Contacts of the helix formed by residues 215 - 229 (chain D) 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 215 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174D ASP* 2.9 33.3 + - - +
210D PRO* 3.3 27.0 + - - +
211D LYS* 3.6 22.3 - - + +
213D GLY 3.4 6.7 + - - -
214D TYR* 1.3 76.9 - - - +
216D VAL* 1.3 61.4 + - - +
217D LEU 3.4 2.0 - - - -
218D ASP* 3.3 12.8 + - + +
219D LYS* 2.8 32.4 + - + +
222D ARG* 5.1 0.2 + - - -
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Residues in contact with VAL 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D TYR* 3.5 39.0 - - + -
172D PRO* 3.6 16.8 + - + +
173D ARG* 3.2 37.0 - - - +
174D ASP* 3.4 17.6 + - - +
213D GLY 4.1 0.2 - - - +
214D TYR 3.7 0.2 - - - -
215D ASN* 1.3 75.7 - - - +
217D LEU* 1.3 65.6 + - + +
219D LYS* 3.1 8.5 + - - +
220D TYR* 3.0 38.1 + - + -
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Residues in contact with LEU 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C ILE* 4.3 16.4 - - + -
161C PRO* 5.0 3.6 - - + -
27D PHE* 3.8 29.5 - - + -
93D CYS* 3.9 24.0 - - + +
96D MET* 3.6 16.6 - - + +
97D THR* 3.5 44.4 - - - +
100D TYR* 5.0 4.9 - - + -
172D PRO* 4.2 19.6 + - + +
214D TYR 5.5 0.2 - - - -
215D ASN* 3.4 1.0 - - - +
216D VAL* 1.3 77.7 - - - +
218D ASP* 1.3 62.6 + - - +
220D TYR* 3.5 4.7 + - + +
221D TYR* 3.1 21.7 + - - +
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Residues in contact with ASP 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ALA 4.7 9.8 - - - +
26D ASP* 4.9 4.2 - - - +
27D PHE* 3.5 23.1 - - - -
211D LYS* 2.7 30.9 + - - -
215D ASN* 3.3 13.5 + - + +
216D VAL 3.3 0.4 - - - -
217D LEU* 1.3 73.4 - - - +
219D LYS* 1.3 66.9 + - - +
221D TYR* 3.0 9.6 + - - +
222D ARG* 2.9 37.3 + - + +
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Residues in contact with LYS 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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215D ASN* 2.8 21.7 + - + +
216D VAL* 3.4 8.3 - - - +
218D ASP* 1.3 73.1 - - - +
220D TYR* 1.3 66.5 + - + +
222D ARG* 3.1 27.7 + - - +
223D ARG* 2.9 31.6 + - + +
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Residues in contact with TYR 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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96D MET* 3.6 17.5 - - + +
99D LEU* 4.0 20.2 - - + -
100D TYR* 3.5 48.9 - + + -
103D ASP* 2.7 41.6 + - - +
177D ILE* 4.4 4.3 - - - +
216D VAL* 3.0 35.7 + - + +
217D LEU* 3.8 3.6 - - - +
219D LYS* 1.3 86.3 - - + +
221D TYR* 1.3 56.7 + - - +
223D ARG* 3.9 6.8 - - + +
224D ILE* 3.1 35.9 + - + +
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Residues in contact with TYR 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU* 3.3 24.6 - - + +
24D PRO 3.0 27.7 + - - -
25D ALA 3.8 15.9 - - - -
27D PHE* 3.7 35.9 - + + -
30D CYS* 4.2 10.4 - - - +
35D LEU* 3.9 21.3 - - + -
38D LEU* 4.7 2.5 - - + -
96D MET* 3.4 12.7 - - + +
217D LEU 3.1 13.6 + - - +
218D ASP* 3.0 13.8 + - - +
220D TYR* 1.3 74.5 - - - +
222D ARG* 1.3 74.4 + - + +
223D ARG 3.2 0.3 + - - -
224D ILE* 3.2 8.3 - - + +
225D VAL* 3.2 42.1 + - + +
245D LEU* 4.0 11.2 - - + -
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Residues in contact with ARG 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ALA 5.8 2.0 - - - +
218D ASP* 2.9 24.0 + - + +
219D LYS* 3.1 46.4 - - - +
221D TYR* 1.3 76.2 - - + +
223D ARG* 1.3 62.2 + - - +
225D VAL* 3.5 2.8 + - - +
226D GLN* 3.0 24.2 + - - +
245D LEU* 4.0 30.4 - - + +
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Residues in contact with ARG 223 (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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42D MET* 5.4 1.1 - - + -
219D LYS* 2.9 18.4 + - + +
220D TYR* 3.9 8.5 - - + +
222D ARG* 1.3 77.7 - - - +
224D ILE* 1.3 59.1 + - + +
226D GLN* 3.1 22.1 + - - +
227D LEU* 2.8 64.7 + - + +
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Residues in contact with ILE 224 (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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35D LEU* 5.0 1.6 - - + +
38D LEU* 3.5 32.0 - - + +
39D ILE* 3.9 23.3 - - + +
42D MET* 3.5 30.5 - - + -
96D MET* 4.2 15.5 - - + -
99D LEU* 3.3 22.7 - - + -
220D TYR* 3.1 14.6 + - + +
221D TYR* 3.2 15.0 - - + +
223D ARG* 1.3 75.1 - - + +
225D VAL* 1.3 60.7 + - + +
228D VAL* 2.7 40.9 + - + +
229D GLY 3.4 1.4 + - - -
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Residues in contact with VAL 225 (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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23D LEU* 3.8 33.9 - - + -
38D LEU* 3.9 10.1 - - + -
221D TYR* 3.2 34.1 + - + +
222D ARG* 3.7 7.4 - - - +
224D ILE* 1.3 75.3 - - - +
226D GLN* 1.3 58.7 + - - +
229D GLY* 2.9 29.3 + - - +
243D TYR* 4.3 12.1 - - + +
244D VAL* 4.5 0.2 - - - -
245D LEU* 3.9 34.3 - - + +
248D ASN* 5.9 2.0 - - - +
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Residues in contact with GLN 226 (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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222D ARG 3.0 14.4 + - - +
223D ARG* 3.1 41.6 + - - +
225D VAL* 1.3 78.8 - - - +
227D LEU* 1.3 72.6 + - + +
229D GLY 4.5 0.7 + - - -
230D SER* 5.6 1.7 + - - -
248D ASN* 5.0 16.4 - - - +
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Residues in contact with LEU 227 (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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42D MET* 3.5 33.2 - - + -
46D LEU* 6.2 1.1 - - + -
223D ARG* 2.8 59.7 + - + +
226D GLN* 1.3 88.3 - - - +
228D VAL* 1.3 65.4 + - + +
229D GLY 3.6 0.6 + - - -
230D SER* 4.7 7.3 + - - -
232D ASN 5.2 5.2 - - - +
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Residues in contact with VAL 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D LEU* 3.6 14.8 - - - +
41D ARG* 2.9 59.5 + - + +
42D MET* 3.6 30.3 - - + +
45D SER* 4.6 9.4 - - - +
224D ILE 2.7 23.2 + - - +
227D LEU* 1.3 79.9 - - + +
229D GLY* 1.3 55.4 + - - +
230D SER 3.3 7.5 - - - +
232D ASN 5.9 0.2 - - - -
233D ALA* 3.6 24.2 - - + -
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Residues in contact with GLY 229 (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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38D LEU* 3.8 14.6 - - - -
41D ARG* 3.1 11.4 + - - -
224D ILE 3.4 1.2 + - - -
225D VAL 2.9 24.4 + - - -
226D GLN 4.5 0.4 + - - -
227D LEU 3.6 1.0 - - - -
228D VAL* 1.3 77.7 - - - +
230D SER* 1.3 57.5 + - - +
242D ASP* 3.7 1.4 - - - -
243D TYR* 2.9 39.5 + - - +
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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