Contacts of the helix formed by residues 324 - 337 (chain K) in PDB entry 1MKD
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 324 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306K ASN* 4.3 3.5 - - - +
322K ASP 3.9 2.8 + - - -
323K SER* 1.3 70.7 - - - +
325K VAL* 1.3 57.1 + - - +
326K LEU 3.4 2.9 - - - -
327K GLU* 3.3 23.5 + - - -
328K ASN* 2.8 39.6 + - - -
366K LEU* 4.3 8.6 + - - +
369K ASP* 2.7 28.9 + - - +
372K LYS* 3.7 18.9 + - - -
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Residues in contact with VAL 325 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306K ASN* 3.5 13.5 + - + +
309K LEU* 4.1 13.5 - - + -
310K ILE* 4.3 9.9 - - + -
316K LEU* 3.5 42.0 - - + +
317K ALA* 3.7 16.4 - - + +
320K TYR* 3.7 13.1 - - + -
322K ASP* 3.6 34.3 - - - +
323K SER 3.1 4.2 - - - +
324K SER* 1.3 76.5 - - - +
326K LEU* 1.3 64.0 + - - +
329K HIS* 3.1 19.8 + - - +
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Residues in contact with LEU 326 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300K ASP 5.2 0.9 - - - +
301K HIS* 3.5 17.0 - - - +
302K PRO* 3.4 31.0 - - + -
304K VAL 3.3 24.5 - - - +
305K SER* 4.5 0.9 - - - -
306K ASN* 2.8 38.4 + - - +
309K LEU* 3.6 17.3 - - + -
316K LEU* 4.7 8.1 - - + -
325K VAL* 1.3 70.8 - - - +
327K GLU* 1.3 68.0 + - - +
329K HIS* 3.0 8.3 + - + +
330K HIS* 2.8 51.0 + - + +
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Residues in contact with GLU 327 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306K ASN* 2.9 28.6 + - - -
324K SER* 3.5 16.0 - - - +
326K LEU* 1.3 78.0 - - - +
328K ASN* 1.3 62.9 + - - +
330K HIS* 3.3 11.0 + - - +
331K LEU* 3.2 26.5 + - - +
365K VAL* 3.8 12.7 - - - +
366K LEU* 4.2 13.9 - - + -
368K THR* 3.6 22.9 - - - +
369K ASP* 3.6 31.4 - - + +
370K MET 4.7 0.9 + - - -
2022K MG 3.8 14.4 - - - -
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Residues in contact with ASN 328 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320K TYR* 3.5 33.9 + - + -
323K SER* 2.9 27.7 + - - -
324K SER* 2.8 24.8 + - - +
325K VAL 3.7 2.0 - - - +
327K GLU* 1.3 71.4 - - - +
329K HIS* 1.3 65.3 + - - +
331K LEU 3.3 2.3 + - - -
332K ALA* 3.0 21.1 + - - +
366K LEU* 3.8 15.6 - - - +
320L TYR* 4.5 6.1 - - - +
321L ASN* 2.9 34.2 + - - +
323L SER* 5.8 1.0 - - - -
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Residues in contact with HIS 329 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299K VAL 4.6 2.0 - - - -
300K ASP* 2.7 41.1 + - + -
316K LEU* 3.7 37.4 - - + +
320K TYR* 3.9 16.6 + - + -
325K VAL 3.1 11.7 + - - +
326K LEU* 3.0 14.3 + - + +
328K ASN* 1.3 80.4 - - - +
330K HIS* 1.3 66.1 + - - +
332K ALA* 3.2 4.5 + - + +
333K VAL* 3.0 44.6 + - + +
319L MET* 6.2 0.8 - - - +
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Residues in contact with HIS 330 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296K ILE* 3.6 20.0 - - - +
297K HIS 3.0 22.9 - - - +
298K ASP* 3.2 32.2 + - - -
299K VAL* 2.7 35.1 + - - +
300K ASP 4.6 0.7 - - - -
301K HIS* 3.8 22.1 - + + -
326K LEU* 2.8 49.9 + - + +
327K GLU* 3.5 12.1 - - - +
328K ASN 3.3 0.2 - - - -
329K HIS* 1.3 73.6 - + - +
331K LEU* 1.3 59.2 + - - +
334K GLY* 2.9 26.3 + - - -
365K VAL* 4.5 2.7 - - + -
2022K MG 4.0 4.1 - - - -
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Residues in contact with LEU 331 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296K ILE* 4.2 6.0 - - + +
327K GLU 3.2 9.5 + - - +
328K ASN 3.5 4.7 - - - +
330K HIS* 1.3 79.2 - - - +
332K ALA* 1.3 63.8 + - - +
334K GLY* 3.4 0.7 + - - -
335K PHE* 3.0 54.0 + - + -
361K VAL* 3.7 14.1 - - + +
362K ILE* 3.7 15.0 - - + +
365K VAL* 3.5 35.9 - - + -
366K LEU* 3.7 32.3 - - + -
321L ASN* 3.3 22.2 - - - +
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Residues in contact with ALA 332 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320K TYR* 3.6 23.3 - - - +
328K ASN 3.0 8.6 + - - +
329K HIS* 3.2 11.4 + - + +
331K LEU* 1.3 77.3 - - - +
333K VAL* 1.3 57.8 + - + +
335K PHE* 3.8 2.0 - - - +
336K LYS* 2.8 32.0 + - - +
318L LEU* 4.2 15.8 - - + +
319L MET* 4.3 17.7 - - + +
321L ASN* 3.8 6.2 + - - -
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Residues in contact with VAL 333 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249K HIS* 4.4 15.3 - - + -
299K VAL* 4.0 25.4 - - + -
300K ASP* 4.3 9.4 - - + +
329K HIS* 3.0 48.8 + - + +
330K HIS 3.8 3.4 - - - +
332K ALA* 1.3 74.6 - - + +
334K GLY* 1.3 64.1 + - - +
336K LYS* 3.3 6.4 + - - +
337K LEU* 3.0 37.0 + - + +
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Residues in contact with GLY 334 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242K TYR* 2.7 32.9 + - - -
246K LEU* 4.7 4.3 - - - -
292K PHE* 4.2 1.0 - - - -
296K ILE* 4.1 22.2 - - - -
299K VAL* 4.1 4.2 - - - +
330K HIS 2.9 17.3 + - - -
331K LEU 3.8 0.9 - - - -
333K VAL* 1.3 78.5 - - - +
335K PHE* 1.3 61.7 + - - +
337K LEU* 3.8 4.3 + - - -
338K LEU* 3.9 3.1 - - - +
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Residues in contact with PHE 335 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292K PHE* 4.2 16.2 - + - -
296K ILE* 5.0 1.3 - - + -
331K LEU* 3.0 49.1 + - + +
332K ALA* 3.9 2.9 - - - +
334K GLY* 1.3 73.5 - - - +
336K LYS* 1.3 67.2 + - - +
338K LEU* 3.0 38.1 + - + +
339K GLN* 4.0 5.6 + - - +
346K PHE* 5.6 0.2 - + - -
357K LEU* 5.3 4.7 - - + -
358K ARG* 3.2 54.1 - - + +
361K VAL* 3.5 28.3 - - + -
362K ILE* 3.7 9.4 - - + -
318L LEU* 4.7 9.2 - - + -
321L ASN* 4.2 3.4 - - - -
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Residues in contact with LYS 336 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332K ALA 2.8 20.2 + - - +
333K VAL* 3.5 8.1 - - - +
335K PHE* 1.3 77.5 - - - +
337K LEU* 1.3 66.7 + - + +
339K GLN* 3.0 53.5 + - - +
340K GLU* 4.2 3.6 + - - +
315L GLU* 4.1 19.6 + - - +
318L LEU* 4.6 14.8 - - + +
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Residues in contact with LEU 337 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242K TYR* 3.7 15.7 - - + +
245K THR* 3.7 13.2 - - + +
246K LEU* 3.7 45.1 - - + +
249K HIS* 3.5 42.0 - - + +
333K VAL* 3.0 26.8 + - + +
334K GLY 4.0 1.3 - - - +
335K PHE 3.3 0.2 - - - -
336K LYS* 1.3 80.0 - - + +
338K LEU* 1.3 60.8 + - - +
339K GLN 3.3 0.3 + - - -
340K GLU* 3.4 24.2 + - - +
343K CYS* 3.2 20.1 - - - +
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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
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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