Contacts of the helix formed by residues 324 - 337 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306L ASN* 4.3 3.7 - - - +
322L ASP 3.9 3.4 + - - -
323L SER* 1.3 72.0 - - - +
325L VAL* 1.3 66.7 + - - +
326L LEU 3.3 2.8 + - - -
327L GLU* 3.3 19.7 + - - -
328L ASN* 2.8 30.7 + - - -
366L LEU* 4.3 7.9 + - - +
369L ASP* 2.7 31.3 + - - +
372L LYS* 3.6 19.2 + - - -
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Residues in contact with VAL 325 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306L ASN* 3.5 13.7 + - + +
309L LEU* 4.1 13.5 - - + -
310L ILE* 4.3 9.4 - - + -
316L LEU* 3.5 42.6 - - + +
317L ALA* 3.7 16.8 - - + +
320L TYR* 3.7 14.1 - - + -
322L ASP* 3.6 34.1 - - - +
323L SER 3.1 3.6 - - - +
324L SER* 1.3 77.4 - - - +
326L LEU* 1.3 63.1 + - - +
329L HIS* 3.1 19.9 + - - +
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Residues in contact with LEU 326 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300L ASP 5.3 0.4 - - - +
301L HIS* 3.5 18.2 - - - +
302L PRO* 3.4 30.5 - - + -
304L VAL 3.4 23.8 - - - +
305L SER* 4.2 1.1 - - - -
306L ASN* 2.8 36.7 + - - +
309L LEU* 3.6 16.8 - - + -
316L LEU* 4.7 7.9 - - + -
325L VAL* 1.3 70.8 - - - +
327L GLU* 1.3 69.8 + - - +
329L HIS* 3.0 8.8 + - + +
330L HIS* 2.8 51.2 + - + +
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Residues in contact with GLU 327 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306L ASN* 2.9 28.5 + - - -
324L SER* 3.5 16.2 - - - +
326L LEU* 1.3 77.2 - - - +
328L ASN* 1.3 62.9 + - - +
330L HIS* 3.4 10.9 + - + +
331L LEU* 3.2 27.0 + - - +
365L VAL* 3.8 12.3 - - - +
366L LEU* 4.2 13.5 - - + -
368L THR* 3.6 22.2 - - - +
369L ASP* 3.5 32.2 - - + +
370L MET 4.7 0.7 + - - -
2024L MG 3.5 17.1 - - - -
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Residues in contact with ASN 328 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320K TYR* 4.4 5.2 - - - +
321K ASN* 2.9 39.0 + - - +
323K SER* 5.4 3.1 + - - -
320L TYR* 3.5 33.0 + - + -
323L SER* 2.9 28.1 + - - -
324L SER* 2.8 24.8 + - - +
325L VAL 3.7 1.6 - - - +
327L GLU* 1.3 73.4 - - - +
329L HIS* 1.3 63.0 + - - +
331L LEU 3.3 1.6 + - - -
332L ALA* 3.0 13.3 + - - +
366L LEU* 3.8 16.6 - - - +
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Residues in contact with HIS 329 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319K MET* 6.2 1.4 - - - +
299L VAL 4.6 1.8 - - - -
300L ASP* 2.7 41.5 + - + -
316L LEU* 3.7 36.0 - - + +
320L TYR* 4.0 17.1 + - + -
325L VAL 3.1 11.2 + - - +
326L LEU* 3.0 13.2 + - + +
328L ASN* 1.3 77.4 - - - +
330L HIS* 1.3 69.2 + + - +
332L ALA* 3.2 3.8 + - + +
333L VAL* 3.0 48.0 + - + +
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Residues in contact with HIS 330 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296L ILE* 3.6 19.0 - - - +
297L HIS 3.0 22.9 - - - +
298L ASP* 3.2 32.0 + - - -
299L VAL* 2.8 34.8 + - - +
300L ASP 4.7 0.9 - - - -
301L HIS* 3.9 21.5 - + + -
326L LEU* 2.8 51.2 + - + +
327L GLU* 3.5 13.2 - - + +
328L ASN 3.3 0.2 - - - -
329L HIS* 1.3 74.8 - + - +
331L LEU* 1.3 58.0 + - - +
333L VAL 3.3 0.2 + - - -
334L GLY* 2.9 27.0 + - - -
365L VAL* 4.5 3.1 - - + -
2024L MG 3.9 4.5 - - - -
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Residues in contact with LEU 331 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321K ASN* 3.2 20.6 - - - +
296L ILE* 4.2 5.6 - - + -
327L GLU 3.2 9.9 + - - +
328L ASN 3.6 4.7 - - - +
329L HIS 3.2 0.2 - - - -
330L HIS* 1.3 80.1 - - - +
332L ALA* 1.3 62.9 + - - +
334L GLY* 3.8 0.3 - - - -
335L PHE* 2.9 51.8 + - + -
361L VAL* 3.7 14.1 - - + +
362L ILE* 3.7 19.5 - - + +
365L VAL* 3.5 36.1 - - + -
366L LEU* 3.7 32.8 - - + -
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Residues in contact with ALA 332 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318K LEU* 3.9 16.9 - - + +
319K MET* 4.0 19.1 - - + +
321K ASN* 3.3 6.9 + - - +
320L TYR* 3.6 22.9 - - - +
328L ASN 3.0 7.8 + - - +
329L HIS* 3.2 10.5 + - + +
331L LEU* 1.3 76.4 - - - +
333L VAL* 1.3 58.3 + - + +
335L PHE* 4.9 0.4 - - - -
336L LYS* 2.8 32.7 + - - +
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Residues in contact with VAL 333 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249L HIS* 4.4 13.9 - - + -
299L VAL* 4.0 24.9 - - + -
300L ASP* 4.3 9.6 - - + +
329L HIS* 3.0 46.9 + - + +
330L HIS 3.8 3.1 - - - +
332L ALA* 1.3 74.0 - - + +
334L GLY* 1.3 66.2 + - - +
336L LYS* 3.3 6.4 + - + +
337L LEU* 3.0 36.3 + - + +
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Residues in contact with GLY 334 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242L TYR* 2.7 32.9 + - - -
246L LEU* 4.7 4.5 - - - -
292L PHE* 4.3 0.8 - - - -
296L ILE* 4.1 22.0 - - - -
299L VAL* 4.0 4.2 - - - +
330L HIS 2.9 16.4 + - - -
331L LEU 3.8 0.9 - - - -
333L VAL* 1.3 78.4 - - - +
335L PHE* 1.3 62.3 + - - +
337L LEU* 3.8 4.3 + - - +
338L LEU* 3.9 3.1 - - - +
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Residues in contact with PHE 335 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318K LEU* 4.8 9.6 - - + -
321K ASN* 4.2 3.8 - - - -
292L PHE* 4.2 15.0 - + - -
296L ILE* 5.0 1.6 - - + -
331L LEU* 2.9 50.5 + - + +
332L ALA* 4.0 2.5 - - - +
334L GLY* 1.3 74.0 - - - +
336L LYS* 1.3 66.4 + - - +
338L LEU* 3.0 38.6 + - + +
339L GLN* 4.0 6.3 + - - +
357L LEU* 5.2 5.6 - - + -
358L ARG* 3.2 55.2 - - + +
361L VAL* 3.5 26.7 - - + -
362L ILE* 3.7 9.2 - - + -
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Residues in contact with LYS 336 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315K GLU* 3.8 24.6 + - - -
318K LEU* 4.0 18.3 - - + +
332L ALA 2.8 21.1 + - - +
333L VAL* 3.6 7.6 - - + +
335L PHE* 1.3 77.3 - - - +
337L LEU* 1.3 66.8 + - + +
339L GLN* 3.0 50.9 + - - +
340L GLU* 4.2 3.6 + - - +
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Residues in contact with LEU 337 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242L TYR* 3.7 16.4 - - + +
245L THR* 3.8 12.3 - - + +
246L LEU* 3.7 44.2 - - + +
249L HIS* 3.6 42.8 - - + +
333L VAL* 3.0 28.0 + - + +
334L GLY 4.0 0.9 - - - +
335L PHE 3.3 0.4 - - - -
336L LYS* 1.3 80.7 - - + +
338L LEU* 1.3 62.0 + - - +
339L GLN 3.3 0.3 + - - -
340L GLU* 3.4 24.4 + - - +
343L CYS* 3.3 18.5 - - - +
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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