Contacts of the helix formed by residues 258 - 274 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250J TYR* 3.4 17.8 - - - -
251J HIS 3.6 20.9 - - - +
252J ALA* 5.6 1.1 + - - +
254J VAL 2.8 21.6 + - - +
255J ALA 3.0 19.6 + - - -
256J TYR 2.7 14.8 + - - +
257J HIS* 1.3 73.6 - - - +
259J ASN* 1.3 67.0 + - - +
260J ILE* 2.7 41.2 + - - +
261J HIS* 3.0 6.4 + - - +
262J ALA 3.0 23.0 + - - -
429J TRP* 5.3 1.0 - - - -
432J ARG* 4.0 8.7 - - - +
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Residues in contact with ASN 259 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212J ASN* 3.5 29.6 + - - +
214J PRO* 3.2 22.3 - - - +
215J LEU* 3.9 4.2 - - + +
247J GLU* 2.7 44.5 + - + +
250J TYR* 3.5 26.9 - - + +
251J HIS 5.3 0.7 - - - +
252J ALA* 5.8 2.8 - - - -
258J ASN* 1.3 80.1 - - - +
260J ILE* 1.3 59.9 + - - +
262J ALA* 3.7 6.4 - - - +
263J ALA* 2.9 28.2 + - - +
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Residues in contact with ILE 260 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203J VAL* 3.8 25.2 - - + +
204J PHE* 4.0 17.0 - - + -
207J ALA* 4.2 22.4 - - + -
212J ASN* 4.7 6.5 - - - +
214J PRO* 4.1 9.2 - - + -
258J ASN* 2.7 18.4 + - - +
259J ASN* 1.3 78.0 - - - +
261J HIS* 1.3 61.8 + - - +
263J ALA* 3.3 2.9 + - - +
264J ASP* 2.9 27.7 + - - +
429J TRP* 3.8 16.6 - - + -
432J ARG* 3.7 31.0 - - - +
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Residues in contact with HIS 261 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256J TYR* 3.1 59.8 + + - +
257J HIS* 4.3 6.1 - + - -
258J ASN* 3.0 8.0 + - - +
260J ILE* 1.3 79.0 - - - +
262J ALA* 1.3 63.6 + - - +
264J ASP* 3.0 8.3 + - - +
265J VAL* 2.9 39.4 + - + +
297J HIS* 3.1 11.7 + + - -
298J ASP* 3.2 13.7 - - + -
415J ASP* 2.9 20.3 + - - -
418J ASN* 5.2 1.9 + - - -
429J TRP* 3.7 17.2 - - + -
2019J ZN 2.2 31.4 - - - -
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Residues in contact with ALA 262 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215J LEU* 3.9 8.1 - - + -
250J TYR* 3.3 44.9 - - + +
258J ASN 3.0 6.5 + - - +
259J ASN* 3.7 8.5 - - - +
260J ILE 3.3 0.2 - - - -
261J HIS* 1.3 77.9 - - - +
263J ALA* 1.3 62.9 + - - +
265J VAL* 3.3 2.3 + - - +
266J VAL* 3.0 27.0 + - - +
294J SER 4.3 1.4 - - - +
295J ALA 3.9 7.2 - - - +
297J HIS* 4.5 11.9 - - - -
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Residues in contact with ALA 263 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203J VAL* 4.2 2.2 - - + -
214J PRO* 3.7 14.4 - - + +
215J LEU* 3.6 32.7 - - - +
218J ILE* 3.9 18.1 - - + +
259J ASN 2.9 19.8 + - - +
260J ILE 3.5 4.9 - - - +
262J ALA* 1.3 75.4 - - - +
264J ASP* 1.3 56.7 + - - +
266J VAL* 3.4 3.8 + - - +
267J GLN* 3.0 29.5 + - - +
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Residues in contact with ASP 264 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201J LEU 5.7 0.7 - - - +
203J VAL* 4.4 16.2 - - + +
260J ILE 2.9 14.1 + - - +
261J HIS* 3.0 11.3 + - - +
263J ALA* 1.3 74.3 - - - +
265J VAL* 1.3 62.9 + - + +
267J GLN* 3.3 9.6 + - - +
268J SER* 2.8 34.8 + - - -
414J ALA 5.9 0.2 - - - -
417J SER* 4.4 2.3 + - - -
418J ASN* 3.3 25.5 + - - -
421J LYS* 3.0 26.4 + - - -
429J TRP* 3.5 24.6 + - + -
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Residues in contact with VAL 265 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261J HIS* 2.9 34.4 + - + +
262J ALA 3.9 2.0 - - - +
264J ASP* 1.3 76.5 - - + +
266J VAL* 1.3 58.3 + - - +
268J SER* 4.4 5.2 - - - -
269J THR* 2.9 34.5 + - - +
294J SER* 4.0 15.9 - - - +
297J HIS* 3.3 37.5 - - + +
411J VAL* 4.3 8.5 - - + +
414J ALA* 3.8 21.9 - - + +
415J ASP* 3.7 17.9 - - + +
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Residues in contact with VAL 266 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215J LEU* 3.9 9.2 - - + -
218J ILE* 4.7 3.6 - - + -
219J MET* 3.6 24.5 - - + -
222J ILE* 3.8 18.2 - - + -
262J ALA 3.0 19.6 + - - +
263J ALA* 3.5 8.7 - - - +
265J VAL* 1.3 77.2 - - - +
267J GLN* 1.3 64.0 + - - +
269J THR* 3.2 3.8 + - - -
270J HIS* 2.9 21.8 + - - +
291J ILE* 4.1 11.8 - - + +
294J SER* 3.8 8.3 - - - -
295J ALA* 3.4 39.0 - - + +
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Residues in contact with GLN 267 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196J VAL* 2.8 37.9 + - + +
198J LYS 2.9 21.8 + - - -
199J TRP* 3.7 10.2 + - - +
201J LEU* 3.5 39.8 - - + +
203J VAL* 6.2 0.4 - - + +
218J ILE* 4.1 8.3 - - + -
222J ILE* 4.0 8.7 - - - -
263J ALA 3.0 15.0 + - - +
264J ASP* 3.8 10.1 - - - +
266J VAL* 1.3 79.9 - - - +
268J SER* 1.3 68.8 + - - +
270J HIS* 3.1 4.3 - - - +
271J VAL* 3.0 40.5 + - - +
421J LYS* 5.0 0.2 + - - -
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Residues in contact with SER 268 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199J TRP* 3.7 22.7 - - - -
264J ASP* 2.8 18.6 + - - -
265J VAL* 3.8 3.6 - - - -
267J GLN* 1.3 77.2 + - - +
269J THR* 1.3 67.0 + - - +
271J VAL* 3.2 1.8 + - - -
272J LEU* 2.9 29.2 + - - +
414J ALA* 3.9 15.0 - - - -
417J SER* 3.7 7.4 + - - -
421J LYS* 3.0 28.1 + - - -
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Residues in contact with THR 269 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265J VAL 2.9 19.5 + - - -
266J VAL 3.5 3.8 - - - -
268J SER* 1.3 77.1 - - - +
270J HIS* 1.3 58.6 + - - +
272J LEU* 3.3 6.6 + - - +
273J LEU* 2.8 49.4 + - + +
290J ALA* 4.2 19.3 - - + +
291J ILE* 4.5 3.8 - - + +
294J SER* 2.8 25.3 + - - +
410J MET* 4.3 7.0 - - - -
411J VAL* 4.0 10.9 - - + +
414J ALA* 3.4 16.0 - - - +
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Residues in contact with HIS 270 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196J VAL* 3.4 24.6 - - + +
197J ASN* 2.8 27.9 + - - -
222J ILE* 3.3 40.2 - - + +
225J GLU* 4.1 11.7 - - + +
226J ARG* 2.8 69.8 + - + +
266J VAL 2.9 12.9 + - - +
267J GLN 3.1 9.2 - - - +
269J THR* 1.3 80.6 - - - +
271J VAL* 1.3 63.5 + - - +
273J LEU* 4.6 4.9 - - - -
274J SER* 3.4 10.3 + - - -
291J ILE* 4.9 3.1 - - + -
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Residues in contact with VAL 271 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196J VAL 4.0 3.4 - - - +
197J ASN* 3.8 27.1 - - - +
198J LYS 4.0 3.8 - - - +
199J TRP* 3.7 30.5 - - + +
267J GLN* 3.0 37.5 + - - +
268J SER 3.2 6.3 + - - +
270J HIS* 1.3 76.8 - - + +
272J LEU* 1.3 66.7 + - + +
274J SER* 3.0 18.3 + - - -
275J THR* 3.5 7.4 + - - -
492J ILE* 6.2 0.7 - - + -
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Residues in contact with LEU 272 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199J TRP* 4.0 18.2 - - + -
268J SER 2.9 20.7 + - - +
269J THR 3.7 3.1 - - - +
271J VAL* 1.3 76.2 - - + +
273J LEU* 1.3 63.5 + - - +
275J THR* 3.0 31.8 + - - +
410J MET* 3.7 46.6 - - + +
413J CYS* 4.2 3.8 - - + -
414J ALA* 4.2 11.0 - - + +
478J TRP* 4.0 29.2 - - + -
481J TRP* 4.1 19.5 - - + +
489J ALA* 6.4 0.2 - - + -
492J ILE* 4.6 7.4 - - + -
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Residues in contact with LEU 273 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226J ARG* 3.5 17.8 + - - +
269J THR* 2.8 25.3 + - + +
271J VAL 3.2 0.2 - - - -
272J LEU* 1.3 76.8 - - - +
274J SER* 1.3 59.2 + - - +
275J THR 3.2 4.7 + - - +
278J LEU* 4.4 13.7 - - - +
282J PHE* 4.2 14.1 - - + -
287J ILE* 3.8 33.2 - - + +
290J ALA* 4.4 2.7 - - + -
291J ILE* 3.8 31.4 - - + -
407J LEU* 4.1 16.6 - - + -
410J MET* 3.5 29.1 - - + -
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Residues in contact with SER 274 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197J ASN* 6.6 0.2 - - - -
226J ARG* 2.9 23.0 + - - +
270J HIS* 3.4 8.3 + - - -
271J VAL* 3.0 13.6 + - - -
273J LEU* 1.3 75.0 - - - +
275J THR* 1.3 67.0 + - - +
276J PRO* 3.4 5.2 - - - +
279J GLU* 5.7 0.2 - - - +
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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