Contacts of the helix formed by residues 344 - 367 (chain A) in PDB entry 3KMR
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 GLN 344 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A LEU* 5.1 0.7 - - + +
253A THR* 3.8 21.3 + - + +
256A ASP* 2.9 15.6 + - - +
342A LEU* 4.7 0.7 - - - -
343A GLU* 1.3 88.0 - - + +
345A PRO* 1.4 63.1 - - - +
346A ASP 3.4 2.9 - - - -
347A ARG* 2.7 51.0 + - + +
348A VAL* 3.3 23.0 + - + +
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Residues in contact with PRO 345 (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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337A GLY* 3.4 23.2 - - - +
339A ARG 5.7 0.4 - - - +
342A LEU* 3.7 26.6 - - + +
343A GLU 3.5 9.0 - - - +
344A GLN* 1.4 89.0 - - - +
346A ASP* 1.3 63.1 + - - +
348A VAL* 3.2 4.6 + - + +
349A ASP* 3.0 33.4 + - - +
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Residues in contact with ASP 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A GLN 3.4 1.0 - - - -
345A PRO* 1.3 82.9 - - - +
347A ARG* 1.3 58.0 + - - +
349A ASP* 3.2 17.2 + - - +
350A MET* 2.9 41.6 + - + +
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Residues in contact with ARG 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A THR* 3.1 40.4 + - - -
252A LEU* 3.9 21.5 - - + +
253A THR* 4.5 4.6 - - - +
344A GLN* 2.7 60.3 + - + +
345A PRO 3.3 0.4 - - - -
346A ASP* 1.3 78.6 - - - +
348A VAL* 1.3 56.5 + - - +
350A MET* 3.4 9.7 + - + +
351A LEU* 3.0 27.7 + - - +
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Residues in contact with VAL 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A LEU* 4.3 23.1 - - + -
256A ASP* 4.7 4.7 - - + +
260A LEU* 4.2 11.2 - - + -
335A ILE* 3.6 14.0 - - + +
336A CYS 3.4 41.7 - - - +
337A GLY* 3.9 3.1 - - - -
342A LEU* 4.2 17.7 - - + -
344A GLN* 3.4 14.8 - - + +
345A PRO 3.2 7.9 + - - +
347A ARG* 1.3 73.7 - - - +
349A ASP* 1.3 65.0 + - - +
351A LEU* 3.2 5.4 + - - +
352A GLN* 3.0 20.3 + - - +
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Residues in contact with ASP 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A GLY* 3.2 26.1 + - - +
338A ASP 4.5 0.2 + - - -
345A PRO* 3.0 18.7 + - - +
346A ASP* 3.3 21.9 - - - +
348A VAL* 1.3 75.3 - - - +
350A MET* 1.3 63.4 + - + +
352A GLN* 3.3 16.0 + - - +
353A GLU* 3.2 26.4 + - - +
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Residues in contact with MET 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ASP* 2.9 28.9 + - + +
347A ARG* 3.5 11.7 - - + +
348A VAL 3.2 0.2 - - - -
349A ASP* 1.3 77.3 - - - +
351A LEU* 1.3 61.2 + - - +
353A GLU* 3.4 27.2 + - - +
354A PRO* 3.1 18.9 - - - +
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Residues in contact with LEU 351 (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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247A PRO* 3.5 21.5 - - + +
248A GLY* 3.7 34.1 - - - +
249A PHE* 3.9 4.7 - - - +
251A THR* 5.6 0.7 - - - +
252A LEU* 4.4 15.5 - - + -
335A ILE* 3.9 27.1 - - + -
347A ARG 3.0 13.6 + - - +
348A VAL* 3.2 8.5 + - - +
350A MET* 1.3 75.7 - - - +
352A GLN* 1.3 61.1 + - - +
354A PRO* 3.2 15.8 - - + +
355A LEU* 4.1 11.3 - - + +
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Residues in contact with GLN 352 (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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332A ILE* 3.1 45.1 + - + +
335A ILE* 3.0 27.8 + - + +
336A CYS* 4.1 13.9 - - - +
337A GLY 5.1 0.3 + - - -
348A VAL 3.0 8.8 + - - +
349A ASP* 3.3 19.0 + - - +
351A LEU* 1.3 76.7 - - - +
353A GLU* 1.3 65.1 + - - +
355A LEU* 2.9 18.1 + - + +
356A LEU* 3.2 29.0 + - + +
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Residues in contact with GLU 353 (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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349A ASP* 3.2 19.6 + - + +
350A MET* 3.5 26.6 - - - +
352A GLN* 1.3 76.8 - - - +
354A PRO* 1.4 69.8 - - + +
356A LEU* 3.2 13.2 + - + +
357A GLU* 3.1 22.0 + - - +
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Residues in contact with PRO 354 (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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184A VAL* 6.1 0.2 - - - +
187A LEU* 3.3 21.7 - - + +
350A MET 3.1 17.3 - - - +
351A LEU* 3.2 16.6 - - + +
353A GLU* 1.4 91.9 - - + +
355A LEU* 1.3 56.2 + - + +
357A GLU* 3.8 14.6 - - + +
358A ALA* 2.9 30.1 + - - +
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Residues in contact with LEU 355 (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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187A LEU* 3.9 26.2 - - + -
191A VAL* 4.0 19.1 - - + -
246A LEU* 5.6 1.8 - - + -
247A PRO* 5.8 1.8 - - + -
328A LEU* 4.1 12.1 - - + +
331A ALA* 3.8 36.6 - - + +
332A ILE* 3.8 17.8 - - + +
335A ILE* 4.0 19.3 - - + -
351A LEU* 4.1 13.9 - - + +
352A GLN* 2.9 15.4 + - - +
354A PRO* 1.3 74.0 - - + +
356A LEU* 1.3 61.3 + - - +
358A ALA* 3.3 4.8 + - - +
359A LEU* 2.9 31.0 + - - +
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Residues in contact with LEU 356 (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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332A ILE* 3.8 26.0 - - + -
352A GLN* 3.2 34.4 + - + +
353A GLU* 3.7 13.5 - - + +
355A LEU* 1.3 74.0 - - - +
357A GLU* 1.3 65.0 + - - +
359A LEU* 3.5 0.4 + - - -
360A LYS* 3.1 24.7 + - - +
374A PHE* 3.6 12.8 - - + -
378A LEU* 3.8 29.8 - - + -
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Residues in contact with GLU 357 (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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184A VAL* 4.2 20.8 - - + +
353A GLU 3.1 15.5 + - - +
354A PRO* 3.8 12.3 - - + +
356A LEU* 1.3 77.6 - - - +
358A ALA* 1.3 61.6 + - - +
360A LYS* 3.2 19.1 + - - +
361A VAL* 3.1 36.5 + - + +
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Residues in contact with ALA 358 (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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184A VAL* 3.9 16.7 - - + +
187A LEU* 3.8 17.0 - - + -
188A ILE* 3.7 19.9 - - + +
328A LEU* 4.3 10.1 - - + -
354A PRO 2.9 19.3 + - - +
355A LEU* 3.3 6.7 + - - +
357A GLU* 1.3 76.1 - - - +
359A LEU* 1.3 61.4 + - - +
361A VAL* 3.3 3.8 - - - +
362A TYR* 3.1 25.5 + - - +
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Residues in contact with LEU 359 (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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325A GLU* 4.1 17.5 - - + +
328A LEU* 3.8 33.8 - - + +
329A LEU* 4.4 19.5 - - + +
332A ILE* 3.8 23.6 - - + -
355A LEU 2.9 17.1 + - - +
356A LEU 3.9 3.8 - - - +
358A ALA* 1.3 73.0 - - - +
360A LYS* 1.3 66.9 + - - +
362A TYR* 3.3 1.7 + - + -
363A VAL* 3.0 51.3 + - + +
374A PHE* 3.8 20.2 - - + -
377A MET* 4.1 11.9 - - + -
378A LEU* 4.8 3.4 - - + -
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Residues in contact with LYS 360 (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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356A LEU 3.1 17.4 + - - +
357A GLU* 3.2 19.2 + - - +
359A LEU* 1.3 77.7 - - - +
361A VAL* 1.3 66.0 + - + +
364A ARG* 2.9 55.6 + - - +
374A PHE* 3.6 35.8 - - + -
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Residues in contact with VAL 361 (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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184A VAL* 3.4 28.7 - - + -
188A ILE* 4.5 3.4 - - + -
357A GLU* 3.1 22.4 + - + +
358A ALA 3.3 15.9 - - - +
360A LYS* 1.3 81.8 - - + +
362A TYR* 1.3 62.5 + - - +
364A ARG* 3.9 3.5 + - - +
365A LYS* 3.3 22.2 + - - +
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Residues in contact with TYR 362 (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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188A ILE* 3.8 27.8 - - + -
192A ARG* 3.1 32.5 + - - -
322A ASP* 2.6 34.8 + - - -
324A ALA* 3.6 10.0 - - + +
325A GLU* 3.6 20.2 - - + -
328A LEU* 4.8 4.9 - - + -
358A ALA 3.1 19.8 + - - +
359A LEU* 3.8 4.5 - - - +
361A VAL* 1.3 77.6 - - - +
363A VAL* 1.3 59.4 + - + +
365A LYS* 3.3 17.3 + - + +
366A ARG* 3.0 52.8 + - + +
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Residues in contact with VAL 363 (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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325A GLU* 3.8 17.5 - - + +
359A LEU* 3.0 33.7 + - + +
360A LYS 4.2 2.5 - - - +
362A TYR* 1.3 75.8 - - - +
364A ARG* 1.3 61.9 + - - +
366A ARG* 3.6 1.2 + - - +
367A ARG* 2.9 31.7 + - - +
370A ARG 5.2 0.9 - - - +
373A MET* 3.6 36.3 - - + -
374A PHE* 4.0 17.0 - - + +
377A MET* 3.6 26.2 - - + -
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Residues in contact with ARG 364 (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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360A LYS* 2.9 46.0 + - - +
361A VAL* 4.5 3.4 - - - +
362A TYR 3.3 0.2 - - - -
363A VAL* 1.3 78.4 - - - +
365A LYS* 1.3 63.8 + - - +
367A ARG 3.9 7.9 - - - +
368A PRO* 3.2 26.3 - - + +
370A ARG 5.0 1.1 + - - +
371A PRO* 3.5 39.4 + - + +
374A PHE* 3.4 37.3 - - - +
375A PRO* 4.3 4.2 - - - +
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Residues in contact with LYS 365 (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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361A VAL 3.3 16.3 + - - +
362A TYR* 3.3 21.1 + - + +
364A ARG* 1.3 79.5 - - - +
366A ARG* 1.3 65.6 + - + +
368A PRO* 3.6 10.0 - - - +
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Residues in contact with ARG 366 (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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320A GLU* 3.4 13.1 + - - +
322A ASP* 3.2 33.2 + - - +
325A GLU* 2.8 42.5 + - - +
362A TYR* 3.0 34.5 + - + +
363A VAL 3.9 2.7 - - - +
365A LYS* 1.3 79.0 - - + +
367A ARG* 1.3 84.9 + - + +
368A PRO* 3.4 7.5 - - - +
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Residues in contact with ARG 367 (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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319A LEU 2.9 27.6 + - - -
320A GLU* 2.9 19.0 + - - +
321A MET* 3.8 1.0 - - - +
325A GLU* 2.8 42.4 + - - -
363A VAL* 2.9 23.8 + - - +
364A ARG* 3.5 8.1 - - - +
366A ARG* 1.3 91.5 - - + +
368A PRO* 1.3 65.5 - - - +
369A SER* 3.2 4.5 - - - +
370A ARG* 3.3 44.2 + - + +
373A MET* 3.8 29.8 - - + +
377A MET* 3.7 12.5 - - - +
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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