Contacts of the helix formed by residues 324 - 337 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306J ASN* 4.2 3.9 - - - +
322J ASP 3.9 3.0 + - - -
323J SER* 1.3 72.1 - - - +
325J VAL* 1.3 65.2 + - - +
326J LEU 3.3 2.4 + - - -
327J GLU* 3.3 24.4 + - - -
328J ASN* 2.8 31.5 + - - -
366J LEU* 4.3 7.4 + - - +
369J ASP* 2.7 26.7 + - - +
372J LYS* 3.7 18.9 + - - -
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Residues in contact with VAL 325 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306J ASN* 3.5 13.0 + - + +
309J LEU* 4.2 13.2 - - + -
310J ILE* 4.3 10.3 - - + -
316J LEU* 3.5 41.5 - - + +
317J ALA* 3.7 17.5 - - + +
320J TYR* 3.7 14.4 - - + -
322J ASP* 3.7 33.0 - - - +
323J SER 3.1 3.8 - - - +
324J SER* 1.3 76.2 - - - +
326J LEU* 1.3 64.1 + - - +
329J HIS* 3.2 19.4 + - - +
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Residues in contact with LEU 326 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300J ASP 5.2 0.7 - - - +
301J HIS* 3.5 18.2 - - + +
302J PRO* 3.4 30.7 - - + -
304J VAL 3.4 23.8 - - - +
305J SER* 4.2 1.1 - - - -
306J ASN* 2.7 39.2 + - - +
309J LEU* 3.6 16.8 - - + -
316J LEU* 4.7 8.1 - - + -
325J VAL* 1.3 69.9 - - - +
327J GLU* 1.3 69.3 + - - +
329J HIS* 3.0 9.1 + - + +
330J HIS* 2.8 51.0 + - + +
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Residues in contact with GLU 327 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298J ASP* 6.0 0.2 - - - +
306J ASN* 2.9 28.8 + - - -
324J SER* 3.3 21.0 + - - +
326J LEU* 1.3 78.6 - - - +
328J ASN* 1.3 63.0 + - - +
330J HIS* 3.4 13.4 + - + +
331J LEU* 3.2 26.0 + - - +
365J VAL* 3.9 12.7 - - - +
366J LEU* 4.2 8.5 - - + -
368J THR* 3.6 22.9 - - - +
369J ASP* 3.6 30.2 - - + +
370J MET 4.7 1.0 + - - -
2020J MG 3.9 13.9 - - - -
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Residues in contact with ASN 328 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320I TYR* 4.2 9.5 - - - +
321I ASN* 2.8 39.5 + - - +
323I SER* 5.4 2.6 - - - -
320J TYR* 3.5 32.6 - - + +
323J SER* 3.0 27.3 + - - -
324J SER* 2.8 26.3 + - - +
325J VAL 3.8 1.6 - - - +
327J GLU* 1.3 72.2 - - - +
329J HIS* 1.3 63.8 + - - +
331J LEU 3.3 1.2 + - - -
332J ALA* 3.0 13.5 + - - +
366J LEU* 3.9 16.1 - - - +
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Residues in contact with HIS 329 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319I MET* 5.6 3.7 - - + +
299J VAL 4.6 1.6 - - - -
300J ASP* 2.7 42.1 + - + -
316J LEU* 3.7 37.2 - - + +
320J TYR* 4.0 16.6 + - + -
325J VAL 3.2 11.4 + - - +
326J LEU* 3.0 14.6 + - + +
328J ASN* 1.3 77.1 - - - +
330J HIS* 1.3 69.3 + - - +
332J ALA* 3.1 4.7 + - + +
333J VAL* 3.0 44.5 + - + +
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Residues in contact with HIS 330 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296J ILE* 3.6 18.0 - - - +
297J HIS 3.0 22.7 - - - +
298J ASP* 3.2 32.7 + - - -
299J VAL* 2.7 34.5 + - - +
300J ASP 4.6 0.9 - - - -
301J HIS* 3.9 22.4 - + + -
326J LEU* 2.8 50.3 + - + +
327J GLU* 3.5 13.2 - - + +
328J ASN 3.3 0.2 - - - -
329J HIS* 1.3 73.6 - + - +
331J LEU* 1.3 63.0 + - - +
334J GLY* 2.9 21.7 + - - -
365J VAL* 4.5 3.4 - - + -
2020J MG 4.3 3.4 - - - -
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Residues in contact with LEU 331 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321I ASN* 3.0 28.0 - - - +
296J ILE* 4.2 6.0 - - + +
327J GLU 3.2 6.6 + - - +
328J ASN 3.5 1.8 - - - +
329J HIS 3.2 0.4 - - - -
330J HIS* 1.3 77.9 - - - +
332J ALA* 1.3 63.4 + - - +
334J GLY* 3.3 0.5 + - - -
335J PHE* 3.0 47.4 + - + -
361J VAL* 3.7 6.7 - - + +
362J ILE* 3.7 39.7 - - + +
365J VAL* 3.5 37.0 - - + -
366J LEU* 3.7 26.0 - - + -
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Residues in contact with ALA 332 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318I LEU* 3.4 28.2 - - + +
319I MET* 3.9 9.9 - - + +
321I ASN* 3.2 6.4 + - - +
320J TYR* 3.7 17.3 - - - +
328J ASN 3.0 13.8 + - - +
329J HIS* 3.5 10.8 - - - +
331J LEU* 1.3 77.1 - - - +
333J VAL* 1.3 57.7 + - + +
335J PHE* 5.0 0.4 - - - -
336J LYS* 2.9 31.9 + - - +
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Residues in contact with VAL 333 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249J HIS* 4.4 14.4 - - + -
299J VAL* 4.0 24.5 - - + -
300J ASP* 4.3 10.8 - - + +
329J HIS* 3.0 47.4 + - + +
330J HIS 3.8 2.9 - - - +
332J ALA* 1.3 75.1 - - + +
334J GLY* 1.3 64.6 + - - +
336J LYS* 3.3 5.6 + - + +
337J LEU* 3.0 37.3 + - + +
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Residues in contact with GLY 334 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242J TYR* 2.8 32.9 + - - -
246J LEU* 4.6 3.6 - - - -
292J PHE* 4.3 0.6 - - - -
296J ILE* 4.2 21.8 - - - -
299J VAL* 4.1 4.2 - - - +
330J HIS 2.9 17.1 + - - -
331J LEU 3.3 1.3 + - - -
333J VAL* 1.3 77.9 - - - +
335J PHE* 1.3 61.6 + - - +
337J LEU* 3.8 4.9 + - - +
338J LEU* 3.9 3.5 - - - +
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Residues in contact with PHE 335 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318I LEU* 4.7 8.5 - - + -
321I ASN* 4.3 3.6 - - - -
292J PHE* 4.2 15.5 - + - -
296J ILE* 5.0 1.3 - - + -
331J LEU* 3.0 41.7 + - + +
332J ALA* 4.0 2.5 - - - +
334J GLY* 1.3 74.8 - - - +
336J LYS* 1.3 66.7 + - - +
338J LEU* 3.0 38.6 + - + +
339J GLN* 4.0 5.9 + - - +
357J LEU* 5.3 4.9 - - + -
358J ARG* 3.1 55.0 - - + +
361J VAL* 3.5 26.7 - - + -
362J ILE* 3.7 17.9 - - + -
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Residues in contact with LYS 336 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315I GLU* 3.4 28.4 + - - +
318I LEU* 3.6 19.6 - - + +
332J ALA 2.9 19.5 + - - +
333J VAL* 3.6 7.2 - - - +
335J PHE* 1.3 76.5 - - - +
337J LEU* 1.3 66.5 + - + +
338J LEU 3.0 1.2 + - - -
339J GLN* 3.0 50.2 + - - +
340J GLU* 4.2 3.7 + - - +
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Residues in contact with LEU 337 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242J TYR* 3.8 15.9 - - + -
245J THR* 3.7 11.7 - - + -
246J LEU* 3.7 45.8 - - + +
249J HIS* 3.6 42.0 - - + +
333J VAL* 3.0 26.4 + - + +
334J GLY 4.0 0.7 - - - +
335J PHE 3.2 0.2 - - - -
336J LYS* 1.3 79.7 - - + +
338J LEU* 1.3 61.7 + - - +
339J GLN 3.2 0.7 + - - -
340J GLU* 3.5 23.9 + - - +
343J CYS* 3.2 20.8 - - - +
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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