Contacts of the helix formed by residues 258 - 274 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250F TYR* 3.4 18.3 - - - -
251F HIS 3.6 21.1 - - - +
252F ALA* 5.6 0.7 - - - -
254F VAL 2.7 22.4 + - - +
255F ALA 3.0 22.4 + - - -
256F TYR 2.7 12.0 + - - +
257F HIS* 1.3 73.4 - - - +
259F ASN* 1.3 67.0 + - - +
260F ILE* 2.8 41.2 + - - +
261F HIS* 3.1 6.2 + - - +
262F ALA 3.0 22.5 + - - -
429F TRP* 5.3 1.5 - - - -
432F ARG* 4.0 7.7 - - - +
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Residues in contact with ASN 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212F ASN* 3.4 31.2 + - - +
214F PRO* 3.2 22.3 - - - +
215F LEU* 3.9 4.4 - - + +
247F GLU* 2.8 42.6 + - + +
250F TYR* 3.5 28.2 - - + +
251F HIS 5.2 0.7 - - - +
252F ALA* 5.7 2.8 - - - -
258F ASN* 1.3 79.1 - - - +
260F ILE* 1.3 60.9 + - - +
262F ALA* 3.7 5.8 - - - +
263F ALA* 2.9 28.1 + - - +
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Residues in contact with ILE 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203F VAL* 3.7 25.9 - - + +
204F PHE* 4.0 16.6 - - + -
207F ALA* 4.2 21.8 - - + -
212F ASN* 4.7 6.5 - - - +
214F PRO* 4.0 10.1 - - + -
258F ASN* 2.8 19.5 + - - +
259F ASN* 1.3 77.8 - - - +
261F HIS* 1.3 62.0 + - - +
263F ALA* 3.2 2.9 + - - +
264F ASP* 2.8 28.2 + - - +
429F TRP* 3.9 16.6 - - + -
432F ARG* 3.7 31.2 - - - +
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Residues in contact with HIS 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256F TYR* 3.1 58.5 + + - +
257F HIS* 4.3 6.7 - + - -
258F ASN* 3.1 8.2 + - - +
260F ILE* 1.3 78.7 - - - +
262F ALA* 1.3 57.6 + - - +
264F ASP* 3.0 7.4 + - - +
265F VAL* 2.8 41.8 + - + +
297F HIS* 3.1 11.9 + + - -
298F ASP* 3.2 20.2 - - + -
415F ASP* 3.0 21.1 + - - -
418F ASN* 5.2 2.1 + - - -
429F TRP* 3.7 17.8 - - + -
2011F ZN 2.4 24.7 - - - -
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Residues in contact with ALA 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215F LEU* 4.0 8.5 - - + -
250F TYR* 3.3 44.4 - - + +
258F ASN 3.0 5.8 + - - +
259F ASN* 3.7 8.1 - - - +
261F HIS* 1.3 77.6 - - - +
263F ALA* 1.3 63.4 + - - +
265F VAL* 3.3 1.7 + - - +
266F VAL* 3.0 28.2 + - - +
294F SER 4.4 0.7 - - - +
295F ALA 3.9 7.2 - - - +
297F HIS* 4.6 12.1 - - - -
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Residues in contact with ALA 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203F VAL* 4.2 1.8 - - + -
214F PRO* 3.7 17.7 - - + +
215F LEU* 3.6 32.9 - - - +
218F ILE* 3.9 15.4 - - + +
259F ASN 2.9 18.8 + - - +
260F ILE 3.5 4.5 - - - +
262F ALA* 1.3 76.4 - - - +
264F ASP* 1.3 56.3 + - - +
266F VAL* 3.4 4.5 + - - +
267F GLN* 3.0 29.6 + - - +
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Residues in contact with ASP 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201F LEU 5.7 0.5 - - - +
203F VAL* 4.4 16.3 - - + +
260F ILE 2.8 12.8 + - - +
261F HIS* 3.3 11.5 + - - +
263F ALA* 1.3 75.1 - - - +
265F VAL* 1.3 61.5 + - + +
267F GLN* 3.3 10.5 + - - +
268F SER* 2.9 34.2 + - - -
414F ALA 5.4 0.3 - - - +
417F SER* 4.4 2.3 + - - -
418F ASN* 3.3 25.8 + - - -
421F LYS* 2.9 27.3 + - - -
429F TRP* 3.5 24.7 + - + -
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Residues in contact with VAL 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261F HIS* 2.8 37.7 + - + +
262F ALA 3.9 2.2 - - - +
264F ASP* 1.3 74.2 - - + +
266F VAL* 1.3 56.9 + - - +
268F SER* 4.4 4.3 - - - -
269F THR* 2.9 35.4 + - - +
294F SER* 4.0 14.8 - - - +
297F HIS* 3.4 36.6 - - + +
411F VAL* 4.3 8.7 - - + +
414F ALA* 3.8 22.0 - - + +
415F ASP* 3.7 18.4 - - + +
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Residues in contact with VAL 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215F LEU* 3.9 9.2 - - + -
218F ILE* 4.7 3.6 - - + -
219F MET* 3.6 24.5 - - + -
222F ILE* 3.8 18.8 - - + -
262F ALA 3.0 20.1 + - - +
263F ALA* 3.5 8.5 - - - +
265F VAL* 1.3 77.0 - - - +
267F GLN* 1.3 58.4 + - - +
269F THR* 3.3 3.1 + - - +
270F HIS* 2.9 26.5 + - - +
291F ILE* 4.1 11.5 - - + +
294F SER* 3.8 8.1 - - - -
295F ALA* 3.4 38.6 - - + +
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Residues in contact with GLN 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196F VAL* 2.8 33.6 + - + +
198F LYS 2.9 21.4 + - - -
199F TRP 3.8 9.9 + - - +
201F LEU* 3.5 38.2 - - + +
218F ILE* 4.1 14.4 - - + -
222F ILE* 4.0 9.2 - - - -
263F ALA 3.0 14.0 + - - +
264F ASP* 3.8 10.7 - - - +
266F VAL* 1.3 79.8 - - - +
268F SER* 1.3 64.5 + - - +
270F HIS* 3.1 4.5 - - - +
271F VAL* 3.0 46.1 + - - +
421F LYS* 5.0 0.3 + - - -
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Residues in contact with SER 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F TRP* 3.6 24.4 - - - -
264F ASP* 2.9 18.5 + - - -
265F VAL* 3.8 4.3 - - - -
267F GLN* 1.3 77.6 + - - +
269F THR* 1.3 60.2 + - - +
271F VAL* 3.2 1.9 + - - -
272F LEU* 2.9 34.7 + - - +
414F ALA* 3.8 16.8 - - - -
417F SER* 3.7 3.5 + - - -
421F LYS* 3.0 28.1 + - - -
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Residues in contact with THR 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265F VAL* 2.9 17.4 + - - +
266F VAL 3.6 4.0 - - - -
268F SER* 1.3 74.5 - - - +
270F HIS* 1.3 58.4 + - - +
272F LEU* 3.2 6.5 + - - +
273F LEU* 2.8 48.4 + - + +
290F ALA* 4.2 18.8 - - + +
291F ILE* 4.5 3.4 - - + +
294F SER* 2.8 27.2 + - - +
410F MET* 4.3 6.7 - - + -
411F VAL* 4.0 11.9 - - + +
414F ALA* 3.4 17.1 - - - +
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Residues in contact with HIS 270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196F VAL* 3.4 24.8 - - + +
197F ASN* 2.9 26.9 + - - +
222F ILE* 3.4 39.5 - - + +
225F GLU* 4.1 11.9 - - + +
226F ARG* 2.8 69.0 + - + +
266F VAL 2.9 13.4 + - - +
267F GLN 3.1 9.0 - - - +
269F THR* 1.3 78.7 - - - +
271F VAL* 1.3 62.6 + - + +
273F LEU* 4.5 5.4 - - - -
274F SER* 3.4 10.4 + - - -
291F ILE* 5.0 3.1 - - + +
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Residues in contact with VAL 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196F VAL 3.9 4.7 - - - +
197F ASN* 3.8 26.7 - - - +
198F LYS 4.0 3.8 - - - +
199F TRP* 3.7 29.8 - - + +
267F GLN* 3.0 39.0 + - - +
268F SER 3.2 5.6 + - - +
270F HIS* 1.3 73.7 - - - +
272F LEU* 1.3 69.5 + - + +
274F SER* 3.0 20.5 + - - -
275F THR* 3.6 4.3 + - - -
492F ILE* 6.2 0.7 - - + -
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Residues in contact with LEU 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199F TRP* 3.9 17.5 - - + -
268F SER 2.9 20.2 + - - +
269F THR 3.7 3.8 - - - +
271F VAL* 1.3 77.1 - - + +
273F LEU* 1.3 62.6 + - - +
275F THR* 3.0 31.8 + - - +
410F MET* 3.7 46.4 - - + +
413F CYS* 4.2 3.6 - - + -
414F ALA* 4.1 11.7 - - + +
478F TRP* 4.0 28.0 - - + -
481F TRP* 4.1 20.5 - - + +
492F ILE* 4.6 7.6 - - + -
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Residues in contact with LEU 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226F ARG* 3.5 16.9 + - - +
269F THR* 2.8 25.7 + - + +
271F VAL 3.2 0.2 - - - -
272F LEU* 1.3 76.8 - - - +
274F SER* 1.3 58.4 + - - +
275F THR* 3.3 4.8 + - - +
278F LEU* 4.4 13.4 - - - +
282F PHE* 4.3 14.6 - - + -
287F ILE* 3.8 32.8 - - + +
290F ALA* 4.4 3.8 - - + -
291F ILE* 3.8 32.1 - - + -
407F LEU* 4.1 16.6 - - + -
410F MET* 3.5 28.9 - - + -
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Residues in contact with SER 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226F ARG* 2.9 22.6 + - - +
270F HIS* 3.4 8.5 + - - -
271F VAL* 3.0 13.6 + - - -
273F LEU* 1.3 76.9 - - - +
275F THR* 1.3 65.1 + - - +
276F PRO* 3.3 5.9 - - - +
279F 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