Contacts of the helix formed by residues 231 - 248 (chain H) 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 231 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230H VAL* 1.3 72.7 - - - +
232H PHE* 1.3 66.4 + - - +
233H ASP* 4.0 6.3 + - - +
234H LYS* 3.0 25.6 + - - +
235H ALA* 2.8 20.6 + - - +
270H TYR* 3.0 8.1 - - - -
343H LYS 4.8 1.6 - - - -
344H THR* 3.6 25.8 - - - -
345H LYS* 4.2 5.2 - - - +
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Residues in contact with PHE 232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B GLN* 3.3 26.7 - - + +
231H SER* 1.3 70.8 - - - +
233H ASP* 1.3 75.5 + - - +
235H ALA* 2.9 13.5 + - - +
236H CYS* 3.0 21.2 + - - -
266H LEU* 5.9 0.7 - - + -
270H TYR* 2.8 57.4 + + + -
273H GLN* 3.5 33.2 - - + +
275H GLY* 3.5 28.3 - - - -
278H LYS* 3.1 34.5 - - + -
343H LYS 5.4 0.2 + - - -
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Residues in contact with ASP 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D ASN* 3.4 38.4 - - - +
231H SER* 3.3 7.9 + - - +
232H PHE* 1.3 81.3 - - - +
234H LYS* 1.3 60.8 + - + +
236H CYS* 2.8 21.8 + - - +
237H GLU* 3.0 11.2 + - - +
278H LYS* 3.0 34.4 + - - +
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Residues in contact with LYS 234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D MET* 4.0 27.8 - - - +
285D ASN* 4.0 23.8 + - - +
230H VAL* 4.4 7.9 - - + -
231H SER* 3.0 21.7 + - - +
233H ASP* 1.3 78.0 - - + +
235H ALA* 1.3 64.7 + - - +
237H GLU* 2.9 37.6 + - - +
238H PHE* 3.0 31.5 + - + -
301H LEU* 4.3 21.1 - - + +
305H LEU* 4.4 19.3 - - + -
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Residues in contact with ALA 235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223H ILE* 5.5 1.9 - - - +
230H VAL* 4.1 8.7 - - + +
231H SER 2.8 16.2 + - - +
232H PHE 3.1 11.9 - - - +
234H LYS* 1.3 73.1 - - - +
236H CYS* 1.3 55.2 + - - +
238H PHE* 3.5 13.0 + - - +
239H ALA* 3.2 19.4 + - - +
265H PHE 4.4 2.3 - - - +
266H LEU* 3.6 14.3 - - + +
267H PRO* 4.0 13.7 - - + +
270H TYR* 3.6 30.5 - - + -
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Residues in contact with CYS 236 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232H PHE* 3.0 45.8 + - - -
233H ASP 2.8 11.0 + - - +
235H ALA* 1.3 76.7 - - - +
237H GLU* 1.3 58.2 + - - +
238H PHE 3.2 0.7 - - - -
239H ALA* 3.3 2.8 + - - +
240H GLY* 2.9 24.1 + - - -
266H LEU* 4.0 19.7 - - - -
275H GLY* 4.5 2.0 - - - -
278H LYS* 4.0 29.8 - - + +
279H ILE* 4.0 15.5 - - + +
282H ALA* 3.9 6.0 - - - +
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Residues in contact with GLU 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D LYS* 4.4 17.4 - - - -
285D ASN* 5.1 3.8 - - - +
233H ASP 3.0 9.7 + - - +
234H LYS* 2.9 38.6 + - - +
236H CYS* 1.3 76.3 - - - +
238H PHE* 1.3 62.1 + - - +
240H GLY* 3.0 10.4 + - - -
241H TYR* 3.1 32.8 + - + -
282H ALA* 4.0 14.9 - - + +
301H LEU* 3.4 27.9 - - + +
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Residues in contact with PHE 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223H ILE* 3.5 27.4 - - + -
230H VAL* 4.0 16.4 - - + -
234H LYS* 3.0 38.6 + - + -
235H ALA* 3.6 11.0 - - - +
236H CYS 3.2 0.2 - - - -
237H GLU* 1.3 77.5 - - - +
239H ALA* 1.3 57.3 + - - +
241H TYR* 3.0 3.3 + + - -
242H GLN* 2.7 25.8 + - - +
265H PHE 5.9 0.4 - - - +
298H TYR* 3.3 58.2 - + - +
301H LEU* 3.4 38.8 - - + -
302H ALA* 3.7 10.3 - - - -
305H LEU* 3.7 17.3 - - + -
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Residues in contact with ALA 239 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235H ALA 3.2 8.7 + - - +
236H CYS 3.3 2.4 + - - +
238H PHE* 1.3 78.9 - - - +
240H GLY* 1.3 56.2 + - - +
242H GLN* 3.5 10.4 - - - +
243H CYS* 2.9 35.5 + - - -
265H PHE* 3.5 30.0 + - + +
266H LEU* 4.2 0.2 - - + -
279H ILE* 3.5 37.0 - - + -
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Residues in contact with GLY 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236H CYS 2.9 14.7 + - - -
237H GLU 3.3 6.1 - - - -
238H PHE 3.0 0.6 - - - -
239H ALA* 1.3 79.9 - - - +
241H TYR* 1.3 61.1 + - - +
243H CYS 3.8 0.2 + - - -
244H GLN* 3.5 16.6 + - - +
279H ILE 3.8 10.3 - - - -
282H ALA* 3.7 19.7 - - - -
283H HIS* 3.6 18.6 - - - +
286H CYS* 4.0 1.9 - - - -
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Residues in contact with TYR 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237H GLU* 3.1 30.2 + - + -
238H PHE 3.0 7.2 + - - +
240H GLY* 1.3 75.9 - - - +
242H GLN* 1.3 67.1 + - - +
243H CYS 3.2 0.4 - - - -
244H GLN* 3.2 2.9 + - + +
245H ILE* 2.9 30.4 + - + +
286H CYS* 3.9 24.9 - - - -
289H MET* 4.0 6.0 - - + +
294H ALA* 4.0 23.6 - - + +
297H ARG* 3.7 49.0 + - + +
298H TYR* 3.7 29.2 - + + -
301H LEU* 4.3 17.5 - - + -
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Residues in contact with GLN 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216H TYR* 3.7 20.9 - - - +
220H ARG* 3.6 27.4 + - - +
224H LEU* 3.8 10.7 - - - +
238H PHE* 2.7 14.3 + - - +
239H ALA* 3.2 7.1 + - - +
241H TYR* 1.3 76.5 - - - +
243H CYS* 1.3 57.1 + - - +
245H ILE* 3.4 1.6 + - - +
246H GLN* 2.8 45.6 + - + +
264H ASP* 3.2 16.5 + - - +
265H PHE* 3.3 49.9 + - + +
298H TYR* 4.5 6.2 + - + -
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Residues in contact with CYS 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239H ALA 2.9 25.0 + - - +
240H GLY 3.9 1.6 - - - +
241H TYR 3.2 0.2 - - - -
242H GLN* 1.3 74.8 - - - +
244H GLN* 1.3 58.7 + - - +
247H PHE* 2.5 49.2 + - + +
248H GLY 3.6 0.5 + - - +
259H PHE* 6.0 0.4 - - - -
260H LEU* 3.6 31.4 - - - -
265H PHE* 3.9 5.2 - - - -
279H ILE* 3.7 14.6 - - - -
280H PHE* 4.8 4.5 - - - -
283H HIS* 3.4 31.4 - - + +
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Residues in contact with GLN 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240H GLY 3.5 10.0 + - - +
241H TYR* 3.2 9.5 + - - +
243H CYS* 1.3 77.7 - - - +
245H ILE* 1.3 60.7 + - - +
248H GLY* 2.9 28.0 + - - -
249H PRO* 3.4 32.9 - - - +
283H HIS* 3.0 23.3 + - - +
286H CYS* 2.8 36.3 - - + +
287H GLY 3.9 2.7 + - - +
289H MET* 3.0 36.9 + - + +
290H SER 4.6 1.6 - - - +
291H GLU* 5.1 4.4 + - - +
294H ALA* 4.1 19.1 - - + -
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Residues in contact with ILE 245 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216H TYR* 3.3 44.9 - - + +
241H TYR* 2.9 20.5 + - + +
242H GLN 3.7 3.4 - - - +
244H GLN* 1.3 78.3 - - - +
246H GLN* 1.3 62.2 + - + +
248H GLY 4.6 0.9 + - - -
291H GLU* 4.0 31.6 - - + +
294H ALA* 3.4 19.7 - - + +
295H LYS* 3.7 45.1 - - + +
298H TYR* 4.8 0.2 - - + -
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Residues in contact with GLN 246 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216H TYR* 6.1 0.2 - - - +
242H GLN* 2.8 31.7 + - + +
245H ILE* 1.3 78.2 - - + +
247H PHE* 1.3 86.7 + - + +
248H GLY 3.7 0.7 - - - -
265H PHE* 2.8 34.4 - - - -
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Residues in contact with PHE 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243H CYS* 2.5 38.4 + - + +
246H GLN* 1.3 104.0 - - + +
248H GLY* 1.3 64.8 + - - +
249H PRO 4.1 2.9 - - - +
255H HIS* 3.8 21.4 + + + +
259H PHE* 3.5 36.8 - + - -
260H LEU* 4.0 12.1 - - + -
265H PHE* 3.5 28.9 - + - -
283H HIS* 4.7 1.6 - + + -
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Residues in contact with GLY 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244H GLN* 2.9 22.1 + - - -
245H ILE 4.6 0.8 + - - -
246H GLN 3.7 1.0 - - - -
247H PHE* 1.3 83.3 - - - +
249H PRO* 1.3 79.2 - - - +
283H HIS* 3.2 15.1 + - - -
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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