Contacts of the helix formed by residues 177 - 194 (chain D) in PDB entry 2WTK
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 177 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175D MET* 3.1 14.0 - - - +
176D SER* 1.3 75.6 + - - +
178D PHE* 1.3 59.5 + - - +
179D ASP* 3.3 23.6 - - - +
180D ILE* 3.4 16.3 + - + +
181D ALA* 2.9 28.2 + - - +
135E ALA* 6.1 1.1 - - - -
136E THR* 3.7 13.5 - - + +
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Residues in contact with PHE 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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175D MET 4.8 1.3 - - - -
176D SER 3.5 2.2 + - - +
177D THR* 1.3 70.0 - - - +
179D ASP* 1.3 58.8 + - - +
181D ALA* 4.1 11.0 - - + -
182D SER* 2.6 61.9 + - - -
222D ASN* 5.4 2.7 - - - -
224D VAL* 3.5 31.2 - - + -
228D GLN* 5.6 0.2 - - - -
104E LEU* 5.5 1.3 - - + -
112E VAL* 4.9 5.8 - - + -
116E GLN* 3.5 29.6 - - + -
119E LEU* 3.8 11.4 - - + -
136E THR* 3.1 11.3 + - - +
137E PHE* 3.8 22.9 - - - +
138E ILE* 3.6 25.6 - - + +
143E LEU* 3.5 29.2 - - + -
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Residues in contact with ASP 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D LEU* 5.4 8.3 - - + +
177D THR* 3.3 26.3 - - - +
178D PHE* 1.3 73.0 - - - +
180D ILE* 1.3 76.6 + - + +
182D SER* 4.1 3.3 - - - -
183D ASP* 3.3 22.0 + - - +
119E LEU* 4.4 20.4 - - + +
120E HIS* 5.4 2.7 - - - +
123E LYS* 3.4 36.0 - - + +
136E THR* 3.3 25.7 - - + +
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Residues in contact with ILE 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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134D TYR* 3.7 30.1 - - + +
137D PRO* 4.2 24.7 - - + +
140D ALA* 3.8 23.1 - - + -
141D LEU* 5.4 4.7 - - + +
175D MET* 3.5 27.4 - - + -
177D THR* 3.4 16.1 + - + +
178D PHE 3.2 0.2 - - - -
179D ASP* 1.3 94.8 + - - +
181D ALA* 1.3 60.9 + - - +
182D SER 3.3 0.2 - - - -
183D ASP* 3.2 5.4 + - - +
184D ALA* 2.9 29.5 + - - +
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Residues in contact with ALA 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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172D TYR 3.8 11.7 - - - -
173D VAL* 3.9 20.4 - - - +
175D MET* 3.3 21.8 - - + +
177D THR 2.9 19.0 + - - +
178D PHE* 3.9 14.1 - - + +
180D ILE* 1.3 77.6 - - - +
182D SER* 1.3 56.1 + - - +
184D ALA* 3.4 2.3 + - - +
185D PHE* 3.0 29.0 + - - +
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Residues in contact with SER 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D PHE* 2.6 56.4 + - - -
179D ASP* 4.1 4.3 - - - -
181D ALA* 1.3 70.8 - - - +
183D ASP* 1.3 63.5 + - - +
185D PHE* 3.5 5.1 + - - +
186D ALA* 3.1 24.9 + - - +
228D GLN* 5.8 0.7 - - - -
116E GLN* 3.5 31.7 + - - +
119E LEU* 6.1 0.9 - - - -
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Residues in contact with ASP 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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134D TYR* 2.8 24.4 + - + -
140D ALA 5.3 1.8 - - - -
141D LEU* 4.1 12.9 - - + +
144D GLY* 3.3 9.7 - - - -
148D ARG* 2.6 53.7 + - - +
179D ASP 3.3 14.2 + - - +
180D ILE* 3.2 11.2 + - - +
182D SER* 1.3 77.8 - - - +
184D ALA* 1.3 61.6 + - - +
186D ALA* 3.1 5.8 + - - +
187D THR 3.1 18.2 + - - -
120E HIS* 4.1 13.9 + - - -
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Residues in contact with ALA 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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134D TYR* 3.6 26.1 - - + -
169D PHE* 3.6 9.0 - - + -
172D TYR* 3.8 35.4 - - + +
173D VAL* 4.0 2.7 - - + -
180D ILE 2.9 18.8 + - - +
181D ALA 3.7 4.5 - - - +
183D ASP* 1.3 72.0 - - - +
185D PHE* 1.3 58.4 + - - +
187D THR 3.5 0.5 + - - -
188D PHE* 3.0 26.7 + - - +
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Residues in contact with PHE 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D VAL* 3.6 28.7 - - + +
181D ALA 3.0 17.1 + - - +
182D SER* 3.5 6.7 + - - +
183D ASP 3.3 0.2 - - - -
184D ALA* 1.3 76.0 - - - +
186D ALA* 1.3 57.9 + - - +
188D PHE* 3.4 18.1 - + - +
189D LYS* 2.7 52.2 + - + +
217D LEU* 4.8 3.4 - - + -
225D THR* 5.3 4.0 - - + -
228D GLN* 3.8 56.5 - - + +
229D SER* 4.0 18.8 - - - -
232D LEU* 3.9 18.2 - - + -
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Residues in contact with ALA 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D ARG* 4.2 15.6 - - - +
182D SER 3.1 18.0 + - - +
183D ASP* 3.1 7.6 + - - +
185D PHE* 1.3 79.3 - - - +
187D THR* 1.3 61.6 + - - +
189D LYS* 3.6 8.1 - - - +
190D ASP* 3.0 24.1 + - - +
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Residues in contact with THR 187 (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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134D TYR* 3.0 13.6 + - - +
144D GLY 4.3 1.4 + - - -
147D LEU* 4.1 20.4 - - + +
148D ARG* 2.8 41.4 + - - +
151D ILE* 3.6 18.5 - - + +
169D PHE* 3.5 24.0 - - + -
183D ASP 3.1 3.8 + - - -
184D ALA 3.8 4.0 - - - -
186D ALA* 1.3 75.7 - - - +
188D PHE* 1.3 54.6 + - - +
190D ASP* 3.0 6.0 + - - +
191D LEU* 2.9 31.1 + - + +
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Residues in contact with PHE 188 (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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166D PHE* 3.8 27.4 - + - -
169D PHE* 3.6 34.7 - + + -
170D PHE* 3.9 35.4 - + - -
173D VAL* 4.5 5.4 - - + -
184D ALA 3.0 18.0 + - - +
185D PHE* 3.4 29.2 - + - +
187D THR* 1.3 74.1 - - - +
189D LYS* 1.3 67.1 + - - +
190D ASP 3.2 0.7 + - - -
191D LEU* 3.4 6.0 + - - +
192D LEU* 3.2 47.4 + - + +
210D PHE* 4.3 1.6 - + - -
214D TYR* 4.0 18.8 - + - -
217D LEU* 4.6 5.4 - - + -
232D LEU* 4.2 5.6 - - + -
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Residues in contact with LYS 189 (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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185D PHE* 2.7 37.5 + - + +
186D ALA* 3.6 8.5 - - - +
188D PHE* 1.3 73.6 - - - +
190D ASP* 1.3 57.0 + - - +
192D LEU* 3.2 9.0 + - - -
193D THR* 2.6 37.9 + - + +
231D LYS* 6.4 0.2 - - - +
232D LEU* 4.0 30.3 - - + -
235D GLU* 4.7 14.0 + - - -
113E THR* 5.8 1.8 + - - -
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Residues in contact with ASP 190 (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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148D ARG* 5.1 9.3 - - + +
151D ILE* 3.0 29.2 - - + +
186D ALA 3.0 15.3 + - - +
187D THR* 3.0 9.8 + - - +
189D LYS* 1.3 74.5 - - - +
191D LEU* 1.3 67.0 + - - +
193D THR* 2.9 17.7 + - - -
194D ARG* 2.8 62.3 + - - +
195D HIS* 5.7 0.2 - - - -
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Residues in contact with LEU 191 (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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151D ILE* 3.6 36.1 - - + -
157D ALA* 3.9 29.4 - - + +
160D ILE* 3.7 16.8 - - + -
161D LEU* 3.5 30.2 - - + +
166D PHE* 3.7 11.9 - - + -
169D PHE* 3.5 37.7 - - + -
187D THR* 2.9 18.5 + - + +
188D PHE* 3.8 4.0 - - - +
190D ASP* 1.3 77.3 + - - +
192D LEU* 1.3 60.4 + - - +
193D THR 3.5 0.5 + - - -
194D ARG 4.6 1.0 + - - -
195D HIS* 5.1 6.8 + - - +
198D LEU* 5.7 0.5 - - - +
199D SER* 4.1 6.2 + - - -
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Residues in contact with LEU 192 (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 LEU* 4.6 3.4 - - + -
166D PHE* 4.3 10.5 - - + -
188D PHE* 3.2 51.1 + - + +
189D LYS 3.2 4.7 + - - +
190D ASP 3.0 1.4 - - - -
191D LEU* 1.3 76.8 - - - +
193D THR* 1.3 62.0 + - + +
199D SER* 3.2 22.9 - - - -
202D PHE* 3.9 21.5 - - + -
203D LEU* 4.6 8.8 - - + +
210D PHE* 3.7 31.4 - - + -
214D TYR* 4.9 0.2 - - + -
232D LEU* 4.1 12.8 - - + -
236D LEU* 3.9 22.9 - - + +
242D ASN* 5.5 1.4 + - - -
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Residues in contact with THR 193 (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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189D LYS* 2.6 32.8 + - + +
190D ASP* 3.4 4.5 + - - -
191D LEU 3.3 0.6 + - - -
192D LEU* 1.3 83.1 - - + +
194D ARG* 1.3 67.6 + - - +
195D HIS 3.7 0.9 - - - -
196D LYS* 3.2 36.3 + - - +
199D SER* 4.4 2.5 - - - -
232D LEU* 4.1 23.6 - - + -
235D GLU* 5.9 4.0 - - + +
236D LEU* 4.1 10.3 - - + -
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Residues in contact with ARG 194 (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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151D ILE 3.9 7.6 - - - -
152D ARG* 3.5 36.1 + - - +
190D ASP* 2.8 46.8 + - - +
193D THR* 1.3 81.0 + - - +
195D HIS* 1.3 91.9 + - + +
196D LYS* 3.2 15.3 + - - +
342D SO4 3.1 42.4 + - - -
108F LYS* 5.4 0.8 - - - +
165F GLU* 4.5 6.8 - - - +
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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