Contacts of the helix formed by residues 258 - 274 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250L TYR* 3.4 17.8 - - - -
251L HIS 3.6 15.7 - - - +
252L ALA* 5.6 1.1 + - - +
254L VAL 2.8 27.6 + - - +
255L ALA 3.0 22.0 + - - -
256L TYR 2.7 11.6 + - - +
257L HIS* 1.3 73.6 - - - +
259L ASN* 1.3 66.2 + - - +
260L ILE* 2.7 41.8 + - - +
261L HIS* 3.0 6.8 + - - +
262L ALA 3.0 23.0 + - - -
429L TRP* 5.3 1.0 - - - -
432L ARG* 4.0 8.7 - - - +
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Residues in contact with ASN 259 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212L ASN* 3.4 30.6 + - - +
214L PRO* 3.1 22.7 - - - +
215L LEU* 3.9 3.6 - - + +
247L GLU* 2.8 42.6 + - + +
250L TYR* 3.4 28.6 - - + +
251L HIS 5.2 0.9 - - - +
252L ALA* 5.7 2.8 - - - -
258L ASN* 1.3 80.2 - - - +
260L ILE* 1.3 60.6 + - - +
262L ALA* 3.6 6.5 - - - +
263L ALA* 2.9 28.4 + - - +
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Residues in contact with ILE 260 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203L VAL* 3.8 25.9 - - + +
204L PHE* 4.0 15.7 - - + -
207L ALA* 4.2 15.3 - - + -
212L ASN* 4.7 6.5 - - - +
214L PRO* 4.0 16.2 - - + -
258L ASN* 2.7 20.0 + - - +
259L ASN* 1.3 77.9 - - - +
261L HIS* 1.3 61.1 + - - +
263L ALA* 3.2 2.4 + - - +
264L ASP* 2.8 28.9 + - - +
429L TRP* 3.8 16.6 - - + -
432L ARG* 3.7 30.3 - - - +
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Residues in contact with HIS 261 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256L TYR* 3.1 58.2 + + - +
257L HIS* 4.3 7.6 - + - -
258L ASN* 3.0 7.5 + - - +
260L ILE* 1.3 79.4 - - - +
262L ALA* 1.3 63.5 + - - +
264L ASP* 2.9 9.2 + - - +
265L VAL* 2.9 38.9 + - + +
297L HIS* 3.1 11.4 + + - -
298L ASP* 3.2 20.6 - - + -
415L ASP* 2.9 20.1 + - - -
418L ASN* 5.2 2.2 + - - -
429L TRP* 3.7 16.8 - - + -
2023L ZN 2.3 25.0 - - - -
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Residues in contact with ALA 262 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215L LEU* 4.0 9.0 - - + -
250L TYR* 3.4 45.5 - - + +
258L ASN 3.0 6.4 + - - +
259L ASN* 3.6 8.3 - - - +
261L HIS* 1.3 79.0 - - - +
263L ALA* 1.3 63.1 + - - +
265L VAL* 3.2 2.6 + - - +
266L VAL* 3.0 26.5 + - - +
294L SER 4.4 0.7 - - - +
295L ALA 3.9 7.4 - - - +
297L HIS* 4.5 13.0 - - - -
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Residues in contact with ALA 263 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203L VAL* 4.2 2.0 - - + -
214L PRO* 3.7 12.8 - - + -
215L LEU* 3.6 33.8 - - - +
218L ILE* 3.9 19.1 - - + +
259L ASN 2.9 19.5 + - - +
260L ILE 3.2 4.9 + - - +
262L ALA* 1.3 76.2 - - - +
264L ASP* 1.3 57.6 + - - +
266L VAL* 3.5 4.6 + - - +
267L GLN* 3.0 29.5 + - - +
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Residues in contact with ASP 264 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201L LEU 5.7 0.7 - - - +
203L VAL* 4.4 16.1 - - + +
260L ILE 2.8 13.9 + - - +
261L HIS* 2.9 11.8 + - - +
263L ALA* 1.3 74.1 - - - +
265L VAL* 1.3 62.3 + - + +
267L GLN* 3.4 9.9 + - - +
268L SER* 2.8 35.1 + - - -
414L ALA 5.4 0.3 - - - +
417L SER* 4.4 2.1 + - - -
418L ASN* 3.3 25.8 + - - -
421L LYS* 2.9 26.4 + - - -
429L TRP* 3.4 24.3 + - + -
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Residues in contact with VAL 265 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261L HIS* 2.9 34.4 + - + +
262L ALA 3.8 2.5 - - - +
264L ASP* 1.3 75.8 - - + +
266L VAL* 1.3 58.0 + - - +
268L SER* 3.4 4.8 + - - -
269L THR* 2.9 35.3 + - - +
294L SER* 4.0 15.7 - - - +
297L HIS* 3.3 36.8 - - + +
411L VAL* 4.3 9.2 - - + +
414L ALA* 3.8 21.9 - - + +
415L ASP* 3.6 18.4 - - + +
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Residues in contact with VAL 266 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215L LEU* 3.9 9.6 - - + -
218L ILE* 4.7 3.4 - - + -
219L MET* 3.6 24.7 - - + -
222L ILE* 3.7 18.6 - - + -
262L ALA 3.0 19.2 + - - +
263L ALA* 3.5 8.7 - - - +
265L VAL* 1.3 76.7 - - - +
267L GLN* 1.3 58.7 + - - +
269L THR* 3.2 4.0 + - - -
270L HIS* 2.9 27.5 + - - +
291L ILE* 4.1 11.8 - - + +
294L SER* 3.8 7.9 - - - -
295L ALA* 3.4 40.6 - - + +
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Residues in contact with GLN 267 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196L VAL* 2.8 33.0 + - + +
198L LYS 2.9 22.2 + - - -
199L TRP 3.7 10.2 + - - +
201L LEU* 3.4 39.2 - - + +
203L VAL* 6.1 0.4 - - + +
218L ILE* 4.1 13.5 - - + -
222L ILE* 3.9 9.4 - - - -
263L ALA 3.0 14.1 + - - +
264L ASP* 3.8 10.6 - - - +
266L VAL* 1.3 80.3 - - - +
268L SER* 1.3 63.7 + - - +
270L HIS* 3.1 4.3 - - - +
271L VAL* 2.9 46.0 + - - +
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Residues in contact with SER 268 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199L TRP* 3.6 23.9 - - - -
264L ASP* 2.8 22.4 + - - -
265L VAL* 3.8 4.3 - - - -
267L GLN* 1.3 77.4 + - - +
269L THR* 1.3 67.2 + - - +
271L VAL* 3.2 1.1 + - - -
272L LEU* 2.9 28.3 + - - +
414L ALA* 3.9 15.7 - - - -
417L SER* 3.7 6.0 + - - -
421L LYS* 3.1 27.4 + - - -
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Residues in contact with THR 269 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265L VAL* 2.9 20.0 + - - +
266L VAL 3.6 3.8 - - - -
268L SER* 1.3 76.7 - - - +
270L HIS* 1.3 56.9 - - - +
272L LEU* 3.2 6.3 + - - +
273L LEU* 2.8 49.3 + - + +
290L ALA* 4.1 19.3 - - + +
291L ILE* 4.5 3.4 - - + +
294L SER* 2.8 27.1 + - - +
410L MET* 4.3 6.7 - - + -
411L VAL* 4.0 11.9 - - + +
414L ALA* 3.4 15.9 - - - +
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Residues in contact with HIS 270 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196L VAL* 3.4 24.8 - - + +
197L ASN* 2.9 26.7 + - - +
222L ILE* 3.3 39.3 - - + +
225L GLU* 4.1 11.2 - - + +
226L ARG* 2.9 70.0 + - + +
266L VAL 2.9 14.4 + - - +
267L GLN 3.1 9.4 - - - +
269L THR* 1.3 79.0 - - - +
271L VAL* 1.3 62.7 + - - +
273L LEU* 3.5 6.5 + - - -
274L SER* 3.3 8.7 + - - -
291L ILE* 5.0 3.6 - - + +
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Residues in contact with VAL 271 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196L VAL 3.9 4.9 - - - +
197L ASN* 3.8 25.4 - - - +
198L LYS 4.0 4.3 - - - +
199L TRP* 3.7 29.8 - - + +
267L GLN* 2.9 38.6 + - - +
268L SER 3.2 5.6 + - - +
270L HIS* 1.3 78.0 - - - +
272L LEU* 1.3 65.2 + - + +
274L SER* 3.0 21.5 + - - -
275L THR* 3.6 4.3 + - - -
492L ILE* 6.2 0.9 - - + -
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Residues in contact with LEU 272 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199L TRP* 4.0 14.6 - - + -
268L SER 2.9 19.3 + - - +
269L THR* 3.7 4.3 - - - +
271L VAL* 1.3 77.6 - - + +
273L LEU* 1.3 62.9 + - - +
275L THR* 3.0 31.7 + - - +
410L MET* 3.7 46.5 - - + +
413L CYS* 4.2 3.8 - - + -
414L ALA* 4.1 11.4 - - + +
478L TRP* 4.0 32.1 - - + -
481L TRP* 4.0 20.4 - - + +
489L ALA* 6.3 0.4 - - + -
492L ILE* 4.6 7.9 - - + -
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Residues in contact with LEU 273 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226L ARG* 3.5 17.7 - - - +
269L THR* 2.8 25.1 + - + +
271L VAL 3.2 0.2 - - - -
272L LEU* 1.3 76.4 - - - +
274L SER* 1.3 58.8 + - - +
275L THR 3.2 7.3 + - - +
278L LEU* 4.3 14.2 - - - +
282L PHE* 4.3 14.7 - - + -
287L ILE* 3.8 33.0 - - + +
290L ALA* 4.3 3.8 - - + -
291L ILE* 3.8 31.4 - - + -
407L LEU* 4.1 16.6 - - + -
410L MET* 3.5 27.1 - - + -
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Residues in contact with SER 274 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197L ASN* 6.6 0.4 - - - -
226L ARG* 2.9 22.8 + - - +
270L HIS* 3.3 8.8 + - - -
271L VAL* 3.0 14.9 + - - -
273L LEU* 1.3 76.2 - - - +
275L THR* 1.3 65.9 + - - +
276L PRO* 3.3 5.5 - - - +
279L 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
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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