Contacts of the helix formed by residues 316 - 339 (chain C) in PDB entry 2MAK
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 TYR 316 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A ALA* 3.6 36.3 + - + +
330A LYS* 4.7 10.0 - - - +
331A ALA* 4.3 11.6 + - + +
334A GLU* 5.0 4.7 + - - -
313C ARG 3.0 24.3 + - - +
314C GLN* 3.0 20.1 - - + -
315C LYS* 1.3 79.0 - - - +
317C ALA* 1.3 68.4 + - - +
318C GLU 3.1 0.4 - - - -
319C GLU* 2.9 27.0 + - + +
320C GLU* 3.0 36.7 + - + +
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Residues in contact with ALA 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A LEU* 4.3 19.6 - - + +
331A ALA* 3.8 19.3 - - + -
350A TRP* 5.2 12.6 - - + -
354A THR* 5.3 0.9 - - + -
314C GLN 3.3 12.9 + - - +
315C LYS* 4.4 1.8 - - - +
316C TYR* 1.3 86.6 - - - +
318C GLU* 1.3 52.5 + - - +
320C GLU* 3.2 6.4 + - - +
321C LEU* 2.7 41.0 + - + +
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Residues in contact with GLU 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A LEU* 3.7 35.3 - - + +
315C LYS* 2.7 47.7 + - - +
317C ALA* 1.3 77.3 - - - +
319C GLU* 1.3 81.4 + - + +
321C LEU* 3.2 13.9 - - + +
322C GLU* 3.0 28.2 + - - +
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Residues in contact with GLU 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C LYS* 6.1 0.7 - - - +
316C TYR* 2.9 18.1 + - + +
318C GLU* 1.3 94.3 - - + +
320C GLU* 1.3 72.4 + - - +
322C GLU* 4.4 0.8 - - - +
323C GLN* 3.0 53.6 + - - +
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Residues in contact with GLU 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A GLN* 6.1 0.9 - - - +
324A VAL* 3.8 22.1 + - + +
327A ALA* 5.0 8.1 - - + +
328A LEU* 5.2 2.5 - - + -
316C TYR* 3.0 44.0 + - + +
317C ALA* 3.5 7.6 - - - +
319C GLU* 1.3 82.5 - - - +
321C LEU* 1.3 58.0 + - - +
323C GLN* 3.9 3.1 - - - +
324C VAL* 2.8 32.9 + - - +
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Residues in contact with LEU 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A VAL* 4.2 0.9 - - - -
328A LEU* 3.6 38.8 - - + -
329A ARG* 5.7 0.4 - - - +
353A LEU* 4.1 5.4 - - + +
354A THR* 3.5 38.4 - - + +
357A VAL* 3.3 30.8 - - + +
358A GLU 5.6 0.2 - - - +
317C ALA 2.7 26.2 + - - +
318C GLU* 3.2 21.3 - - + +
320C GLU* 1.3 74.3 - - - +
322C GLU* 1.3 73.7 + - - +
324C VAL* 3.1 12.3 - - + +
325C ARG* 2.9 28.6 + - - +
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Residues in contact with GLU 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A GLU* 6.2 0.2 - - - +
357A VAL* 3.8 22.3 - - + +
318C GLU 3.0 20.0 + - - +
319C GLU* 4.4 0.7 - - - +
321C LEU* 1.3 74.1 - - - +
323C GLN* 1.3 66.7 + - + +
325C ARG* 3.1 32.1 + - - +
326C GLU* 3.1 35.9 + - - +
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Residues in contact with GLN 323 (chain C).
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* 5.5 4.3 - - - +
319C GLU* 3.0 47.7 + - - +
320C GLU* 4.0 4.0 - - - +
322C GLU* 1.3 77.1 - - + +
324C VAL* 1.3 52.7 + - - +
326C GLU* 3.2 14.4 + - + +
327C ALA* 2.7 39.6 + - + +
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Residues in contact with VAL 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLU* 3.9 34.1 - - + +
321A LEU 4.0 1.1 - - - +
324A VAL* 3.8 33.7 - - + -
328A LEU* 5.9 0.9 - - + -
361A TYR* 6.3 2.7 - - + -
320C GLU 2.8 18.0 + - - +
321C LEU* 3.1 20.9 - - + +
323C GLN* 1.3 73.2 - - - +
325C ARG* 1.3 63.8 + - - +
327C ALA* 4.0 4.9 - - - -
328C LEU* 2.8 53.9 + - + +
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Residues in contact with ARG 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A GLU* 6.1 0.4 - - - +
357A VAL* 3.8 17.1 - - + +
360A GLN* 3.4 45.9 + - - +
361A TYR* 4.0 27.8 - - + +
364A ILE* 3.6 20.2 - - + +
321C LEU 2.9 15.0 + - - +
322C GLU* 3.1 40.9 + - - +
324C VAL* 1.3 76.9 - - - +
326C GLU* 1.3 62.9 + - - +
329C ARG* 3.0 37.7 + - - +
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Residues in contact with GLU 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A ILE* 6.2 0.9 - - - -
322C GLU* 3.3 22.6 - - - +
323C GLN* 3.3 21.8 - - - +
325C ARG* 1.3 87.6 + - + +
327C ALA* 1.3 57.3 + - - +
329C ARG* 4.4 1.5 - - - +
330C LYS* 2.9 51.4 + - - +
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Residues in contact with ALA 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A TYR* 3.9 27.9 + - + +
320A GLU* 4.4 12.6 - - + +
323C GLN* 2.7 25.4 + - + +
324C VAL* 4.0 4.7 - - - +
326C GLU* 1.3 75.5 - - + +
328C LEU* 1.3 57.5 + - + +
330C LYS* 3.5 7.8 - - - +
331C ALA* 2.8 28.5 + - - +
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Residues in contact with LEU 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ALA* 4.3 15.7 - - + +
320A GLU* 5.2 0.9 - - + -
321A LEU* 3.6 45.1 - - + -
324A VAL* 5.9 0.4 - - + -
324C VAL* 2.8 38.9 + - + +
327C ALA* 1.3 73.5 - - - +
329C ARG* 1.3 89.5 + - - +
331C ALA* 3.4 5.4 - - - +
332C GLU* 2.7 49.4 + - + +
354C THR* 4.0 7.6 - - + -
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Residues in contact with ARG 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU* 5.8 0.4 - - - +
361A TYR* 3.1 50.3 - - + +
364A ILE* 4.0 30.5 - - + -
365A LYS* 3.1 13.5 - - + +
368A ASN* 5.7 0.3 + - - -
325C ARG* 3.0 26.9 + - - +
326C GLU* 4.4 1.6 - - - +
328C LEU* 1.3 102.8 - - - +
330C LYS* 1.3 60.0 + - - +
332C GLU* 2.6 46.5 + - - +
333C LYS* 3.0 29.6 + - - +
354C THR* 5.2 3.0 + - - -
358C GLU* 2.7 24.0 + - - -
361C TYR* 5.7 2.4 - - - -
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Residues in contact with LYS 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A TYR* 5.1 8.1 - - - +
326C GLU* 2.9 41.6 + - - +
327C ALA* 3.5 6.9 - - - +
329C ARG* 1.3 75.1 - - - +
331C ALA* 1.3 59.6 + - - +
333C LYS* 3.3 4.1 + - - +
334C GLU* 2.9 44.7 + - + +
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Residues in contact with ALA 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A GLN* 3.7 28.2 - - + +
316A TYR* 4.7 6.9 + - + +
317A ALA* 3.8 17.5 - - + -
327C ALA 2.8 18.2 + - - +
328C LEU 3.4 5.4 - - - +
330C LYS* 1.3 73.2 - - - +
332C GLU* 1.3 54.9 + - - +
334C GLU* 3.4 11.0 + - - +
335C LEU* 2.7 39.2 + - + +
350C TRP* 4.5 2.0 - - - +
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Residues in contact with GLU 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A LYS* 2.9 25.6 + - - +
368A ASN* 5.7 2.2 - - - +
328C LEU* 2.7 29.6 + - + +
329C ARG* 2.6 57.8 + - - +
330C LYS 3.3 0.2 - - - -
331C ALA* 1.3 71.8 - - - +
333C LYS* 1.3 56.9 + - - +
336C GLU* 2.8 34.4 + - - +
350C TRP* 3.3 32.6 - - + +
351C LEU* 6.1 0.7 - - - +
354C THR* 4.1 11.8 + - + +
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Residues in contact with LYS 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A ASN* 3.8 24.6 - - - +
371A LYS* 5.0 11.4 - - - +
329C ARG 3.0 17.2 + - - +
330C LYS* 3.9 4.9 - - - +
332C GLU* 1.3 75.6 - - - +
334C GLU* 1.3 60.1 + - - +
336C GLU* 3.0 24.7 + - - +
337C SER* 3.0 31.9 + - - -
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Residues in contact with GLU 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A GLN* 2.8 41.0 + - + +
316A TYR* 5.1 3.8 + - - -
330C LYS* 2.9 34.8 + - + +
331C ALA* 3.4 9.6 - - - +
333C LYS* 1.3 78.3 - - - +
335C LEU* 1.3 55.0 + - - +
337C SER* 3.2 7.1 + - - -
338C HIS* 2.7 41.4 + - + +
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Residues in contact with LEU 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A SER* 5.5 3.4 - - - -
314A GLN* 3.7 29.2 - - + +
315A LYS* 5.3 6.1 - - + +
331C ALA 2.7 18.3 + - - +
332C GLU 3.4 3.8 - - - +
334C GLU* 1.3 79.0 - - - +
336C GLU* 1.3 54.4 + - - +
338C HIS* 2.9 6.1 + - - -
339C SER* 2.7 35.9 + - - -
342C TYR* 3.2 25.8 - - + +
346C ALA* 4.8 2.2 - - + +
347C LEU* 4.3 10.5 - - - +
350C TRP* 3.4 53.2 - - + +
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Residues in contact with GLU 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A ASN* 2.9 33.5 + - - +
369A ALA* 6.0 0.2 - - - -
372A GLN* 3.1 29.1 + - - +
332C GLU* 2.8 19.4 + - - +
333C LYS* 3.0 34.6 + - - +
335C LEU* 1.3 72.5 - - - +
337C SER* 1.3 56.6 + - - +
339C SER* 2.7 17.5 + - - -
350C TRP* 3.9 20.5 - - + -
284D ASP* 3.2 35.1 - - + +
288D HIS* 3.5 7.1 - - - -
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Residues in contact with SER 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333C LYS* 3.0 24.3 + - - -
334C GLU* 3.5 8.1 - - - -
335C LEU 3.0 0.4 - - - -
336C GLU* 1.3 77.5 - - - +
338C HIS* 1.3 63.4 + - - +
339C SER 3.3 0.2 - - - -
340C SER* 3.8 5.9 + - - -
341C TRP* 4.1 6.3 + - - -
288D HIS* 3.4 26.4 + - - -
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Residues in contact with HIS 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1A ALA* 6.4 0.2 - - + -
0A SER 6.1 0.7 - - - -
312A SER* 6.5 0.4 - - - -
314A GLN* 3.9 20.8 + - - +
334C GLU* 2.7 26.2 + - + +
335C LEU* 3.6 4.0 - - - +
337C SER* 1.3 70.6 - - - +
339C SER* 1.3 57.3 + - - +
340C SER 3.0 5.6 - - - -
341C TRP* 2.9 66.2 + + + +
342C TYR* 3.2 27.8 - + - +
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Residues in contact with SER 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C LEU 2.7 14.5 + - - -
336C GLU 2.7 24.4 + - - -
338C HIS* 1.3 70.1 - - - +
340C SER* 1.3 56.5 + - - +
341C TRP 3.0 2.4 + - - -
342C TYR* 2.9 48.9 + - - +
343C ALA 4.9 0.3 - - - -
344C PRO* 5.9 0.9 - - - -
347C LEU* 4.0 25.4 - - - -
284D ASP* 3.5 4.7 + - - -
288D HIS 3.2 14.6 + - - +
289D ARG 3.7 3.0 - - - +
290D GLY* 3.2 2.4 - - - -
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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
------------------------------------------------------------
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