Contacts of the helix formed by residues 258 - 274 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B TYR* 3.4 18.7 - - - -
251B HIS 3.7 15.3 - - - +
252B ALA* 5.6 0.9 - - - +
254B VAL 2.8 27.4 + - - +
255B ALA 2.9 23.0 + - - -
256B TYR 2.7 12.8 + - - +
257B HIS* 1.3 74.3 - - - +
259B ASN* 1.3 66.4 + - - +
260B ILE* 2.8 41.5 + - - +
261B HIS* 3.1 7.0 + - - +
262B ALA 3.0 22.9 + - - -
429B TRP* 5.3 1.1 - - - -
432B ARG* 4.0 7.5 - - - +
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Residues in contact with ASN 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ASN* 3.5 29.9 + - - +
214B PRO* 3.2 20.5 - - - +
215B LEU* 3.9 5.2 - - + +
247B GLU* 2.7 44.3 + - + +
250B TYR* 3.5 25.9 - - + +
251B HIS 5.3 0.5 - - - +
252B ALA* 5.8 2.9 - - - -
258B ASN* 1.3 80.7 - - - +
260B ILE* 1.3 61.0 + - - +
262B ALA* 3.6 5.4 - - - +
263B ALA* 2.9 28.4 + - - +
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Residues in contact with ILE 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B VAL* 3.8 25.7 - - + +
204B PHE* 4.0 16.6 - - + -
207B ALA* 4.2 16.6 - - + -
212B ASN* 4.7 6.7 - - - +
214B PRO* 4.1 15.3 - - + -
258B ASN* 2.8 17.8 + - - +
259B ASN* 1.3 79.0 - - - +
261B HIS* 1.3 67.6 + - - +
263B ALA* 3.2 2.6 + - - +
264B ASP* 2.8 22.7 + - - +
429B TRP* 3.9 16.6 - - + -
432B ARG* 3.7 30.7 - - - +
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Residues in contact with HIS 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B TYR* 3.2 58.3 + + - +
257B HIS* 4.3 6.5 - + - -
258B ASN* 3.1 7.9 + - - +
260B ILE* 1.3 78.6 - - - +
262B ALA* 1.3 63.2 + - - +
264B ASP* 2.9 8.2 + - - +
265B VAL* 2.9 35.7 + - + +
297B HIS* 3.1 11.9 + + - -
298B ASP* 3.3 20.9 - - + -
415B ASP* 3.0 20.3 + - - -
418B ASN* 5.3 1.9 + - - -
429B TRP* 3.7 15.9 - - + -
2003B ZN 2.3 25.5 - - - -
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Residues in contact with ALA 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU* 3.9 8.7 - - + -
250B TYR* 3.3 44.9 - - + +
258B ASN 3.0 6.9 + - - +
259B ASN* 3.6 7.4 - - - +
261B HIS* 1.3 77.7 - - - +
263B ALA* 1.3 63.1 + - - +
265B VAL* 3.3 2.3 + - - +
266B VAL* 3.0 27.4 + - - +
294B SER 4.3 1.5 - - - +
295B ALA 3.9 7.6 - - - +
297B HIS* 4.6 11.9 - - - -
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Residues in contact with ALA 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B VAL* 4.2 2.2 - - + -
214B PRO* 3.7 18.2 - - + +
215B LEU* 3.6 32.5 - - - +
218B ILE* 3.9 14.2 - - + +
259B ASN 2.9 18.3 + - - +
260B ILE 3.5 4.9 - - - +
262B ALA* 1.3 76.0 - - - +
264B ASP* 1.3 57.5 + - - +
266B VAL* 3.4 4.4 + - - +
267B GLN* 3.0 29.6 + - - +
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Residues in contact with ASP 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B LEU 5.7 0.7 - - - +
203B VAL* 4.4 15.8 - - + +
260B ILE 2.8 13.4 + - - +
261B HIS* 2.9 11.6 + - - +
263B ALA* 1.3 74.9 - - - +
265B VAL* 1.3 60.8 + - + +
267B GLN* 3.3 10.3 + - - +
268B SER* 2.9 34.3 + - - -
414B ALA 5.9 0.2 - - - -
417B SER* 4.5 2.0 + - - -
418B ASN* 3.3 25.6 + - - -
421B LYS* 3.0 24.9 + - - -
429B TRP* 3.4 25.9 + - + -
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Residues in contact with VAL 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B HIS* 2.9 33.3 + - + +
262B ALA 3.9 2.5 - - - +
264B ASP* 1.3 77.3 - - + +
266B VAL* 1.3 63.1 + - - +
268B SER* 4.4 4.7 - - - -
269B THR* 3.0 29.2 + - - -
294B SER* 4.0 15.7 - - - +
297B HIS* 3.4 36.8 - - + +
411B VAL* 4.3 8.7 - - + +
414B ALA* 3.8 21.5 - - + +
415B ASP* 3.7 17.7 - - + +
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Residues in contact with VAL 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU* 3.9 8.7 - - + -
218B ILE* 4.7 4.0 - - + -
219B MET* 3.6 24.2 - - + -
222B ILE* 3.8 18.8 - - + -
262B ALA 3.0 19.3 + - - +
263B ALA* 3.5 9.4 - - - +
265B VAL* 1.3 78.6 - - - +
267B GLN* 1.3 57.6 + - - +
269B THR* 3.2 2.6 + - - -
270B HIS* 2.9 26.7 + - - +
291B ILE* 4.1 11.6 - - + +
294B SER* 3.8 7.9 - - - -
295B ALA* 3.4 39.3 - - + +
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Residues in contact with GLN 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B VAL* 2.9 32.6 + - + +
198B LYS 3.0 21.0 + - - -
199B TRP 3.7 9.9 + - - +
201B LEU* 3.4 40.7 - - + +
203B VAL* 6.1 0.2 - - - +
218B ILE* 4.1 13.5 - - + -
222B ILE* 4.0 9.0 - - - -
263B ALA 3.0 14.1 + - - +
264B ASP* 3.3 10.7 + - - +
266B VAL* 1.3 81.1 - - - +
268B SER* 1.3 63.5 + - - +
270B HIS* 3.1 4.7 - - - +
271B VAL* 3.0 45.9 + - - +
421B LYS* 5.0 0.3 + - - -
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Residues in contact with SER 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B TRP* 3.6 23.8 - - - -
264B ASP* 2.9 19.0 + - - -
265B VAL* 4.4 0.7 - - - -
267B GLN* 1.3 76.7 + - - +
269B THR* 1.3 61.5 + - - +
271B VAL* 3.2 1.6 + - - -
272B LEU* 2.9 35.8 + - - +
414B ALA* 3.9 20.6 - - - -
417B SER* 3.7 4.1 + - - -
421B LYS* 3.1 28.1 + - - -
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Residues in contact with THR 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B VAL 3.0 19.8 + - - -
266B VAL 3.6 3.6 - - - -
268B SER* 1.3 76.1 - - - +
270B HIS* 1.3 57.7 + - - +
272B LEU* 3.2 7.0 + - - +
273B LEU* 2.8 48.5 + - + +
290B ALA* 4.1 18.8 - - + +
291B ILE* 4.5 3.8 - - + +
294B SER* 2.8 26.8 + - - +
410B MET* 4.3 6.3 - - + -
411B VAL* 3.9 12.7 - - + +
414B ALA* 3.4 16.0 - - - +
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Residues in contact with HIS 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B VAL* 3.4 24.8 - - + +
197B ASN* 2.9 26.4 + - - +
222B ILE* 3.4 40.6 - - + +
225B GLU* 4.1 11.2 - - + +
226B ARG* 2.8 70.5 + - + +
266B VAL 2.9 13.9 + - - +
267B GLN 3.1 8.7 - - - +
269B THR* 1.3 78.5 - - - +
271B VAL* 1.3 64.1 + - - +
273B LEU* 3.5 7.3 + - - -
274B SER* 3.4 8.6 + - - -
291B ILE* 5.0 2.7 - - + -
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Residues in contact with VAL 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B VAL 3.9 4.7 - - - +
197B ASN* 3.8 25.8 - - - +
198B LYS 4.0 4.0 - - - +
199B TRP* 3.7 30.7 - - + +
267B GLN* 3.0 37.7 + - - +
268B SER 3.6 5.8 - - - +
270B HIS* 1.3 77.6 - - + +
272B LEU* 1.3 63.8 + - + +
274B SER* 3.0 20.2 + - - -
275B THR* 3.6 5.0 + - - -
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Residues in contact with LEU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B TRP* 4.0 17.3 - - + -
268B SER 2.9 21.5 + - - +
269B THR* 3.7 3.8 - - - +
271B VAL* 1.3 75.8 - - + +
273B LEU* 1.3 62.1 + - - +
275B THR* 3.0 31.1 + - - +
410B MET* 3.7 47.2 - - + +
413B CYS* 4.2 3.8 - - + -
414B ALA* 4.2 11.0 - - + +
478B TRP* 4.0 29.4 - - + -
481B TRP* 4.1 19.0 - - + +
489B ALA* 6.4 0.2 - - + -
492B ILE* 4.6 7.6 - - + -
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Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B ARG* 3.5 17.2 + - - +
269B THR* 2.8 25.5 + - + +
270B HIS* 4.6 0.2 - - - -
271B VAL 3.2 0.2 - - - -
272B LEU* 1.3 76.4 - - - +
274B SER* 1.3 60.4 + - - +
275B THR 3.2 4.4 + - - +
278B LEU* 4.4 14.2 - - - +
282B PHE* 4.3 14.8 - - + -
287B ILE* 3.8 32.3 - - + +
290B ALA* 4.4 3.8 - - + -
291B ILE* 3.8 31.4 - - + -
407B LEU* 4.1 16.4 - - + -
410B MET* 3.5 28.2 - - + -
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Residues in contact with SER 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ASN* 6.6 0.2 - - - -
226B ARG* 2.9 22.8 + - - +
270B HIS* 3.4 9.0 + - - -
271B VAL* 3.0 13.9 + - - -
273B LEU* 1.3 73.8 - - - +
275B THR* 1.3 67.5 + - - +
276B PRO* 3.3 5.7 - - - +
279B 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