Contacts of the helix formed by residues 258 - 274 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250H TYR* 3.4 17.4 - - - -
251H HIS 3.6 16.2 - - - +
252H ALA* 5.6 0.9 - - - +
254H VAL 2.8 27.1 + - - +
255H ALA 3.0 22.4 + - - -
256H TYR 2.7 11.6 + - - +
257H HIS* 1.3 74.3 - - - +
259H ASN* 1.3 65.8 + - - +
260H ILE* 2.8 40.3 + - - +
261H HIS* 3.0 20.8 + - - +
262H ALA 3.0 10.2 + - - -
429H TRP* 5.3 1.1 - - - -
432H ARG* 4.0 8.1 - - - +
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Residues in contact with ASN 259 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212H ASN* 3.4 31.1 + - - +
214H PRO* 3.1 23.0 - - - +
215H LEU* 3.9 4.6 - - + +
247H GLU* 2.7 42.1 + - + +
250H TYR* 3.4 27.3 - - + +
251H HIS 5.3 0.9 - - - +
252H ALA* 5.7 3.1 - - - -
258H ASN* 1.3 84.9 - - - +
260H ILE* 1.3 61.5 + - - +
262H ALA* 3.7 6.2 - - - +
263H ALA* 2.9 27.5 + - - +
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Residues in contact with ILE 260 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203H VAL* 3.8 25.9 - - + +
204H PHE* 4.0 15.0 - - + -
207H ALA* 4.3 16.8 - - + -
212H ASN* 4.7 6.5 - - - +
214H PRO* 4.0 16.2 - - + -
258H ASN* 2.8 19.5 + - - +
259H ASN* 1.3 78.0 - - - +
261H HIS* 1.3 61.3 + - - +
263H ALA* 3.3 2.6 + - - +
264H ASP* 2.8 28.6 + - - +
429H TRP* 3.9 16.4 - - + -
432H ARG* 3.7 31.2 - - - +
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Residues in contact with HIS 261 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256H TYR* 3.1 58.9 + + - +
257H HIS* 4.3 6.1 - + - -
258H ASN* 3.0 8.4 + - - +
260H ILE* 1.3 78.7 - - - +
262H ALA* 1.3 64.3 + - - +
264H ASP* 2.9 7.9 + - - +
265H VAL* 2.9 40.1 + - + +
297H HIS* 3.0 11.9 + + - -
298H ASP* 3.2 20.4 - - + -
415H ASP* 3.0 20.5 + - - -
418H ASN* 5.4 1.7 + - - -
429H TRP* 3.7 15.9 - - + -
2015H ZN 2.3 25.2 - - - -
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Residues in contact with ALA 262 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215H LEU* 4.0 9.0 - - + -
250H TYR* 3.4 45.3 - - + +
258H ASN 3.0 6.0 + - - +
259H ASN* 3.7 8.1 - - - +
261H HIS* 1.3 78.5 - - - +
263H ALA* 1.3 63.3 + - - +
265H VAL* 3.2 2.1 + - - +
266H VAL* 3.0 26.5 + - - +
294H SER 4.3 1.4 - - - +
295H ALA 3.9 7.6 - - - +
297H HIS* 4.5 12.1 - - - -
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Residues in contact with ALA 263 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203H VAL* 4.2 1.8 - - + -
214H PRO* 3.7 15.3 - - + +
215H LEU* 3.6 31.8 - - - +
218H ILE* 3.9 17.2 - - + +
259H ASN 2.9 19.4 + - - +
260H ILE 3.5 5.4 - - - +
262H ALA* 1.3 76.2 - - - +
264H ASP* 1.3 56.4 + - - +
266H VAL* 3.4 5.1 + - - +
267H GLN* 3.0 30.0 + - - +
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Residues in contact with ASP 264 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201H LEU 5.7 0.7 - - - +
203H VAL* 4.4 16.5 - - + +
260H ILE 2.8 13.9 + - - +
261H HIS* 2.9 11.2 + - - +
263H ALA* 1.3 75.6 - - - +
265H VAL* 1.3 62.0 + - + +
267H GLN* 3.3 9.6 + - - +
268H SER* 2.9 35.0 + - - -
417H SER* 4.4 2.2 + - - -
418H ASN* 3.3 25.8 + - - -
421H LYS* 2.9 26.8 + - - -
429H TRP* 3.5 23.9 + - + -
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Residues in contact with VAL 265 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261H HIS* 2.9 33.9 + - + +
262H ALA 3.8 2.2 - - - +
264H ASP* 1.3 76.5 - - + +
266H VAL* 1.3 58.0 + - - +
268H SER* 4.4 0.4 - - - -
269H THR* 2.9 35.0 + - - -
294H SER* 4.0 15.7 - - - +
297H HIS* 3.4 36.6 - - + +
411H VAL* 4.3 9.4 - - + +
414H ALA* 3.7 25.5 - - + +
415H ASP* 3.7 18.4 - - + +
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Residues in contact with VAL 266 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215H LEU* 3.9 9.4 - - + -
218H ILE* 4.8 4.3 - - + -
219H MET* 3.6 24.2 - - + -
222H ILE* 3.8 18.6 - - + -
262H ALA 3.0 19.5 + - - +
263H ALA* 3.5 8.3 - - - +
265H VAL* 1.3 75.8 - - - +
267H GLN* 1.3 57.5 + - - +
269H THR* 3.2 4.0 + - - -
270H HIS* 2.9 27.0 + - - +
291H ILE* 4.1 11.7 - - + +
294H SER* 3.8 8.1 - - - -
295H ALA* 3.4 39.9 - - + +
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Residues in contact with GLN 267 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196H VAL* 2.8 32.4 + - + +
198H LYS 2.9 22.2 + - - -
199H TRP 3.7 10.0 - - - +
201H LEU* 3.5 39.1 + - + +
203H VAL* 6.5 0.4 - - + -
218H ILE* 4.1 13.7 - - + -
222H ILE* 4.0 9.2 - - - -
263H ALA 3.0 14.1 + - - +
264H ASP* 3.8 10.7 - - - +
266H VAL* 1.3 80.2 - - - +
268H SER* 1.3 64.2 + - - +
270H HIS* 3.2 4.0 - - - +
271H VAL* 3.0 45.7 + - - +
421H LYS* 5.0 0.2 + - - -
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Residues in contact with SER 268 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199H TRP* 3.6 24.0 - - - -
264H ASP* 2.9 18.5 + - - -
265H VAL* 3.8 4.0 - - - -
267H GLN* 1.3 79.4 + - - +
269H THR* 1.3 60.9 + - - +
271H VAL* 3.2 1.4 + - - -
272H LEU* 2.9 35.0 + - - +
414H ALA* 3.9 15.0 - - - -
417H SER* 3.6 6.3 + - - -
421H LYS* 3.1 27.9 + - - -
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Residues in contact with THR 269 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265H VAL 2.9 18.7 + - - -
266H VAL 3.6 3.8 - - - -
268H SER* 1.3 75.7 - - - +
270H HIS* 1.3 58.0 + - - +
272H LEU* 3.2 6.2 + - - +
273H LEU* 2.8 49.5 + - + +
290H ALA* 4.2 18.2 - - + +
291H ILE* 4.5 3.4 - - + +
294H SER* 2.8 27.7 + - - +
410H MET* 4.4 7.0 - - + -
411H VAL* 4.0 12.3 - - + +
414H ALA* 3.4 16.1 - - - +
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Residues in contact with HIS 270 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196H VAL* 3.4 24.3 - - - +
197H ASN* 2.8 27.6 + - - +
222H ILE* 3.3 39.3 - - + +
225H GLU* 4.1 11.4 - - + +
226H ARG* 2.9 69.7 + - + +
266H VAL 2.9 13.1 + - - +
267H GLN 3.2 9.2 - - - +
269H THR* 1.3 79.2 - - - +
271H VAL* 1.3 63.0 + - - +
273H LEU* 3.4 6.9 + - - -
274H SER* 3.3 8.5 + - - -
291H ILE* 4.9 4.0 - - + +
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Residues in contact with VAL 271 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196H VAL 4.0 2.5 - - - +
197H ASN* 3.8 27.8 - - - +
198H LYS 4.0 3.8 - - - +
199H TRP* 3.7 30.1 - - + +
267H GLN* 3.0 38.3 + - - +
268H SER 3.2 6.0 + - - +
270H HIS* 1.3 77.4 - - - +
272H LEU* 1.3 64.6 + - + +
274H SER* 3.0 20.2 + - - -
275H THR* 3.6 5.0 + - - -
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Residues in contact with LEU 272 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199H TRP* 4.0 17.7 - - + -
268H SER 2.9 20.7 + - - +
269H THR* 3.7 3.6 - - - +
271H VAL* 1.3 76.5 - - + +
273H LEU* 1.3 63.1 + - - +
275H THR* 3.0 31.6 + - - +
410H MET* 3.6 46.9 - - + +
413H CYS* 4.2 5.4 - - + -
414H ALA* 4.2 8.7 - - + +
478H TRP* 4.0 29.2 - - + -
481H TRP* 4.1 20.4 - - + +
489H ALA* 6.4 0.2 - - + -
492H ILE* 4.6 7.6 - - + -
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Residues in contact with LEU 273 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226H ARG* 3.5 16.9 + - - +
269H THR* 2.8 25.8 + - + +
270H HIS* 4.6 0.2 - - - -
271H VAL 3.2 0.2 - - - -
272H LEU* 1.3 76.2 - - - +
274H SER* 1.3 59.7 + - - +
275H THR 3.2 4.4 + - - +
278H LEU* 4.4 14.4 - - - +
282H PHE* 4.3 15.0 - - + -
287H ILE* 3.9 32.5 - - + +
290H ALA* 4.4 3.1 - - + -
291H ILE* 3.8 31.9 - - + -
407H LEU* 4.1 16.6 - - + -
410H MET* 3.6 27.8 - - + -
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Residues in contact with SER 274 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197H ASN* 6.6 0.4 - - - -
226H ARG* 2.9 23.1 + - - +
270H HIS* 3.3 8.8 + - - -
271H VAL* 3.0 13.8 + - - -
273H LEU* 1.3 76.6 - - - +
275H THR* 1.3 67.0 + - - +
276H PRO* 3.3 5.5 - - - +
279H GLU* 5.7 0.3 - - - +
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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
------------------------------------------------------------
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