Contacts of the helix formed by residues 290 - 304 (chain D) in PDB entry 1MK9
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 SER 290 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288D ASN 3.4 3.9 + - - -
289D MET* 1.3 79.6 - - - +
291D GLU* 1.3 59.6 + - - +
292D ILE* 3.3 7.5 + - - +
293D GLU* 2.6 47.6 + - - +
294D ALA* 3.0 29.5 + - - +
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Residues in contact with GLU 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D GLN 4.8 4.0 + - - +
245D ILE* 2.5 50.1 - - + +
246D GLN* 4.7 1.6 - - - -
289D MET 3.9 0.4 + - - -
290D SER* 1.3 73.4 - - - +
292D ILE* 1.3 64.4 + - + +
294D ALA* 4.7 0.4 - - - -
295D LYS* 2.8 40.6 + - - +
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Residues in contact with ILE 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746C LEU 6.0 0.4 - - - +
209D PRO* 5.1 17.7 - - + +
212D LEU* 3.2 24.9 - - + -
290D SER* 3.3 6.5 + - - +
291D GLU* 1.3 83.8 - - + +
293D GLU* 1.3 63.1 + - + +
294D ALA 3.0 5.2 - - - -
295D LYS* 3.1 24.8 + - + +
296D VAL* 3.1 30.8 + - + +
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Residues in contact with GLU 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746C LEU 5.6 1.4 - - - +
289D MET* 4.0 16.8 - - + -
290D SER* 2.6 31.5 + - - +
292D ILE* 1.3 77.9 - - + +
294D ALA* 1.3 57.5 + - - +
296D VAL* 3.8 16.6 - - - +
297D ARG* 3.1 32.9 + - - +
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Residues in contact with ALA 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D TYR* 4.2 9.6 - - + +
244D GLN* 4.2 15.5 - - + -
245D ILE* 3.8 22.4 - - + -
289D MET* 3.7 18.8 - - - -
290D SER 3.0 16.9 + - - +
291D GLU* 4.0 0.7 - - - +
293D GLU* 1.3 76.9 - - - +
295D LYS* 1.3 66.1 + - - +
296D VAL 3.1 1.3 - - - -
297D ARG* 3.2 3.7 + - - +
298D TYR* 2.9 25.6 + - - +
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Residues in contact with LYS 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D PRO 5.9 0.2 - - - +
212D LEU* 4.0 19.7 - - + -
213D ASN* 3.3 32.2 + - + +
216D TYR* 4.1 21.9 - - + +
245D ILE* 3.4 36.7 - - + +
291D GLU* 2.8 33.5 + - - +
292D ILE* 3.1 24.4 + - + +
294D ALA* 1.3 77.8 - - - +
296D VAL* 1.3 63.3 + - - +
298D TYR* 3.4 1.9 + - - +
299D VAL* 3.1 30.5 + - - +
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Residues in contact with VAL 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746C LEU* 3.4 42.2 - - + +
747C TYR* 5.2 4.3 - - + -
212D LEU* 3.8 24.2 - - + -
292D ILE* 3.1 19.4 + - + +
293D GLU* 3.8 19.1 - - - +
294D ALA 3.1 0.2 - - - -
295D LYS* 1.3 74.1 - - - +
297D ARG* 1.3 71.6 + - + +
299D VAL* 2.9 16.5 + - - +
300D LYS* 2.9 27.8 + - + +
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Residues in contact with ARG 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373B TYR* 5.7 8.7 - - - +
241D TYR* 4.0 26.9 + - + +
289D MET* 3.2 39.6 - - - +
293D GLU* 3.1 16.6 + - - +
294D ALA* 3.2 7.3 + - - +
296D VAL* 1.3 83.7 - - + +
298D TYR* 1.3 52.2 + - - +
300D LYS* 3.0 9.7 + - - +
301D LEU* 2.8 35.3 + - - +
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Residues in contact with TYR 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D TYR* 3.9 25.8 - + + -
219D ALA* 4.1 11.2 - - + -
220D ARG* 3.4 46.9 + - + +
223D ILE* 4.0 11.5 - - + +
224D LEU* 5.3 1.7 - - - +
238D PHE* 3.2 68.3 - + + +
241D TYR* 3.6 22.8 - - + -
242D GLN* 4.5 10.1 + - + -
294D ALA 2.9 17.5 + - - +
295D LYS* 3.5 5.8 - - - +
297D ARG* 1.3 76.9 - - - +
299D VAL* 1.3 57.8 + - - +
301D LEU* 4.5 1.6 - - - -
302D ALA* 3.0 23.0 + - - +
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Residues in contact with VAL 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746C LEU* 4.7 9.9 - - + -
212D LEU* 4.9 4.9 - - + +
215D LEU* 4.0 16.2 - - + +
216D TYR* 3.6 34.5 - - + +
219D ALA* 4.7 6.1 - - + -
295D LYS 3.1 15.4 + - - +
296D VAL* 2.9 10.6 + - - +
298D TYR* 1.3 76.3 - - + +
300D LYS* 1.3 61.5 + - - +
302D ALA* 3.8 7.5 - - - +
303D ARG* 3.0 55.7 + - + +
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Residues in contact with LYS 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B ASN* 3.5 30.7 + - - +
370B PHE 3.0 15.9 + - - -
371B GLY 4.1 10.1 + - - -
372B ASP* 4.5 5.1 - - - +
746C LEU* 4.2 11.4 - - + -
747C TYR* 3.0 34.8 + - - -
296D VAL* 2.9 21.2 + - + +
297D ARG* 3.0 11.0 + - - +
299D VAL* 1.3 75.6 - - - +
301D LEU* 1.3 60.4 + - - +
302D ALA 3.3 0.4 - - - -
303D ARG* 3.6 5.2 + - - +
304D SER* 3.1 29.3 + - - -
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Residues in contact with LEU 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D LYS* 4.7 11.0 - - + +
237D GLU* 3.7 47.1 - - + +
238D PHE* 3.2 36.8 - - + -
241D TYR* 4.3 10.5 - - + +
297D ARG 2.8 15.1 + - - +
298D TYR* 4.3 1.6 - - - -
300D LYS* 1.3 77.1 - - - +
302D ALA* 1.3 63.2 + - - +
304D SER* 2.9 22.4 + - - +
305D LEU* 3.4 18.5 - - + +
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Residues in contact with ALA 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D ALA* 3.8 26.9 - - + -
223D ILE* 4.6 6.5 - - + -
228D HIS* 3.3 11.5 - - + +
238D PHE* 3.7 16.1 - - + -
298D TYR 3.0 18.6 + - - +
299D VAL 3.9 5.8 - - - +
301D LEU* 1.3 78.9 - - - +
303D ARG* 1.3 52.7 + - - +
304D SER 3.5 0.2 - - - -
305D LEU* 4.1 3.2 + - - -
308D TYR* 2.7 36.7 - - + +
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Residues in contact with ARG 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B SER* 4.9 12.6 + - - +
354B THR* 2.6 55.7 + - - -
355B ASN* 3.3 19.5 + - - +
746C LEU* 3.6 14.9 - - - +
215D LEU* 3.6 29.5 - - - +
299D VAL* 3.0 38.6 + - + +
300D LYS* 4.1 3.6 - - - +
301D LEU 3.3 0.4 - - - -
302D ALA* 1.3 75.4 - - - +
304D SER* 1.3 59.6 - - - +
305D LEU 3.1 13.2 + - - +
308D TYR* 3.6 41.8 + - + +
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Residues in contact with SER 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B SER* 5.8 1.1 - - - -
300D LYS 3.1 16.0 + - - -
301D LEU* 2.9 27.9 + - - +
303D ARG* 1.3 76.6 - - - +
305D LEU* 1.3 61.9 + - - +
306D LYS 3.8 1.6 + - - -
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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