Contacts of the helix formed by residues 258 - 275 (chain E) 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 ALA 258 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E HIS* 3.1 60.7 + - + +
191E TYR 4.8 2.7 - - - +
192E VAL* 4.2 9.4 - - + +
220E MET* 4.2 5.3 - - - -
257E ASP* 1.3 77.8 - - + +
259E LYS* 1.3 59.0 + - + +
260E SER 3.1 5.7 + - - -
261E ASP* 3.3 8.9 + - - +
262E ILE* 4.0 2.6 + - - +
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Residues in contact with LYS 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247E GLU* 4.6 0.2 - - - -
257E ASP* 2.8 21.4 + - - +
258E ALA* 1.3 77.8 - - + +
260E SER* 1.3 56.5 + - - +
261E ASP 3.5 0.2 - - - -
262E ILE* 3.8 9.5 + - - +
263E TYR 3.7 4.9 + - - -
364E PRO* 3.5 23.9 + - + +
365E ASP* 3.6 19.7 + - - +
367E ARG* 2.7 64.8 + - + +
368E PRO* 4.5 8.6 - - - +
369E SER* 4.5 19.2 - - - +
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Residues in contact with SER 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192E VAL* 3.6 8.8 - - - +
194E ARG* 5.4 0.5 - - - +
245E SER* 3.2 30.5 + - - -
247E GLU* 3.8 8.2 + - - -
248E VAL* 3.7 13.3 - - - +
256E TYR* 3.4 14.8 - - - -
257E ASP* 2.5 24.5 + - - +
259E LYS* 1.3 77.9 - - - +
261E ASP* 1.3 65.4 + - - +
262E ILE 3.2 0.4 - - - -
263E TYR* 3.3 14.9 - - - +
264E SER* 3.3 13.6 + - - -
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Residues in contact with ASP 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183E LEU* 3.8 11.2 - - + +
187E HIS* 2.7 31.1 + - + +
192E VAL* 3.4 13.6 - - - +
193E HIS* 2.8 28.3 + - - +
194E ARG* 3.0 25.8 + - - +
196E VAL* 4.4 6.7 + - + +
258E ALA 3.3 7.0 + - - +
260E SER* 1.3 75.6 + - - +
262E ILE* 1.3 56.7 + - - +
264E SER* 3.2 12.3 + - - -
265E VAL* 2.8 35.0 + - - +
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Residues in contact with ILE 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180E LEU* 3.9 28.7 - - + -
183E LEU* 4.8 4.7 - - + -
187E HIS* 5.0 4.5 - - + +
258E ALA 4.0 8.9 + - - +
259E LYS* 3.8 13.1 + - + +
260E SER 3.2 0.8 - - - -
261E ASP* 1.3 77.8 - - - +
263E TYR* 1.3 63.7 + - - +
265E VAL* 3.2 6.6 + - + +
266E GLY 3.1 18.0 + - - -
359E CYS* 3.3 26.8 - - - +
367E ARG* 4.2 10.3 - - + -
368E PRO* 3.5 26.7 - - + +
369E SER* 4.4 5.8 - - - -
370E ALA* 4.2 16.4 - - + +
373E LEU* 3.9 16.2 - - + -
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Residues in contact with TYR 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243E TRP 4.2 0.4 - - - -
244E LEU 3.5 18.6 - - - -
245E SER* 3.4 26.9 - - - -
246E PRO* 3.7 22.5 - - + +
259E LYS 3.7 3.4 + - - -
260E SER 3.3 11.4 + - - +
262E ILE* 1.3 78.9 - - - +
264E SER* 1.3 56.3 + - - +
266E GLY 3.3 2.3 + - - -
267E ILE* 3.0 56.5 + - + +
279E PHE* 4.2 4.0 - - - -
291E LYS* 3.4 25.3 + - - +
295E THR 4.6 0.7 + - - -
296E VAL* 3.8 16.9 - - + +
359E CYS 3.4 12.6 + - - +
360E LEU* 3.6 40.2 - - + +
361E GLN 5.0 0.4 - - - -
362E ARG* 6.2 0.2 - - - -
367E ARG* 4.0 16.4 - - - +
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Residues in contact with SER 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194E ARG* 5.8 2.1 - - - -
196E VAL* 3.5 29.4 + - - +
243E TRP* 2.4 30.7 + - - -
244E LEU* 4.3 5.4 - - - +
260E SER 3.3 12.4 + - - -
261E ASP* 3.2 14.3 + - - -
263E TYR* 1.3 74.2 - - - +
265E VAL* 1.3 61.5 + - - +
267E ILE* 3.6 5.1 - - - +
268E THR* 2.7 35.0 + - - -
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Residues in contact with VAL 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176E LEU* 4.1 12.8 - - + +
179E VAL* 4.1 11.2 - - + -
180E LEU* 3.8 21.8 - - + -
183E LEU* 3.7 26.0 - - + -
196E VAL* 4.1 6.3 - - + -
261E ASP 2.8 17.9 + - - +
262E ILE* 3.2 13.0 + - + +
264E SER* 1.3 76.1 - - - +
266E GLY* 1.3 52.2 + - - +
268E THR* 3.1 4.5 + - - -
269E ALA* 2.7 34.4 + - - +
355E PHE* 3.8 27.6 - - + -
359E CYS* 4.0 5.6 - - - -
373E LEU* 4.8 0.2 - - + -
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Residues in contact with GLY 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E ILE 3.1 11.1 + - - -
263E TYR 3.3 3.3 + - - -
265E VAL* 1.3 75.7 - - - +
267E ILE* 1.3 60.5 + - - +
269E ALA* 3.2 9.9 - - - +
270E CYS* 3.1 26.7 + - - -
356E VAL* 4.5 3.0 - - - +
359E CYS* 3.4 25.7 - - - +
360E LEU* 4.0 13.4 - - - +
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Residues in contact with ILE 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242E PRO 4.2 15.9 - - - +
243E TRP* 3.5 31.0 - - + +
263E TYR* 3.0 49.7 + - + +
264E SER* 3.6 7.9 - - - +
265E VAL 3.3 0.2 - - - -
266E GLY* 1.3 73.4 - - - +
268E THR* 1.3 64.9 + - - +
270E CYS* 3.0 7.9 + - - +
271E GLU* 3.0 19.6 + - - +
277E VAL* 5.0 0.9 - - + -
278E PRO* 3.8 21.2 - - + +
279E PHE* 4.4 4.5 - - + -
297E PRO* 4.1 17.5 - - + -
360E LEU* 3.6 14.1 - - + -
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Residues in contact with THR 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176E LEU* 4.7 4.9 - - + -
179E VAL* 6.5 0.4 - - + -
196E VAL* 3.3 9.1 + - + +
197E LYS* 3.2 23.3 + - - -
198E ALA* 3.8 13.9 - - - +
201E ILE* 3.7 29.8 - - + -
243E TRP* 3.8 2.0 - - - +
264E SER 2.7 23.0 + - - -
265E VAL* 3.6 6.3 - - - -
267E ILE* 1.3 70.9 - - - +
269E ALA* 1.3 57.7 + - - +
271E GLU* 3.5 9.2 - - - +
272E LEU* 2.9 40.7 + - + +
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Residues in contact with ALA 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172E ILE* 4.9 0.2 - - - +
176E LEU* 4.0 27.3 - - + +
265E VAL 2.7 16.7 + - - +
266E GLY* 3.2 15.0 - - - +
268E THR* 1.3 73.4 - - - +
270E CYS* 1.3 56.3 + - - +
272E LEU* 3.5 4.7 + - - +
273E ALA* 3.0 30.9 + - - +
352E PHE* 4.0 8.5 - - + -
355E PHE* 4.1 4.5 - - + -
356E VAL* 3.9 20.9 - - + -
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Residues in contact with CYS 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266E GLY 3.1 17.4 + - - -
267E ILE 3.0 8.3 + - - +
269E ALA* 1.3 75.5 - - - +
271E GLU* 1.3 58.3 + - - +
273E ALA* 4.4 2.0 - - - -
274E ASN* 2.8 50.3 + - - +
278E PRO* 3.8 17.0 - - + -
297E PRO* 3.8 11.4 - - + -
298E CYS* 3.7 34.8 - - - -
356E VAL* 4.0 15.9 - - - -
360E LEU* 4.2 2.7 - - - -
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Residues in contact with GLU 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E LYS* 2.8 40.9 + - - +
159E ILE* 3.4 8.5 - - + +
198E ALA* 3.2 32.0 + - + +
199E SER 4.9 0.7 + - - -
243E TRP* 3.0 36.9 + - - +
267E ILE 3.0 11.1 + - - +
268E THR* 3.2 8.9 + - - +
270E CYS* 1.3 76.4 - - - +
272E LEU* 1.3 58.8 + - - +
275E GLY* 2.8 31.4 + - - -
276E HIS 3.9 9.2 - - - +
277E VAL* 4.2 9.4 - - - +
278E PRO* 4.2 8.2 - - + +
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Residues in contact with LEU 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E ALA* 3.7 30.1 - - + -
159E ILE* 3.7 11.9 - - + +
166E GLY* 3.3 4.9 - - - -
167E MET* 2.8 49.3 + - - +
172E ILE* 3.8 27.6 - - + -
175E ILE* 3.8 26.2 - - + -
176E LEU* 4.1 14.1 - - + -
198E ALA* 4.2 7.4 - - + -
201E ILE* 5.2 0.2 - - + -
268E THR* 2.9 34.4 + - + +
269E ALA 3.9 2.5 - - - +
271E GLU* 1.3 75.5 - - - +
273E ALA* 1.3 56.4 + - - +
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Residues in contact with ALA 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E ASP 3.8 4.5 - - - +
166E GLY* 3.7 10.2 - - - -
167E MET 4.6 1.8 - - - +
172E ILE* 3.6 9.6 - - + +
269E ALA 3.0 18.5 + - - +
270E CYS* 4.4 1.3 - - - -
272E LEU* 1.3 78.4 - - - +
274E ASN* 1.3 67.4 + - - +
298E CYS 6.1 0.7 - - - +
348E PHE* 3.5 35.1 - - + -
352E PHE* 3.8 19.1 - - + -
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Residues in contact with ASN 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E MET 4.0 1.9 - - - +
165E ASP* 3.5 17.8 - - - +
270E CYS* 2.8 35.1 + - - +
273E ALA* 1.3 91.6 - - - +
275E GLY* 1.3 56.8 + - - +
276E HIS* 3.3 39.6 + - + +
278E PRO* 5.8 1.4 - - - +
297E PRO* 5.8 1.2 - - - +
298E CYS 4.2 20.6 - - - +
348E PHE* 4.8 5.2 - - - -
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Residues in contact with GLY 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E LYS* 4.8 3.4 + - - -
159E ILE* 3.3 29.9 - - - +
164E MET 3.4 19.5 - - - +
166E GLY* 3.8 9.0 - - - -
271E GLU 2.8 20.4 + - - -
273E ALA 3.8 0.8 - - - -
274E ASN* 1.3 72.4 - - - +
276E HIS* 1.3 59.7 + - - +
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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