Contacts of the helix formed by residues 290 - 305 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B GLN* 5.6 0.7 - - - -
288B ASN 3.7 1.7 + - - -
289B MET* 1.3 77.7 - - - +
291B GLU* 1.3 77.1 + - - +
292B ILE* 3.2 16.9 + - - +
293B GLU* 3.1 16.6 + - - +
294B ALA* 2.9 22.3 + - - +
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Residues in contact with GLU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B GLN 4.9 4.0 + - - +
245B ILE* 3.8 32.8 - - + +
248B GLY* 6.3 1.8 - - - -
289B MET 4.0 0.6 + - - -
290B SER* 1.3 82.3 - - - +
292B ILE* 1.3 68.7 + - + +
294B ALA* 3.2 7.3 + - - +
295B LYS* 3.0 35.0 + - - +
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Residues in contact with ILE 292 (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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746A LEU 5.7 0.4 - - - +
749A GLU* 6.1 6.1 - - + -
209B PRO* 5.2 18.2 - - + -
212B LEU* 3.4 18.6 - - + +
290B SER* 3.1 9.3 + - - +
291B GLU* 1.3 87.0 + - + +
293B GLU* 1.3 72.9 + - + +
295B LYS* 3.3 14.1 + - + +
296B VAL* 3.2 23.4 + - + +
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Residues in contact with GLU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746A LEU 5.2 2.3 - - - +
747A TYR* 6.1 0.7 - - - -
289B MET* 4.0 19.1 - - + +
290B SER* 3.1 13.2 + - - +
292B ILE* 1.3 81.4 - - + +
294B ALA* 1.3 66.7 + - - +
296B VAL* 3.9 17.7 - - - +
297B ARG* 3.2 38.6 + - + +
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Residues in contact with ALA 294 (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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241B TYR* 3.5 17.1 - - + -
244B GLN* 4.3 15.0 - - + -
245B ILE* 3.4 21.5 - - + -
289B MET* 3.7 20.1 - - - +
290B SER 2.9 12.2 + - - +
291B GLU* 3.3 11.0 - - - +
293B GLU* 1.3 78.0 - - - +
295B LYS* 1.3 56.5 + - - +
297B ARG 3.6 0.2 + - - -
298B TYR* 3.0 28.9 + - - +
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Residues in contact with LYS 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B PRO 5.4 1.4 + - - +
212B LEU* 3.9 21.3 - - + -
213B ASN* 2.7 38.6 + - - +
216B TYR* 3.8 24.4 - - + +
245B ILE* 3.2 38.7 - - + +
291B GLU* 3.0 21.6 + - - +
292B ILE* 3.3 13.5 - - + +
294B ALA* 1.3 75.9 - - - +
296B VAL* 1.3 65.1 + - - +
298B TYR* 3.2 5.6 + - - +
299B VAL* 2.9 27.2 + - - +
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Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746A LEU* 3.0 52.8 - - + +
747A TYR* 5.2 5.2 - - + -
212B LEU* 3.5 22.0 - - + -
292B ILE* 3.2 18.7 + - + +
293B GLU* 3.4 21.3 + - - +
295B LYS* 1.3 74.5 - - - +
297B ARG* 1.3 57.9 + - + +
299B VAL* 3.0 6.6 + - - +
300B LYS* 2.7 40.0 + - + +
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Residues in contact with ARG 297 (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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241B TYR* 3.9 29.6 + - + +
289B MET* 5.6 4.0 - - + -
293B GLU* 3.2 26.4 + - + +
296B VAL* 1.3 82.2 - - + +
298B TYR* 1.3 57.0 + - - +
300B LYS* 3.7 26.1 - - - +
301B LEU* 2.8 30.7 + - - +
371D GLY 3.4 22.1 + - - -
372D ASP* 3.4 22.2 + - - +
373D TYR* 3.5 23.8 - - - +
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Residues in contact with TYR 298 (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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216B TYR* 3.5 27.6 - + + -
219B ALA* 4.6 7.6 - - + -
220B ARG* 3.6 41.6 + - + +
223B ILE* 4.6 9.3 - - + +
224B LEU* 5.1 2.9 - - - +
238B PHE* 3.3 56.0 - + + +
241B TYR* 3.6 29.6 - - + -
242B GLN* 4.3 9.7 + - + -
294B ALA 3.0 19.5 + - - +
295B LYS* 3.3 9.9 - - - +
296B VAL 3.1 0.2 - - - -
297B ARG* 1.3 75.7 - - - +
299B VAL* 1.3 60.7 + - - +
301B LEU* 3.3 5.2 + - - +
302B ALA* 3.1 23.9 + - + +
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Residues in contact with VAL 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746A LEU* 5.2 6.5 - - + -
212B LEU* 4.9 4.7 - - + +
215B LEU* 3.4 16.6 - - + +
216B TYR* 3.4 39.7 - - + +
219B ALA* 4.2 7.6 - - + -
295B LYS 2.9 13.2 + - - +
296B VAL* 3.6 8.7 - - - +
298B TYR* 1.3 76.7 - - + +
300B LYS* 1.3 59.7 + - - +
302B ALA* 3.8 7.0 - - - +
303B ARG* 3.1 59.1 + - + +
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Residues in contact with LYS 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746A LEU* 4.1 8.7 - - + -
747A TYR* 3.5 15.0 + - - -
296B VAL* 2.7 26.9 + - + +
297B ARG* 3.8 29.0 - - - +
298B TYR 3.2 0.2 - - - -
299B VAL* 1.3 72.3 - - - +
301B LEU* 1.3 63.0 + - - +
303B ARG* 3.6 6.0 + - - +
304B SER* 3.2 19.2 + - - -
355D ASN* 3.2 50.6 + - - +
370D PHE* 3.2 30.6 + - - +
371D GLY 4.0 12.3 + - - -
372D ASP* 5.2 2.8 - - - +
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Residues in contact with LEU 301 (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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234B LYS* 4.1 24.0 - - + +
237B GLU* 4.0 30.7 - - + +
238B PHE* 3.5 34.3 - - + -
241B TYR* 4.5 12.6 - - + +
297B ARG 2.8 17.1 + - - +
298B TYR* 3.6 4.7 - - - +
300B LYS* 1.3 76.3 - - - +
302B ALA* 1.3 64.7 + - - +
304B SER* 2.5 36.3 + - - +
305B LEU* 3.5 4.8 + - + +
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Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B ALA* 4.3 21.8 - - + -
223B ILE* 4.8 3.1 - - + -
228B HIS* 3.2 32.0 - - + +
238B PHE* 3.7 19.9 - - + -
298B TYR* 3.1 14.3 + - + +
299B VAL* 3.8 6.5 - - + +
300B LYS 3.4 0.2 - - - -
301B LEU* 1.3 81.5 - - - +
303B ARG* 1.3 60.0 + - + +
305B LEU* 3.8 4.3 + - - +
308B TYR* 3.4 13.8 - - + +
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Residues in contact with ARG 303 (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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746A LEU* 3.9 13.9 - - - +
215B LEU* 3.8 30.7 - - - +
299B VAL* 3.1 41.5 + - + +
300B LYS* 3.9 4.7 - - - +
301B LEU 3.1 0.6 - - - -
302B ALA* 1.3 75.1 - - + +
304B SER* 1.3 69.3 + - - +
305B LEU 3.3 7.8 + - - +
308B TYR* 4.0 39.8 + - + +
352D SER* 4.8 14.4 + - - +
354D THR* 2.9 48.8 + - - +
355D ASN* 4.4 12.1 - - - +
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Residues in contact with SER 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LYS* 5.3 1.4 + - - -
300B LYS 3.2 12.0 + - - -
301B LEU* 2.5 33.6 + - - +
303B ARG* 1.3 78.6 - - - +
305B LEU* 1.3 76.7 + - - +
306B LYS* 3.4 2.9 + - - +
352D SER* 5.5 3.4 - - - -
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Residues in contact with LEU 305 (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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228B HIS* 3.8 15.5 - - + +
230B VAL* 3.6 34.8 - - + -
234B LYS* 4.3 29.2 - - + -
238B PHE* 4.2 18.8 - - + -
301B LEU* 3.5 4.2 + - + +
302B ALA 3.9 3.1 - - - +
303B ARG 3.3 2.8 - - - +
304B SER* 1.3 93.3 + - - +
306B LYS* 1.3 59.5 + - - +
307B THR* 3.0 21.2 + - + +
308B TYR* 3.2 18.0 + - - +
323H ASN* 5.9 4.7 - - - +
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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