Contacts of the helix formed by residues 167 - 184 (chain D) in PDB entry 2PK2
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 SER 167 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165D ARG 3.6 1.3 + - - -
166D ALA* 1.3 80.3 - - - +
168D LYS* 1.3 60.4 + - - +
169D ASP* 4.3 4.7 + - - +
170D LEU* 3.4 23.0 + - - +
171D ALA* 3.2 26.2 + - - +
210D TRP* 4.0 19.1 - - - -
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Residues in contact with LYS 168 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167D SER* 1.3 71.5 - - - +
169D ASP* 1.3 84.4 + - + +
170D LEU 3.2 1.1 - - - -
171D ALA* 3.1 6.3 + - - +
172D GLN* 3.0 52.3 + - - +
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Residues in contact with ASP 169 (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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167D SER* 4.3 4.6 + - - +
168D LYS* 1.3 90.0 - - + +
170D LEU* 1.3 59.8 + - - +
172D GLN* 3.4 15.9 - - - +
173D THR* 3.0 15.5 + - - -
258D TRP* 4.6 1.7 - - - -
262D GLU* 3.6 33.7 - - - +
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Residues in contact with LEU 170 (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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161D THR* 5.6 2.2 - - + -
166D ALA* 4.4 11.9 - - + -
167D SER* 3.4 19.3 + - - +
168D LYS 3.2 0.4 - - - -
169D ASP* 1.3 76.6 - - - +
171D ALA* 1.3 69.5 + - - +
173D THR* 2.9 18.6 + - - +
174D SER* 2.9 14.3 + - - +
204D ALA* 4.3 14.4 - - + -
205D CYS* 5.0 2.0 - - - +
208D SER* 3.2 31.6 - - - +
210D TRP* 3.7 47.3 - - + +
212D ILE* 4.1 17.0 - - + -
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Residues in contact with ALA 171 (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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157D VAL* 5.1 0.7 - - + +
161D THR* 4.3 21.3 - - + +
166D ALA* 5.4 0.2 - - - +
167D SER 3.2 19.5 + - - +
168D LYS* 3.1 8.9 + - - +
170D LEU* 1.3 78.2 - - - +
172D GLN* 1.3 55.7 - - - +
174D SER* 2.6 33.1 + - - -
175D TYR* 2.9 14.0 + - - +
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Residues in contact with GLN 172 (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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168D LYS* 3.0 56.2 + - - +
169D ASP* 3.4 17.5 - - - +
170D LEU 3.1 0.2 - - - -
171D ALA* 1.3 77.1 - - - +
173D THR* 1.3 56.1 + - - +
175D TYR* 4.0 4.7 - - - +
176D PHE* 2.8 40.5 + - + +
258D TRP* 3.6 23.8 - - + +
262D GLU* 4.3 6.6 - - - +
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Residues in contact with THR 173 (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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169D ASP 3.0 16.3 + - - -
170D LEU* 3.1 15.1 + - - +
172D GLN* 1.3 76.6 - - - +
174D SER* 1.3 59.6 + - - +
176D PHE* 4.7 1.8 - - - -
177D MET* 3.1 24.9 + - + +
200D CYS 3.8 1.7 - - - +
204D ALA* 3.3 30.1 - - + +
207D TRP* 4.2 14.4 - - + -
208D SER* 4.9 2.7 - - - +
258D TRP* 3.8 22.3 - - + -
259D ARG* 4.1 22.7 + - - +
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Residues in contact with SER 174 (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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157D VAL* 3.9 14.9 - - - +
161D THR* 3.7 9.3 - - - +
170D LEU* 2.9 15.5 + - - +
171D ALA* 2.6 27.4 + - - -
173D THR* 1.3 69.9 - - - +
175D TYR* 1.3 66.0 + - - +
177D MET* 3.2 11.8 + - - +
178D ALA 3.4 7.1 + - - -
200D CYS* 3.7 17.2 - - - +
201D ILE* 3.5 27.0 - - - +
204D ALA* 4.5 2.1 - - - +
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Residues in contact with TYR 175 (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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56D GLN* 4.9 18.5 - - + +
57D LEU* 4.9 9.5 - - - +
60D ASN* 4.9 4.2 + - - -
154D HIS* 3.8 38.6 - + + +
157D VAL* 3.8 20.1 - - + +
158D VAL* 4.7 13.2 - - + -
171D ALA 2.9 15.4 + - - +
172D GLN* 4.0 4.9 - - - +
174D SER* 1.3 72.7 - - - +
176D PHE* 1.3 60.6 + - - +
178D ALA* 2.8 29.3 + - - +
179D THR* 3.6 8.5 + - - -
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Residues in contact with PHE 176 (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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172D GLN* 2.8 25.0 + - + +
173D THR* 4.6 3.8 - - - +
175D TYR* 1.3 77.2 - - - +
177D MET* 1.3 61.3 + - - +
179D THR* 3.4 18.0 + - + -
180D ASN* 3.2 23.4 + - - -
251D ARG* 4.6 18.8 - - - -
254D ARG 5.3 1.6 - - - -
255D ILE* 4.3 35.4 - - + -
258D TRP* 4.1 46.2 - + + -
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Residues in contact with MET 177 (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 THR 3.1 20.0 + - - +
174D SER 3.2 4.9 + - - +
175D TYR 3.1 0.8 - - - -
176D PHE* 1.3 76.8 - - - +
178D ALA* 1.3 65.9 + - - +
180D ASN* 3.2 23.2 + - + -
181D SER 3.4 8.1 + - - -
200D CYS* 3.6 18.7 - - + +
203D LEU* 3.3 39.5 - - + -
204D ALA 5.3 1.6 - - - +
207D TRP* 4.6 19.3 - - + -
241D PHE* 3.3 47.5 - - + -
245D LEU* 4.1 14.6 - - + -
255D ILE* 4.6 6.1 - - + -
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Residues in contact with ALA 178 (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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153D PRO* 3.7 28.2 - - + +
154D HIS* 3.9 21.7 + - + +
157D VAL* 5.1 1.3 - - + -
174D SER 3.4 4.8 + - - +
175D TYR* 2.8 16.6 + - - +
177D MET* 1.3 78.1 - - - +
179D THR* 1.3 57.3 + - - +
180D ASN 3.0 0.2 - - - -
181D SER* 2.9 26.6 + - - -
182D LEU* 3.5 6.6 + - - +
200D CYS* 3.4 17.6 - - + +
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Residues in contact with THR 179 (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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46D GLN* 5.2 1.6 - - + -
56D GLN* 4.7 18.3 - - - +
60D ASN* 4.4 16.3 + - - +
154D HIS* 4.5 8.5 + - - -
175D TYR* 3.6 10.8 + - - -
176D PHE* 3.4 16.6 + - + -
177D MET 3.2 0.2 - - - -
178D ALA* 1.3 77.3 - - - +
180D ASN* 1.3 61.2 + - - +
182D LEU* 4.3 3.1 - - - -
183D HIS* 3.2 49.8 + - + +
251D ARG* 5.9 4.5 - - - +
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Residues in contact with ASN 180 (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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176D PHE* 3.2 30.3 + - - -
177D MET* 3.2 17.7 + - - +
178D ALA 3.0 0.6 - - - -
179D THR* 1.3 81.4 - - - +
181D SER* 1.3 64.7 + - - +
182D LEU 3.0 2.9 + - - -
183D HIS* 4.1 3.0 + - - +
184D LEU* 3.1 37.9 + - + +
185D THR* 3.6 2.3 + - - +
241D PHE* 4.1 15.9 - - + -
245D LEU* 4.5 0.7 - - + -
251D ARG* 3.5 22.0 + - - +
255D ILE* 3.0 40.8 - - + +
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Residues in contact with SER 181 (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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153D PRO* 3.8 7.3 - - - +
177D MET 3.4 4.7 + - - -
178D ALA 2.9 12.5 + - - -
180D ASN* 1.3 78.2 - - - +
182D LEU* 1.3 60.5 + - - +
185D THR* 2.7 30.4 + - - +
187D PHE* 4.1 11.9 + - - +
188D SER 5.1 0.9 + - - -
196D VAL* 3.2 32.6 - - - +
199D VAL* 6.3 0.2 - - - -
200D CYS* 3.9 15.0 - - - -
241D PHE* 3.7 13.8 - - - -
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Residues in contact with LEU 182 (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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60D ASN* 4.0 15.7 - - + +
63D ILE* 4.0 16.6 - - + -
64D VAL* 4.0 29.4 - - + +
67D HIS* 2.7 44.8 + - + -
152D HIS* 4.1 7.6 - - + +
153D PRO* 4.0 30.1 - - + -
154D HIS* 4.8 4.9 - - + -
178D ALA 3.5 6.2 + - - +
179D THR* 4.5 2.9 - - - +
180D ASN 3.0 0.4 - - - -
181D SER* 1.3 80.0 + - - +
183D HIS* 1.3 67.3 + - + +
184D LEU 3.4 0.2 - - - -
185D THR 2.8 6.8 - - - +
188D SER* 4.3 14.4 - - - +
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Residues in contact with HIS 183 (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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39D GLN* 3.1 23.4 + - - -
42D ALA* 3.3 24.4 + - + +
46D GLN* 3.7 36.6 + - + +
59D ILE* 4.7 0.2 - - - +
60D ASN* 3.9 7.9 + - - -
63D ILE* 3.4 32.0 - - + +
67D HIS* 3.7 6.6 - - - -
179D THR* 3.2 42.7 + - + +
180D ASN* 3.7 2.8 + - - +
182D LEU* 1.3 87.0 - - + +
184D LEU* 1.3 74.2 + - + +
251D ARG* 5.9 5.3 + - - +
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Residues in contact with LEU 184 (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* 4.8 4.7 - - - +
38D ARG* 5.3 0.9 - - - +
39D GLN* 3.1 47.1 + - + +
67D HIS* 4.6 1.4 + - - -
180D ASN* 3.1 24.1 + - + +
183D HIS* 1.3 89.2 - - + +
185D THR* 1.3 68.5 + - + +
186D THR* 4.8 2.4 - - - +
241D PHE* 5.7 0.2 - - + -
244D ILE* 4.2 7.0 - - + +
245D LEU* 3.9 23.6 - - + -
248D THR* 3.5 39.5 - - + +
251D ARG* 4.0 20.9 - - + -
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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