Contacts of the helix formed by residues 258 - 274 (chain E) in PDB entry 1MKD
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 258 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250E TYR* 3.4 17.7 - - - -
251E HIS 3.6 15.9 - - - +
252E ALA* 5.6 0.7 - - - +
254E VAL 2.8 26.7 + - - +
255E ALA 3.0 19.4 + - - -
256E TYR 2.7 15.9 + - - +
257E HIS* 1.3 72.4 - - - +
259E ASN* 1.3 70.9 + - - +
260E ILE* 2.7 41.5 + - - +
261E HIS* 3.0 6.4 + - - +
262E ALA* 3.0 18.0 + - - +
429E TRP* 5.3 1.3 - - - -
432E ARG* 4.0 8.9 - - - +
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Residues in contact with ASN 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212E ASN* 3.5 30.0 + - - +
214E PRO* 3.2 21.8 - - - +
215E LEU* 4.0 3.9 - - + +
247E GLU* 2.7 44.1 + - + +
250E TYR* 3.5 26.7 - - + +
251E HIS 5.3 0.9 - - - +
252E ALA* 5.8 2.9 - - - -
258E ASN* 1.3 78.9 - - - +
260E ILE* 1.3 61.0 + - - +
262E ALA* 3.7 5.8 - - - +
263E ALA* 2.9 28.6 + - - +
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Residues in contact with ILE 260 (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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203E VAL* 3.8 21.4 - - + +
204E PHE* 4.0 15.7 - - + -
207E ALA* 4.3 20.6 - - + -
212E ASN* 4.7 6.7 - - - +
214E PRO* 4.1 15.5 - - + -
258E ASN* 2.7 19.1 + - - +
259E ASN* 1.3 78.7 - - - +
261E HIS* 1.3 60.6 + - - +
263E ALA* 3.2 2.6 + - - +
264E ASP* 2.8 28.6 + - - +
429E TRP* 3.8 17.3 - - + -
432E ARG* 3.7 31.4 - - - +
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Residues in contact with HIS 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256E TYR* 3.2 59.7 + + - +
257E HIS* 4.3 6.3 - + - -
258E ASN* 3.0 7.7 + - - +
260E ILE* 1.3 78.2 - - - +
262E ALA* 1.3 63.1 + - - +
264E ASP* 3.0 7.9 + - - +
265E VAL* 2.9 35.3 + - + +
297E HIS* 3.0 11.6 + + - -
298E ASP* 3.2 13.9 - - + -
415E ASP* 2.9 20.1 + - - -
418E ASN* 5.4 1.9 + - - -
429E TRP* 3.7 16.1 - - + -
2009E ZN 2.3 31.4 - - - -
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Residues in contact with ALA 262 (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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215E LEU* 4.0 8.7 - - + -
250E TYR* 3.4 44.6 - - + +
258E ASN 3.0 6.4 + - - +
259E ASN* 3.7 8.1 - - - +
261E HIS* 1.3 77.6 - - - +
263E ALA* 1.3 64.3 + - - +
265E VAL* 3.2 2.3 + - - +
266E VAL* 3.0 27.0 + - - +
294E SER 4.4 0.8 - - - +
295E ALA 3.9 7.6 - - - +
297E HIS* 4.5 12.3 - - - -
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Residues in contact with ALA 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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203E VAL* 4.2 1.8 - - + -
214E PRO* 3.7 16.8 - - + -
215E LEU* 3.6 32.3 - - - +
218E ILE* 3.9 16.5 - - + +
259E ASN 2.9 18.9 + - - +
260E ILE 3.2 4.7 + - - +
262E ALA* 1.3 76.3 - - - +
264E ASP* 1.3 57.8 + - - +
266E VAL* 3.4 4.7 + - - +
267E GLN* 3.0 29.3 + - - +
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Residues in contact with ASP 264 (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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201E LEU 5.7 0.7 - - - +
203E VAL* 4.4 16.2 - - + +
260E ILE 2.8 13.4 + - - +
261E HIS* 3.3 11.3 + - - +
263E ALA* 1.3 74.9 - - - +
265E VAL* 1.3 62.4 + - + +
267E GLN* 3.4 9.3 + - - +
268E SER* 2.8 35.0 + - - -
414E ALA 5.4 0.2 - - - +
417E SER* 4.4 2.3 + - - -
418E ASN* 3.3 26.2 + - - -
421E LYS* 3.0 26.7 + - - -
429E TRP* 3.5 24.0 + - + -
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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
----------------------------------------------------------
261E HIS* 2.9 33.3 + - + +
262E ALA 3.8 2.7 - - - +
264E ASP* 1.3 77.1 - - + +
266E VAL* 1.3 62.7 + - - +
268E SER* 4.5 4.0 - - - -
269E THR* 2.9 29.4 + - - +
294E SER* 4.0 16.8 - - - +
297E HIS* 3.3 37.0 - - + +
411E VAL* 4.3 8.1 - - + +
414E ALA* 3.8 23.0 - - + +
415E ASP* 3.7 17.0 - - + +
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Residues in contact with VAL 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215E LEU* 3.9 8.5 - - + -
218E ILE* 4.7 4.0 - - + -
219E MET* 3.6 23.6 - - + -
222E ILE* 3.8 18.8 - - + -
262E ALA 3.0 18.6 + - - +
263E ALA* 3.4 8.7 - - - +
265E VAL* 1.3 77.7 - - - +
267E GLN* 1.3 58.1 + - - +
269E THR* 3.2 3.3 + - - +
270E HIS* 2.9 26.3 + - - +
291E ILE* 4.1 11.0 - - + +
294E SER* 3.8 8.3 - - - -
295E ALA* 3.4 40.2 - - + +
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Residues in contact with GLN 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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196E VAL* 2.8 37.3 + - + +
198E LYS 2.9 22.2 + - - -
199E TRP* 3.7 9.5 - - - +
201E LEU* 3.5 40.4 - - + +
203E VAL* 6.1 0.4 - - + +
218E ILE* 4.1 8.5 - - + -
222E ILE* 4.0 9.6 - - - -
263E ALA 3.0 14.3 + - - +
264E ASP* 3.4 10.5 + - - +
266E VAL* 1.3 79.8 - - - +
268E SER* 1.3 63.5 + - - +
270E HIS* 3.1 4.5 - - - +
271E VAL* 3.0 45.7 + - - +
421E LYS* 5.0 0.2 + - - -
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Residues in contact with SER 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199E TRP* 3.7 22.8 - - - -
264E ASP* 2.8 19.3 + - - -
265E VAL* 3.8 3.8 - - - -
267E GLN* 1.3 76.8 + - - +
269E THR* 1.3 66.5 + - - +
271E VAL* 3.2 3.0 + - - +
272E LEU* 2.9 29.9 + - - +
414E ALA* 3.9 14.4 - - - -
417E SER* 3.7 6.6 + - - -
421E LYS* 3.0 28.2 + - - -
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Residues in contact with THR 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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265E VAL 2.9 17.2 + - - -
266E VAL 3.5 3.8 - - - -
268E SER* 1.3 75.3 - - - +
270E HIS* 1.3 55.7 + - - +
272E LEU* 3.2 7.0 + - - +
273E LEU* 2.8 53.0 + - + +
290E ALA* 4.1 19.1 - - + +
291E ILE* 4.5 3.4 - - + +
294E SER* 2.8 27.5 + - - +
410E MET* 4.4 6.5 - - + -
411E VAL* 4.0 11.8 - - + +
414E ALA* 3.4 16.5 - - - +
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Residues in contact with HIS 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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196E VAL* 3.4 25.4 - - - +
197E ASN* 2.8 27.4 + - - +
222E ILE* 3.4 38.8 - - + +
225E GLU* 4.1 11.4 - - + +
226E ARG* 2.9 70.5 + - + +
266E VAL 2.9 13.3 + - - +
267E GLN 3.1 8.7 - - - +
269E THR* 1.3 79.3 - - - +
271E VAL* 1.3 63.2 + - + +
273E LEU* 3.5 7.7 + - - -
274E SER* 3.4 7.9 + - - -
291E ILE* 5.0 2.9 - - + -
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Residues in contact with VAL 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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196E VAL 4.0 2.5 - - - +
197E ASN* 3.8 27.8 - - - +
198E LYS 3.9 4.5 - - - +
199E TRP* 3.7 30.5 - - + +
267E GLN* 3.0 38.0 + - - +
268E SER 3.2 6.3 + - - +
270E HIS* 1.3 75.7 - - - +
272E LEU* 1.3 66.9 + - + +
274E SER* 3.0 20.9 + - - -
275E THR* 3.5 4.3 + - - -
492E ILE* 6.2 0.7 - - + -
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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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199E TRP* 4.0 17.7 - - + -
268E SER 2.9 20.3 + - - +
269E THR* 3.7 3.8 - - - +
271E VAL* 1.3 76.4 - - + +
273E LEU* 1.3 62.8 + - - +
275E THR* 3.0 30.4 + - - +
410E MET* 3.7 45.9 - - + +
413E CYS* 4.2 4.0 - - + -
414E ALA* 4.2 11.2 - - + +
478E TRP* 4.0 29.2 - - + -
481E TRP* 4.1 20.3 - - + +
492E ILE* 4.6 7.6 - - + -
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Residues in contact with LEU 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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226E ARG* 3.5 17.4 + - - +
269E THR* 2.8 29.3 + - + +
270E HIS* 4.6 0.2 - - - -
271E VAL 3.2 0.2 - - - -
272E LEU* 1.3 73.8 - - - +
274E SER* 1.3 59.7 + - - +
275E THR 3.2 5.1 + - - +
278E LEU* 4.4 13.6 - - - +
282E PHE* 4.3 14.8 - - + -
287E ILE* 3.8 32.8 - - + +
290E ALA* 4.4 2.9 - - + -
291E ILE* 3.8 31.0 - - + -
407E LEU* 4.1 15.7 - - + -
410E MET* 3.5 28.0 - - + -
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Residues in contact with SER 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197E ASN* 6.6 0.2 - - - -
226E ARG* 2.9 22.2 + - - +
270E HIS* 3.4 8.9 + - - -
271E VAL* 3.0 14.9 + - - -
273E LEU* 1.3 74.8 - - - +
275E THR* 1.3 67.4 + - - +
276E PRO* 3.3 5.5 - - - +
279E GLU* 5.8 0.2 - - - +
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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