6 + - - +
211D THR 3.2 2.7 - - - -
212D ILE* 3.7 4.7 + - - +
213D ASN* 3.1 28.2 + - - +
238D VAL* 5.3 0.2 - - - -
239D ASP* 5.8 1.6 - - - -
242D LEU 5.2 1.5 - - - +
243D VAL* 4.9 8.8 - - - +
607D PCP 3.4 7.0 + - - -
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Residues in contact with GLY 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D TYR* 3.4 14.7 - - - +
176D VAL* 3.2 31.1 + - - -
208D ALA* 3.6 5.0 - - - +
209D GLY* 1.3 77.8 - - - +
211D THR* 1.3 56.8 + - - +
213D ASN* 3.7 5.9 - - - +
214D GLY 3.0 21.0 + - - -
607D PCP 2.9 3.8 + - - -
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Residues in contact with THR 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D VAL* 3.6 33.4 - - + -
161D LYS* 5.5 1.6 + - - +
175D TYR* 3.5 20.4 - - + +
177D SER* 3.8 3.6 + - - -
186D MET* 3.4 15.8 - - + +
203D ASP* 4.5 1.8 - - - +
210D GLY* 1.3 70.5 - - - +
212D ILE* 1.3 66.4 + - - +
213D ASN 3.2 0.9 - - - -
214D GLY 3.3 1.2 + - - -
215D MET* 3.1 22.0 + - + +
607D PCP 2.6 54.4 + - + +
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Residues in contact with ILE 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D ILE* 4.2 19.3 - - + -
203D ASP* 4.2 15.5 - - + +
206D MET* 3.7 34.5 - - + -
209D GLY* 3.7 6.6 + - - +
211D THR* 1.3 76.4 - - - +
213D ASN* 1.3 58.4 + - - +
215D MET* 3.0 16.4 + - + +
216D ILE* 2.9 44.8 + - + +
229D ILE* 4.0 22.9 - - + -
231D VAL* 3.8 22.4 - - + -
243D VAL* 4.4 14.1 - - + -
607D PCP 5.3 1.5 + - - +
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Residues in contact with ASN 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D GLY 3.1 20.9 + - - +
210D GLY* 3.7 7.4 - - - +
212D ILE* 1.3 75.4 - - - +
214D GLY* 1.3 65.7 + - - +
216D ILE* 3.2 11.7 + - - +
217D ASN* 2.9 36.2 + - - +
242D LEU* 3.6 37.0 + - - +
243D VAL* 4.0 7.6 - - - -
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Residues in contact with GLY 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D ILE* 3.6 10.5 - - - +
175D TYR* 4.0 15.9 - - - +
186D MET* 3.5 13.9 - - - -
210D GLY 3.0 16.6 + - - -
211D THR 3.3 4.2 + - - -
213D ASN* 1.3 73.9 - - - +
215D MET* 1.3 58.3 + - - +
217D ASN* 3.2 7.4 + - - +
218D LEU* 2.8 28.6 + - - +
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Residues in contact with MET 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D MET* 3.7 33.4 - - - +
136D THR* 4.1 4.0 - - - -
137D VAL* 3.8 37.5 - - + +
159D VAL* 4.4 5.6 - - + -
186D MET* 3.5 17.4 - - + -
201D ILE* 3.9 33.4 - - + -
202D ILE 4.9 0.7 - - - +
203D ASP* 4.7 8.1 - - - -
211D THR* 3.1 19.8 + - + +
212D ILE* 3.0 21.1 + - + +
214D GLY* 1.3 75.3 - - - +
216D ILE* 1.3 59.8 + - - +
218D LEU* 3.3 5.2 + - - +
219D LEU* 2.9 34.3 + - - +
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Residues in contact with ILE 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D ILE* 3.9 15.7 - - + -
212D ILE* 2.9 32.5 + - + +
213D ASN* 3.7 18.4 - - - +
215D MET* 1.3 72.1 - - - +
217D ASN* 1.3 70.7 + - - +
219D LEU* 3.2 9.6 + - - +
220D ASP* 3.1 33.4 + - - +
226D VAL* 4.0 15.7 - - + -
229D ILE* 4.1 7.2 - - + -
243D VAL 4.6 2.7 - - - +
244D ASP* 3.5 34.5 - - + +
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Residues in contact with ASN 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D ILE* 4.0 21.0 - - + +
174D ASN 4.8 5.2 - - - +
175D TYR* 5.9 0.2 - - - +
213D ASN* 2.9 25.6 + - - +
214D GLY* 3.2 12.3 - - - +
216D ILE* 1.3 80.7 - - - +
218D LEU* 1.3 63.1 + - - +
220D ASP* 3.1 26.9 + - - +
221D GLU* 3.6 10.7 + - - +
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Residues in contact with LEU 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D MET* 4.9 4.3 - - + -
159D VAL* 3.8 41.5 - - + -
171D VAL* 3.6 43.3 - - + +
173D ILE* 3.7 18.8 - - + +
186D MET* 4.5 7.9 - - + +
187D SER 4.6 1.3 - - - -
188D LEU* 4.0 15.9 - - + -
214D GLY 2.8 17.2 + - - +
215D MET* 3.5 5.8 - - - +
216D ILE 3.2 0.2 - - - -
217D ASN* 1.3 76.6 - - - +
219D LEU* 1.3 62.3 + - + +
221D GLU* 3.1 21.8 + - - +
222D PHE* 3.4 20.4 - - + -
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Residues in contact with LEU 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D MET* 3.6 22.2 - - + -
193D MET* 3.1 32.1 - - + -
199D VAL* 3.8 31.9 - - + -
201D ILE* 4.2 10.3 - - + -
215D MET 2.9 19.4 + - - +
216D ILE* 3.5 7.0 - - - +
218D LEU* 1.3 76.9 - - + +
220D ASP* 1.3 62.5 + - - +
222D PHE* 3.1 8.9 + - + -
224D ALA* 2.8 37.2 + - + +
225D ASN 4.5 3.1 - - - +
226D VAL* 3.8 28.3 - - + +
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Residues in contact with ASP 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D ILE* 3.1 29.2 + - - +
217D ASN* 3.2 17.9 + - - +
218D LEU 3.1 0.6 - - - -
219D LEU* 1.3 77.3 - - - +
221D GLU* 1.3 65.8 + - - +
223D ASN* 3.1 15.0 + - - +
224D ALA 4.5 7.4 - - - +
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Residues in contact with GLU 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D VAL* 3.6 34.4 - - + +
173D ILE* 4.5 17.4 - - + +
195D THR* 5.8 0.3 - - - +
217D ASN 4.0 10.1 - - - +
218D LEU 3.1 14.1 + - - +
220D ASP* 1.3 81.7 - - - +
222D PHE* 1.3 58.4 + - + +
223D ASN 3.3 0.6 + - - -
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Residues in contact with PHE 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D VAL* 3.8 30.7 - - + -
188D LEU* 4.1 26.9 - - + -
189D ALA 4.2 3.8 - - - -
190D LYS* 3.8 28.7 - - + -
193D MET* 3.8 50.9 - - + -
195D THR* 3.3 26.1 - - + -
196D GLY 3.1 15.8 + - - -
218D LEU* 3.4 24.5 - - + -
219D LEU 3.1 8.3 + - - +
221D GLU* 1.3 77.4 - - + +
223D ASN* 1.3 70.0 + - - +
224D ALA* 4.1 2.5 - - + +
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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