Contacts of the helix formed by residues 258 - 274 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A TYR* 3.4 18.2 - - - -
251A HIS 3.6 15.7 - - - +
252A ALA* 5.6 1.1 - - - +
254A VAL 2.8 27.8 + - - +
255A ALA 3.0 19.4 + - - -
256A TYR 2.7 15.4 + - - +
257A HIS* 1.3 73.0 - - - +
259A ASN* 1.3 70.7 + - - +
260A ILE* 2.7 40.6 + - - +
261A HIS* 3.0 6.6 + - - +
262A ALA 3.0 18.0 + - - -
429A TRP* 5.3 0.9 - - - -
432A ARG* 4.0 8.3 - - - +
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Residues in contact with ASN 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A ASN* 3.4 31.6 + - - +
214A PRO* 3.2 22.5 - - - +
215A LEU* 3.9 4.0 - - + +
247A GLU* 2.8 42.5 + - + +
250A TYR* 3.5 26.2 - - + +
251A HIS 5.2 0.9 - - - +
252A ALA* 5.7 2.6 - - - -
258A ASN* 1.3 84.7 - - - +
260A ILE* 1.3 61.3 + - - +
262A ALA* 3.7 5.8 - - - +
263A ALA* 2.9 27.7 + - - +
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Residues in contact with ILE 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A VAL* 3.8 20.0 - - + +
204A PHE* 4.0 16.4 - - + -
207A ALA* 4.2 26.7 - - + -
212A ASN* 4.8 6.7 - - - +
214A PRO* 4.1 9.4 - - + -
258A ASN* 2.7 19.9 + - - +
259A ASN* 1.3 77.6 - - - +
261A HIS* 1.3 61.7 + - - +
263A ALA* 3.2 2.8 + - - +
264A ASP* 2.8 28.1 + - - +
429A TRP* 3.8 18.6 - - + -
432A ARG* 3.7 31.0 - - - +
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Residues in contact with HIS 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A TYR* 3.1 59.8 + + - +
257A HIS* 4.3 6.5 - + - -
258A ASN* 3.0 7.5 + - - +
260A ILE* 1.3 78.7 - - - +
262A ALA* 1.3 63.3 + - - +
264A ASP* 3.0 7.7 + - - +
265A VAL* 2.9 41.0 + - + +
297A HIS* 3.1 11.8 + + - -
298A ASP* 3.3 20.9 - - + -
415A ASP* 2.9 20.7 + - - -
418A ASN* 5.2 1.5 + - - -
429A TRP* 3.7 16.5 - - + -
2001A ZN 2.4 25.0 - - - -
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Residues in contact with ALA 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A LEU* 4.0 8.3 - - + -
250A TYR* 3.4 44.6 - - + +
258A ASN 3.0 6.0 + - - +
259A ASN* 3.7 8.7 - - - +
261A HIS* 1.3 78.3 - - - +
263A ALA* 1.3 61.6 + - - +
265A VAL* 3.3 2.4 + - - +
266A VAL* 3.0 27.7 + - - +
294A SER 4.3 0.9 - - - +
295A ALA 3.9 8.3 - - - +
297A HIS* 4.5 12.3 - - - -
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Residues in contact with ALA 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A VAL* 4.2 2.0 - - + -
214A PRO* 3.7 12.1 - - + -
215A LEU* 3.6 33.8 - - - +
218A ILE* 3.9 19.9 - - + +
259A ASN 2.9 19.7 + - - +
260A ILE 3.2 4.7 + - - +
262A ALA* 1.3 75.1 - - - +
264A ASP* 1.3 57.1 + - - +
266A VAL* 3.5 3.8 + - - +
267A GLN* 3.0 29.6 + - - +
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Residues in contact with ASP 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A LEU 5.7 0.9 - - - +
203A VAL* 4.4 16.3 - - + +
260A ILE 2.8 13.5 + - - +
261A HIS* 3.0 11.3 + - - +
263A ALA* 1.3 74.1 - - - +
265A VAL* 1.3 62.5 + - + +
267A GLN* 3.3 9.4 + - - +
268A SER* 2.8 34.6 + - - -
414A ALA 5.4 0.2 - - - +
417A SER* 4.4 2.4 + - - -
418A ASN* 3.3 26.2 + - - -
421A LYS* 2.9 27.4 + - - -
429A TRP* 3.5 24.9 + - + -
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Residues in contact with VAL 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A HIS* 2.9 39.6 + - + +
262A ALA 3.9 2.7 - - - +
264A ASP* 1.3 73.5 - - + +
266A VAL* 1.3 57.1 + - - +
268A SER* 3.4 4.9 + - - -
269A THR* 2.9 35.0 + - - -
294A SER* 4.0 17.0 - - - +
297A HIS* 3.4 32.8 - - + +
411A VAL* 4.3 8.5 - - + +
414A ALA* 3.7 21.3 - - + +
415A ASP* 3.7 17.7 - - + +
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Residues in contact with VAL 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A LEU* 3.9 9.4 - - + -
218A ILE* 4.7 3.4 - - + -
219A MET* 3.5 24.7 - - + -
222A ILE* 3.8 17.9 - - + -
262A ALA 3.0 21.0 + - - +
263A ALA* 3.5 8.3 - - - +
265A VAL* 1.3 76.5 - - - +
267A GLN* 1.3 59.5 + - - +
269A THR* 3.2 3.6 + - - -
270A HIS* 2.9 27.0 + - - +
291A ILE* 4.1 11.5 - - + +
294A SER* 3.8 7.9 - - - -
295A ALA* 3.4 38.6 - - + +
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Residues in contact with GLN 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A VAL* 2.8 33.2 + - + +
198A LYS 2.9 21.8 + - - -
199A TRP 3.7 10.0 - - - +
201A LEU* 3.5 38.6 - - + +
203A VAL* 6.1 0.6 - - + +
218A ILE* 4.1 13.0 - - + -
222A ILE* 4.0 8.7 - - - -
263A ALA 3.0 14.7 + - - +
264A ASP* 3.8 10.1 - - - +
266A VAL* 1.3 79.5 - - - +
268A SER* 1.3 69.5 + - - +
270A HIS* 3.2 4.0 - - - +
271A VAL* 3.0 39.8 + - - +
421A LYS* 5.0 0.5 + - - -
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Residues in contact with SER 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A TRP* 3.7 23.2 - - - -
264A ASP* 2.8 18.4 + - - -
265A VAL* 3.8 4.5 - - - -
267A GLN* 1.3 77.3 + - - +
269A THR* 1.3 61.8 + - - +
271A VAL* 3.1 3.8 + - - +
272A LEU* 2.8 34.5 + - - +
414A ALA* 3.9 16.8 - - - -
417A SER* 3.7 3.4 + - - -
421A LYS* 3.1 26.9 + - - -
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Residues in contact with THR 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A VAL 2.9 16.2 + - - -
266A VAL 3.5 4.7 - - - -
268A SER* 1.3 76.2 - - - +
270A HIS* 1.3 57.4 + - - +
272A LEU* 3.2 6.8 + - - +
273A LEU* 2.8 49.5 + - + +
290A ALA* 4.1 19.1 - - + +
291A ILE* 4.5 3.6 - - + +
294A SER* 2.8 27.1 + - - +
410A MET* 4.3 8.7 - - - -
411A VAL* 4.0 8.8 - - + +
414A ALA* 3.4 16.2 - - - +
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Residues in contact with HIS 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A VAL* 3.4 24.6 - - + +
197A ASN* 2.8 28.2 + - - +
222A ILE* 3.3 39.5 - - + +
225A GLU* 4.1 15.0 - - + +
226A ARG* 2.9 65.5 + - + +
266A VAL 2.9 13.2 + - - +
267A GLN 3.2 9.6 - - - +
269A THR* 1.3 78.7 - - - +
271A VAL* 1.3 62.8 + - + +
273A LEU* 3.5 6.9 + - - -
274A SER* 3.3 9.3 + - - -
291A ILE* 5.0 4.0 - - + +
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Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A VAL 4.0 4.5 - - - +
197A ASN* 3.8 26.2 - - - +
198A LYS 4.0 3.4 - - - +
199A TRP* 3.7 30.3 - - + +
267A GLN* 3.0 38.2 + - - +
268A SER 3.1 6.0 + - - +
270A HIS* 1.3 74.5 - - + +
272A LEU* 1.3 68.1 + - + +
274A SER* 3.0 20.6 + - - -
275A THR* 3.5 4.9 + - - -
492A ILE* 6.2 0.7 - - + -
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Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A TRP* 4.0 17.7 - - + -
268A SER 2.8 19.9 + - - +
269A THR 3.7 3.6 - - - +
271A VAL* 1.3 76.9 - - + +
273A LEU* 1.3 63.6 + - - +
275A THR* 3.0 30.7 + - - +
410A MET* 3.7 46.1 - - + +
413A CYS* 4.2 4.0 - - + -
414A ALA* 4.2 11.9 - - + +
478A TRP* 4.0 28.5 - - + -
481A TRP* 4.1 19.9 - - + +
492A ILE* 4.6 7.6 - - + -
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Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ARG* 3.5 17.3 - - - +
269A THR* 2.8 25.0 + - + +
270A HIS* 4.6 0.2 - - - -
271A VAL 3.2 0.2 - - - -
272A LEU* 1.3 76.0 - - - +
274A SER* 1.3 59.5 + - - +
275A THR 3.2 4.2 + - - +
278A LEU* 4.3 14.6 - - - +
282A PHE* 4.2 14.8 - - + -
287A ILE* 3.8 33.4 - - + +
290A ALA* 4.4 3.1 - - + -
291A ILE* 3.8 31.4 - - + -
407A LEU* 4.1 16.4 - - + -
410A MET* 3.6 28.5 - - + -
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Residues in contact with SER 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ARG* 2.9 22.2 + - - +
270A HIS* 3.3 8.8 + - - -
271A VAL* 3.0 15.0 + - - -
273A LEU* 1.3 76.6 - - - +
275A THR* 1.3 66.5 + - - +
276A PRO* 3.3 5.5 - - - +
279A 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
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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