Contacts of the helix formed by residues 258 - 274 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250K TYR* 3.4 17.3 - - - -
251K HIS 3.6 16.2 - - - +
252K ALA* 5.6 1.1 + - - -
254K VAL 2.7 27.3 + - - +
255K ALA 2.9 21.8 + - - -
256K TYR 2.7 12.8 + - - +
257K HIS* 1.3 73.2 - - - +
259K ASN* 1.3 70.1 + - - +
260K ILE* 2.7 40.7 + - - +
261K HIS* 3.0 7.1 + - - +
262K ALA* 3.0 18.9 + - - +
429K TRP* 5.3 1.1 - - - -
432K ARG* 4.0 8.7 - - - +
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Residues in contact with ASN 259 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212K ASN* 3.4 31.6 + - - +
214K PRO* 3.2 22.7 - - - +
215K LEU* 4.0 4.2 - - + +
247K GLU* 2.8 43.0 + - + +
250K TYR* 3.4 27.6 - - + +
251K HIS 5.2 0.9 - - - +
252K ALA* 5.7 3.1 - - - -
258K ASN* 1.3 80.2 - - - +
260K ILE* 1.3 61.1 + - - +
262K ALA* 3.7 5.2 - - - +
263K ALA* 2.9 28.9 + - - +
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Residues in contact with ILE 260 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203K VAL* 3.8 21.4 - - + +
204K PHE* 4.0 16.4 - - + -
207K ALA* 4.2 19.7 - - + -
212K ASN* 4.7 6.7 - - - +
214K PRO* 4.1 16.2 - - + -
258K ASN* 2.7 19.2 + - - +
259K ASN* 1.3 78.2 - - - +
261K HIS* 1.3 61.3 + - - +
263K ALA* 3.2 2.6 + - - +
264K ASP* 2.8 28.6 + - - +
429K TRP* 3.8 16.8 - - + -
432K ARG* 3.8 30.5 - - - +
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Residues in contact with HIS 261 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256K TYR* 3.1 57.6 + + - +
257K HIS* 4.3 6.5 - + - -
258K ASN* 3.0 8.0 + - - +
260K ILE* 1.3 80.3 - - - +
262K ALA* 1.3 62.6 + - - +
264K ASP* 2.9 7.9 + - - +
265K VAL* 2.8 35.4 + - + +
297K HIS* 3.1 12.2 + + - -
298K ASP* 3.3 20.4 - - + -
415K ASP* 3.0 20.7 + - - -
418K ASN* 5.4 1.8 + - - -
429K TRP* 3.7 17.0 - - + -
2021K ZN 2.4 25.2 - - - -
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Residues in contact with ALA 262 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215K LEU* 3.9 9.0 - - + -
250K TYR* 3.3 44.4 - - + +
258K ASN 3.0 6.9 + - - +
259K ASN* 3.7 8.3 - - - +
261K HIS* 1.3 77.3 - - - +
263K ALA* 1.3 63.1 + - - +
265K VAL* 3.3 2.3 + - - +
266K VAL* 3.0 27.5 + - - +
294K SER 4.3 1.7 - - - +
295K ALA 3.9 7.2 - - - +
297K HIS* 4.5 12.1 - - - -
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Residues in contact with ALA 263 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203K VAL* 4.2 2.0 - - + -
214K PRO* 3.7 13.5 - - + -
215K LEU* 3.6 32.9 - - - +
218K ILE* 3.9 19.1 - - + +
259K ASN 2.9 18.4 + - - +
260K ILE 3.2 4.9 + - - +
262K ALA* 1.3 75.8 - - - +
264K ASP* 1.3 57.8 + - - +
266K VAL* 3.4 4.5 + - - +
267K GLN* 3.0 29.6 + - - +
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Residues in contact with ASP 264 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201K LEU 5.7 0.7 - - - +
203K VAL* 4.4 14.8 - - + +
260K ILE 2.8 13.4 + - - +
261K HIS* 2.9 11.9 + - - +
263K ALA* 1.3 73.4 - - - +
265K VAL* 1.3 62.7 + - - +
267K GLN* 3.3 10.5 + - - +
268K SER* 2.9 33.5 + - - -
414K ALA 5.4 0.5 - - - +
417K SER* 4.4 2.3 + - - -
418K ASN* 3.3 25.6 + - - -
421K LYS* 3.0 27.4 + - - -
429K TRP* 3.4 25.3 + - + -
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Residues in contact with VAL 265 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261K HIS* 2.8 37.5 + - + +
262K ALA 3.9 2.7 - - - +
264K ASP* 1.3 73.5 - - + +
266K VAL* 1.3 57.2 + - - +
268K SER* 3.4 5.1 + - - -
269K THR* 2.9 35.3 + - - +
294K SER* 4.0 16.4 - - - +
297K HIS* 3.3 35.9 - - + +
411K VAL* 4.3 8.5 - - + +
414K ALA* 3.8 21.2 - - + +
415K ASP* 3.7 18.2 - - + +
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Residues in contact with VAL 266 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215K LEU* 3.9 9.4 - - + -
218K ILE* 4.7 3.6 - - + -
219K MET* 3.6 25.4 - - + -
222K ILE* 3.8 18.2 - - + -
262K ALA 3.0 23.3 + - - +
263K ALA* 3.4 8.7 - - - +
265K VAL* 1.3 78.1 - - - +
267K GLN* 1.3 58.4 + - - +
269K THR* 3.2 3.1 + - - +
270K HIS* 2.9 27.0 + - - +
291K ILE* 4.1 11.8 - - + +
294K SER* 3.8 7.6 - - - -
295K ALA* 3.4 39.7 - - + +
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Residues in contact with GLN 267 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196K VAL* 2.8 32.5 + - + +
198K LYS 2.9 21.8 + - - -
199K TRP 3.7 9.9 - - - +
201K LEU* 3.4 39.9 - - + +
203K VAL* 6.1 0.2 - - - +
218K ILE* 4.1 14.1 - - + -
222K ILE* 4.0 9.9 - - + -
263K ALA 3.0 16.8 + - - +
264K ASP* 3.8 10.9 - - - +
266K VAL* 1.3 76.3 - - - +
268K SER* 1.3 63.3 + - - +
270K HIS* 3.1 4.3 - - - +
271K VAL* 3.0 46.7 + - - +
421K LYS* 5.1 0.3 + - - -
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Residues in contact with SER 268 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199K TRP* 3.6 21.2 - - - -
264K ASP* 2.9 19.1 + - - -
265K VAL* 3.8 4.0 - - - -
267K GLN* 1.3 76.0 + - - +
269K THR* 1.3 60.2 + - - +
271K VAL* 3.1 3.8 + - - +
272K LEU* 2.8 34.4 + - - +
414K ALA* 3.9 15.0 - - - -
417K SER* 3.7 7.2 + - - -
421K LYS* 3.1 27.9 + - - -
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Residues in contact with THR 269 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265K VAL 2.9 17.7 + - - -
266K VAL 3.5 4.3 - - - -
268K SER* 1.3 76.2 - - - +
270K HIS* 1.3 57.3 + - - +
272K LEU* 3.2 7.0 + - - +
273K LEU* 2.8 48.4 + - + +
290K ALA* 4.1 19.7 - - + +
291K ILE* 4.5 3.6 - - + +
294K SER* 2.8 26.7 + - - +
410K MET* 4.4 6.3 - - - -
411K VAL* 4.0 11.6 - - + +
414K ALA* 3.4 16.3 - - - +
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Residues in contact with HIS 270 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196K VAL* 3.4 24.6 - - + +
197K ASN* 2.8 27.6 + - - -
222K ILE* 3.4 39.9 - - + +
225K GLU* 4.1 11.2 - - + +
226K ARG* 2.9 68.9 + - + +
266K VAL 2.9 14.9 + - - +
267K GLN 3.1 8.3 - - - +
269K THR* 1.3 79.0 - - - +
271K VAL* 1.3 62.8 + - - +
273K LEU* 3.5 6.4 + - - -
274K SER* 3.4 8.9 + - - -
291K ILE* 5.0 2.9 - - + -
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Residues in contact with VAL 271 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196K VAL 4.0 2.5 - - - +
197K ASN* 3.8 28.9 - - - +
198K LYS 4.0 4.0 - - - +
199K TRP* 3.7 31.9 - - + +
267K GLN* 3.0 37.7 + - - +
268K SER 3.1 5.4 + - - +
270K HIS* 1.3 75.7 - - - +
272K LEU* 1.3 67.8 + - + +
274K SER* 3.0 21.0 + - - -
275K THR* 3.5 5.4 + - - -
492K ILE* 6.2 1.1 - - + -
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Residues in contact with LEU 272 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199K TRP* 4.0 17.9 - - + -
268K SER 2.8 19.7 + - - +
269K THR* 3.7 4.0 - - - +
271K VAL* 1.3 77.1 - - + +
273K LEU* 1.3 62.7 + - - +
275K THR* 3.0 31.7 + - - +
410K MET* 3.7 45.8 - - + +
413K CYS* 4.2 3.6 - - + -
414K ALA* 4.2 11.4 - - + +
478K TRP* 4.0 28.9 - - + -
481K TRP* 4.1 19.9 - - + +
489K ALA* 6.4 0.2 - - + -
492K ILE* 4.6 8.1 - - + -
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Residues in contact with LEU 273 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226K ARG* 3.5 18.5 + - - +
269K THR* 2.8 25.1 + - + +
271K VAL 3.2 0.2 - - - -
272K LEU* 1.3 76.6 - - - +
274K SER* 1.3 59.7 + - - +
275K THR 3.2 5.1 + - - +
278K LEU* 4.4 13.7 - - - +
282K PHE* 4.3 14.9 - - + -
287K ILE* 3.8 32.3 - - + +
290K ALA* 4.4 3.6 - - + -
291K ILE* 3.8 31.2 - - + -
407K LEU* 4.1 16.2 - - + -
410K MET* 3.5 28.3 - - + -
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Residues in contact with SER 274 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197K ASN* 6.6 0.2 - - - -
226K ARG* 2.9 21.8 + - - +
270K HIS* 3.4 8.6 + - - -
271K VAL* 3.0 14.7 + - - -
273K LEU* 1.3 76.2 - - - +
275K THR* 1.3 66.2 + - - +
276K PRO* 3.4 5.4 - - - +
279K GLU* 5.7 0.5 - - - +
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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