Contacts of the helix formed by residues 222 - 239 (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 ASN 222 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174D GLU* 4.2 4.7 - - - +
175D MET 5.5 4.8 + - - -
176D SER* 6.3 1.0 - - - +
178D PHE* 5.4 3.0 - - - -
220D SER* 2.9 18.2 + - - +
221D GLU* 1.3 76.2 - - - +
223D TYR* 1.3 63.8 + - - +
224D VAL* 2.7 35.8 + - - +
225D THR* 2.8 21.0 + - - +
226D LYS* 2.9 20.3 + - - +
138E ILE* 3.7 29.6 + - - +
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Residues in contact with TYR 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D GLU 3.4 5.9 + - - -
222D ASN* 1.3 73.1 + - - +
224D VAL* 1.3 71.6 + - + +
226D LYS* 3.4 5.1 + - - +
227D ARG* 2.9 73.7 + - - +
267D SER* 3.2 27.9 + - - -
269D ASN* 3.6 2.4 + - - -
270D ILE* 4.1 17.2 - - + +
104E LEU* 4.1 16.4 - - + -
105E GLU* 2.9 29.2 + - - -
138E ILE* 4.8 2.1 - - + +
140E ASP 3.2 24.4 + - - +
141E ASN* 4.2 19.5 - - + -
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Residues in contact with VAL 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D PHE* 3.5 31.0 - - + -
222D ASN* 2.7 13.0 + - - +
223D TYR* 1.3 80.1 - - + +
225D THR* 1.3 62.2 + - - +
227D ARG* 3.8 3.7 - - - +
228D GLN* 3.0 53.7 + - + +
104E LEU* 3.5 33.0 - - + -
112E VAL* 5.1 6.7 - - + -
116E GLN* 4.7 0.2 - - - +
138E ILE* 3.8 18.8 - - + +
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Residues in contact with THR 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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173D VAL* 3.5 19.7 + - + +
174D GLU* 3.1 27.5 + - - +
185D PHE* 6.1 3.4 - - + -
217D LEU* 3.9 16.6 - - + +
220D SER* 3.3 26.0 - - - -
222D ASN* 2.8 21.2 + - - +
224D VAL* 1.3 72.9 - - - +
226D LYS* 1.3 61.8 + - - +
228D GLN* 3.8 4.3 - - - +
229D SER* 2.9 36.3 + - - +
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Residues in contact with LYS 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D LEU 4.0 8.7 - - - +
218D LEU* 3.4 31.6 + - - +
219D HIS* 4.1 9.9 + - - +
220D SER* 3.3 25.3 + - - +
222D ASN 2.9 18.7 + - - +
223D TYR* 3.8 4.7 - - - +
225D THR* 1.3 73.7 - - - +
227D ARG* 1.3 65.9 + - - +
228D GLN 3.1 0.2 + - - -
229D SER* 3.9 1.6 - - - -
230D LEU* 3.1 28.4 + - + +
262D LEU* 3.9 20.8 - - + +
265D ASP* 4.0 14.3 + - - +
270D ILE* 3.9 23.8 - - + -
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Residues in contact with ARG 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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223D TYR* 2.9 52.0 + - + +
224D VAL* 3.8 4.5 - - - +
226D LYS* 1.3 76.9 - - - +
228D GLN* 1.3 61.5 + - + +
230D LEU* 3.4 4.4 + - - +
231D LYS* 3.0 27.0 + - + +
269D ASN* 3.3 24.1 - - + +
270D ILE* 4.1 18.3 - - + +
273D GLU* 4.0 14.7 + - + +
104E LEU* 2.9 27.7 + - - +
107E CYS 2.9 22.0 + - - -
108E SER* 3.6 2.6 + - - +
109E ASN* 3.5 35.6 + - - +
112E VAL* 4.2 9.4 - - - +
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Residues in contact with GLN 228 (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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182D SER* 5.8 0.9 - - - -
185D PHE* 3.8 41.6 - - + +
224D VAL* 3.0 40.7 + - + +
225D THR* 4.0 3.1 - - - +
227D ARG* 1.3 77.8 - - + +
229D SER* 1.3 59.2 + - - +
230D LEU 3.1 1.3 - - - -
231D LYS* 3.5 6.2 + - - +
232D LEU* 2.9 30.8 + - - +
112E VAL* 4.8 7.6 - - + +
113E THR* 5.5 2.8 + - - -
116E GLN* 3.6 27.1 + - - +
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Residues in contact with SER 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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185D PHE* 4.0 9.6 - - - -
214D TYR* 2.5 38.1 + - - -
217D LEU* 3.3 38.0 - - - +
218D LEU* 3.8 16.2 - - - -
225D THR* 2.9 20.7 + - - +
226D LYS 3.9 0.9 - - - -
228D GLN* 1.3 76.3 - - - +
230D LEU* 1.3 56.3 + - - +
233D LEU* 3.0 12.0 + - - +
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Residues in contact with LEU 230 (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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218D LEU* 3.7 18.4 - - + +
226D LYS* 3.1 20.0 + - + +
227D ARG 3.6 4.0 - - - +
229D SER* 1.3 75.2 - - - +
231D LYS* 1.3 66.2 + - - +
233D LEU* 3.1 13.8 + - + +
234D GLY* 3.2 11.1 + - - -
259D MET* 3.9 29.6 - - + -
262D LEU* 3.9 18.8 - - + -
270D ILE* 3.7 42.2 - - + +
273D GLU* 3.7 16.3 - - + +
274D ALA* 4.0 6.7 - - + +
277D VAL* 4.2 11.7 - - + +
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Residues in contact with LYS 231 (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* 6.4 0.2 - - - +
227D ARG* 3.0 17.5 + - + +
228D GLN* 3.5 7.2 + - - +
230D LEU* 1.3 76.0 - - - +
232D LEU* 1.3 64.5 + - - +
234D GLY* 3.3 1.7 + - - -
235D GLU* 3.1 48.8 + - - +
273D GLU* 3.9 28.0 + - - +
109E ASN* 3.8 41.6 - - + +
106F ARG* 5.3 9.8 - - - +
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Residues in contact with LEU 232 (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* 3.9 20.9 - - + -
188D PHE* 4.2 6.7 - - + -
189D LYS* 4.0 31.4 - - + -
192D LEU* 4.1 24.5 - - + -
193D THR* 4.1 20.4 - - + -
214D TYR* 3.3 17.3 - - + +
228D GLN 2.9 18.3 + - - +
230D LEU 3.1 0.2 - - - -
231D LYS* 1.3 77.6 - - - +
233D LEU* 1.3 61.9 + - - +
235D GLU* 3.2 19.7 + - + +
236D LEU* 3.0 31.1 + - + +
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Residues in contact with LEU 233 (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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211D PHE* 4.0 26.7 - - + -
214D TYR* 3.5 15.2 + - + -
218D LEU* 4.2 9.2 - - + -
229D SER 3.0 18.6 + - - +
230D LEU* 3.1 7.6 + - + +
232D LEU* 1.3 76.8 - - - +
234D GLY* 1.3 61.7 + - - +
236D LEU* 3.3 11.1 + - + +
237D LEU* 3.0 46.7 + - + +
249D TYR* 3.3 37.7 - - + +
259D MET* 4.0 14.4 - - + -
277D VAL* 4.1 10.5 - - + -
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Residues in contact with GLY 234 (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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230D LEU 3.2 10.3 + - - -
231D LYS* 3.8 3.4 - - - -
232D LEU 3.2 0.4 - - - -
233D LEU* 1.3 76.6 - - - +
235D GLU* 1.3 62.8 + - - +
237D LEU* 3.4 6.8 + - - +
238D LEU* 3.3 31.2 + - - +
276D HIS* 5.0 10.1 - - - -
277D VAL* 4.0 18.3 - - - +
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Residues in contact with GLU 235 (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* 4.7 11.8 + - - -
193D THR* 6.0 3.4 - - + -
231D LYS* 3.1 51.6 + - - +
232D LEU* 3.2 25.6 + - + +
234D GLY* 1.3 74.3 - - - +
236D LEU* 1.3 63.8 + - + +
238D LEU* 3.4 4.1 + - - +
239D ASP* 3.3 22.0 + - - +
170F GLN* 5.7 2.1 + - - -
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Residues in contact with LEU 236 (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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192D LEU* 3.9 31.0 - - + +
193D THR* 4.1 16.6 - - + -
203D LEU* 4.5 17.7 - - + -
210D PHE* 4.6 22.2 - - + -
211D PHE* 5.3 3.8 - - + -
214D TYR* 4.9 4.9 - - + -
232D LEU* 3.0 28.6 + - + +
233D LEU* 3.3 21.3 + - + +
235D GLU* 1.3 75.1 - - - +
237D LEU* 1.3 64.0 + - + +
238D LEU 3.3 0.7 + - - -
239D ASP* 3.4 5.6 + - - -
242D ASN* 2.7 41.6 + - + +
245D ILE* 6.2 1.8 - - + -
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Residues in contact with LEU 237 (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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211D PHE* 5.6 1.1 - - + -
233D LEU* 3.0 34.9 + - + +
234D GLY* 3.8 6.3 - - - +
235D GLU 3.3 0.4 - - - -
236D LEU* 1.3 78.9 - - + +
238D LEU* 1.3 60.6 + - - +
239D ASP 3.4 4.7 + - - +
242D ASN* 5.1 1.3 - - - -
243D PHE* 5.7 0.2 - - - -
245D ILE* 4.7 9.0 - - + +
246D MET* 3.5 49.3 - - + +
249D TYR* 3.7 46.0 - - + -
250D ILE* 4.8 9.6 - - + -
277D VAL* 3.8 23.8 - - + -
280D VAL* 5.0 13.2 - - + -
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Residues in contact with LEU 238 (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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234D GLY 3.3 18.5 + - - +
235D GLU* 3.9 4.7 - - - +
236D LEU 3.2 0.8 - - - -
237D LEU* 1.3 81.9 - - - +
239D ASP* 1.3 64.5 + - - +
240D ARG* 3.5 6.1 + - - +
246D MET* 4.8 0.9 - - - -
276D HIS 4.8 2.9 - - - +
279D LYS* 4.1 28.0 - - - +
280D VAL* 3.9 28.0 - - + -
169F SER 3.7 5.9 - - - +
170F GLN* 4.9 14.6 - - - +
203F PRO* 4.2 30.1 - - + +
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Residues in contact with ASP 239 (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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196D LYS* 3.4 34.4 + - - +
235D GLU 3.3 12.3 + - - +
236D LEU* 3.4 12.4 + - - +
237D LEU 4.2 2.4 - - - +
238D LEU* 1.3 79.6 - - - +
240D ARG* 1.3 66.8 + - - +
241D HIS* 2.7 33.7 + - - +
242D ASN* 3.0 28.4 + - - +
243D PHE* 3.8 2.9 + - - -
169F SER* 3.5 14.7 + - - -
170F GLN* 4.9 6.2 + - - +
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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