Contacts of the helix formed by residues 213 - 237 (chain B) in PDB entry 1PR1
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 213 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B THR* 1.3 81.9 - - - +
214B ALA* 1.3 65.4 + - - +
215B ALA* 4.2 8.4 - - - +
216B GLU* 2.8 43.5 + - - +
217B ARG* 3.0 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B THR 3.8 0.2 + - - -
213B THR* 1.3 69.3 - - - +
215B ALA* 1.3 53.9 + - - +
217B ARG* 3.5 28.9 - - - +
218B GLN* 2.7 58.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B THR* 3.2 7.5 - - - +
214B ALA* 1.3 79.1 - - - +
216B GLU* 1.3 56.2 + - + +
218B GLN* 3.3 10.6 + - - +
219B THR* 2.7 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ARG* 3.2 39.7 + - - +
212B THR* 4.7 5.4 - - + +
213B THR* 2.8 37.1 + - - +
215B ALA* 1.3 77.3 - - + +
217B ARG* 1.3 62.2 + - - +
219B THR* 3.2 7.5 + - - -
220B THR* 3.1 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ARG* 3.8 17.9 - - + +
201B THR* 5.3 4.9 - - + +
203B SER* 5.5 18.3 + - - -
211B GLN* 3.4 12.5 + - - +
212B THR* 2.9 33.9 + - + -
213B THR 3.0 12.4 + - - +
214B ALA* 3.4 36.1 - - - +
216B GLU* 1.3 77.3 - - - +
218B GLN* 1.3 63.8 + - + +
220B THR* 3.2 5.4 + - - -
221B PHE* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ARG* 6.2 2.9 - - - +
27B TYR* 5.6 6.7 + - - +
214B ALA* 2.7 48.1 + - + +
215B ALA* 3.7 7.4 - - - +
217B ARG* 1.3 74.6 - - + +
219B THR* 1.3 62.4 + - - +
221B PHE* 3.5 7.8 + - - +
222B ASN* 3.1 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ARG* 5.2 2.9 - - - +
215B ALA* 2.7 24.6 + - - +
216B GLU* 3.3 12.5 - - - -
217B ARG 3.1 0.2 - - - -
218B GLN* 1.3 77.4 - - - +
220B THR* 1.3 57.6 + - - +
222B ASN* 3.2 9.9 + - - +
223B ASP* 3.0 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ARG* 3.1 51.7 + - - +
103B VAL* 4.0 14.3 - - + +
146B ILE* 6.3 0.4 - - + -
201B THR* 3.6 18.4 - - + -
216B GLU 3.1 14.1 + - - -
217B ARG 3.2 7.4 + - - -
219B THR* 1.3 73.8 - - - +
221B PHE* 1.3 61.0 + - - +
223B ASP* 3.2 13.4 + - + +
224B MET* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ARG* 3.7 38.6 - - + -
27B TYR* 3.8 26.9 - + - -
28B ILE* 4.9 4.5 - - + -
88B VAL 4.8 7.0 - - - -
89B GLY* 5.3 5.4 - - - -
90B SER* 6.4 1.6 - - - -
201B THR* 4.2 15.2 - - + +
217B ARG 3.1 14.6 + - - +
218B GLN* 3.7 8.3 - - - +
219B THR 3.3 0.2 - - - -
220B THR* 1.3 77.3 - - - +
222B ASN* 1.3 72.3 + - - +
224B MET* 3.4 26.9 + - + +
225B ILE* 3.2 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B TYR* 2.7 38.2 + - - -
31B THR* 5.0 5.1 - - - +
32B PHE* 3.8 20.5 - - + -
218B GLN* 3.1 18.5 + - - +
219B THR* 3.5 10.6 - - - +
221B PHE* 1.3 79.7 - - - +
223B ASP* 1.3 59.7 + - - +
225B ILE* 3.1 5.3 + - - +
226B LYS* 2.9 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B VAL* 5.5 0.4 - - + -
144B LEU* 4.3 4.4 - - + +
146B ILE* 3.8 36.6 - - + +
219B THR* 3.0 30.2 + - - +
220B THR* 3.2 17.0 + - + +
222B ASN* 1.3 76.9 - - - +
224B MET* 1.3 56.8 + - - +
226B LYS* 3.1 20.3 + - - +
227B ILE* 2.8 38.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B VAL* 3.9 22.9 - - + -
89B GLY 3.4 24.9 - - - +
103B VAL* 4.8 5.8 - - + +
199B ILE* 3.5 37.2 - - + +
200B CYS 4.0 0.2 - - - -
201B THR* 3.5 26.5 - - - +
220B THR 3.0 7.1 + - - +
221B PHE* 3.4 46.4 - - + +
222B ASN 3.2 0.2 - - - -
223B ASP* 1.3 76.7 - - - +
225B ILE* 1.3 59.3 + - + +
227B ILE* 3.3 15.5 + - - +
228B ALA* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 4.3 4.7 - - + -
28B ILE* 3.6 37.0 - - + -
32B PHE* 3.7 33.7 - - + -
88B VAL* 3.7 27.4 - - + -
221B PHE* 3.2 30.0 + - + +
222B ASN 3.1 7.3 + - - +
224B MET* 1.3 81.7 - - + +
226B LYS* 1.3 59.5 + - - +
228B ALA* 3.1 5.2 + - - +
229B LEU* 2.8 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PHE* 3.4 23.6 - - + -
52B TYR* 5.1 10.5 - - - +
144B LEU* 3.8 31.8 - - + +
222B ASN* 2.9 22.2 + - + +
223B ASP* 3.5 20.6 + - - +
225B ILE* 1.3 71.8 - - - +
227B ILE* 1.3 58.3 + - - +
229B LEU* 4.4 7.6 - - - +
230B GLU* 2.7 45.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B VAL* 4.3 14.6 - - + -
105B ILE* 5.3 2.5 - - + -
137B ALA* 3.5 27.6 - - + +
140B ALA* 3.6 5.1 - - - +
141B ALA* 3.8 24.0 - - + +
144B LEU* 3.5 20.6 - - + -
146B ILE* 4.1 20.9 - - + -
199B ILE* 4.2 18.2 - - + -
223B ASP 2.8 24.6 + - - +
224B MET* 3.3 12.6 - - - +
226B LYS* 1.3 76.3 - - - +
228B ALA* 1.3 53.4 + - - +
231B SER* 2.8 37.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 3.8 20.2 - - + -
86B ILE* 3.9 14.3 - - + +
88B VAL* 3.9 16.8 - - + -
199B ILE* 4.2 8.7 - - + -
224B MET 3.0 13.5 + - - +
225B ILE 3.1 8.5 + - - +
227B ILE* 1.3 76.8 - - - +
229B LEU* 1.3 63.2 + - - +
231B SER* 2.8 23.3 + - - -
232B VAL* 3.0 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 3.8 22.7 - - + -
28B ILE* 5.4 2.5 - - + -
32B PHE* 3.4 41.3 - - + -
33B LEU* 4.4 6.5 - - + -
52B TYR* 3.6 41.8 - - + -
57B ILE* 4.1 25.7 - - + +
225B ILE* 2.8 29.1 + - + +
226B LYS* 3.8 3.6 - - - +
228B ALA* 1.3 74.5 - - - +
230B GLU* 1.3 62.9 + - - +
232B VAL* 3.4 19.7 + - + +
233B LEU* 3.6 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B TYR* 2.5 33.3 + - - +
53B LYS* 2.8 22.2 + - - -
140B ALA* 4.0 14.8 - - + +
144B LEU* 5.2 11.9 - - + -
226B LYS* 2.7 31.2 + - + +
227B ILE* 3.9 2.5 - - - +
229B LEU* 1.3 70.7 - - - +
231B SER* 1.3 63.3 + - - +
233B LEU* 3.2 21.3 + - - +
234B LEU* 3.2 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ILE* 4.0 11.1 - - - +
133B MET 4.9 1.8 + - - -
136B ASN* 3.2 49.4 + - - +
137B ALA* 3.6 12.9 - - - +
140B ALA* 3.8 1.8 - - - +
197B LEU* 5.3 1.4 - - - +
199B ILE* 5.4 0.2 - - - +
227B ILE 2.8 19.2 + - - -
228B ALA* 2.8 19.6 + - - -
230B GLU* 1.3 72.9 - - - +
232B VAL* 1.3 62.0 + - - +
234B LEU* 3.3 2.7 + - - -
235B GLY 3.1 15.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 4.3 18.2 - - + -
17B LEU* 4.8 3.1 - - + -
55B ARG* 4.2 19.1 - - + +
57B ILE* 3.8 26.2 - - + -
84B LYS* 5.1 10.5 + - + +
86B ILE* 3.8 20.0 - - + -
136B ASN* 5.5 0.2 - - - +
228B ALA 3.0 21.1 - - - +
229B LEU* 3.4 11.9 - - - +
231B SER* 1.3 71.7 - - - +
233B LEU* 1.3 71.4 + - + +
235B GLY* 3.1 3.5 + - - +
236B ASP* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B TYR* 3.9 23.3 - - + +
53B LYS* 4.0 19.1 - - + +
55B ARG* 3.7 36.6 - - + -
229B LEU 3.6 11.9 + - - +
230B GLU* 3.2 27.9 + - - +
232B VAL* 1.3 84.5 - - + +
234B LEU* 1.3 62.0 + - + +
236B ASP* 3.3 22.4 + - - +
237B LYS* 3.5 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ASN* 3.6 36.1 - - - +
139B ASP* 3.7 23.6 - - + +
140B ALA* 3.9 10.3 - - + +
230B GLU* 3.2 13.3 + - + +
231B SER 3.5 8.5 - - - +
232B VAL 3.2 0.4 - - - -
233B LEU* 1.3 81.4 - - + +
235B GLY* 1.3 59.9 + - - +
237B LYS* 3.3 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LYS* 4.2 13.1 + - - -
136B ASN* 3.4 21.7 - - - +
231B SER 3.1 7.4 + - - -
232B VAL 3.1 7.6 + - - -
234B LEU* 1.3 74.9 - - - +
236B ASP* 1.3 63.9 + - - +
237B LYS 3.0 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 5.7 0.2 - - - +
55B ARG* 2.5 52.1 + - - +
84B LYS* 5.6 1.9 + - - -
232B VAL* 2.9 17.7 + - - +
233B LEU* 3.3 16.4 + - - +
235B GLY* 1.3 76.5 - - - +
237B LYS* 1.3 59.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B LEU 3.5 7.7 + - - +
234B LEU* 3.3 18.3 + - - +
235B GLY 3.0 8.8 - - - -
236B ASP* 1.3 82.8 - - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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