Contacts of the helix formed by residues 350 - 366 (chain E) 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 THR 350 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348E ASN 4.1 1.1 + - - +
349E LEU* 1.3 75.9 - - - +
351E LYS* 1.3 64.7 + - - +
352E LYS* 3.2 25.8 - - - +
353E GLN* 2.9 43.7 + - - +
354E ARG* 2.9 19.8 + - - +
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Residues in contact with LYS 351 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349E LEU 3.6 1.0 + - - -
350E THR* 1.3 72.5 - - - +
352E LYS* 1.3 75.4 + - + +
354E ARG* 3.3 15.5 + - - +
355E GLN* 3.1 48.7 + - + +
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Residues in contact with LYS 352 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350E THR* 3.1 23.6 - - - +
351E LYS* 1.3 97.8 - - + +
353E GLN* 1.3 62.6 + - + +
355E GLN* 3.2 16.4 + - - +
356E SER* 3.0 26.5 + - - -
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Residues in contact with GLN 353 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E PHE* 4.3 21.1 - - - -
285E LEU* 3.7 27.6 - - + +
348E ASN 4.7 0.9 - - - +
349E LEU* 3.4 20.4 - - + +
350E THR* 2.9 47.3 + - - +
352E LYS* 1.3 74.0 - - + +
354E ARG* 1.3 62.1 + - - +
356E SER* 3.2 2.4 + - - -
357E LEU* 2.8 32.8 + - - +
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Residues in contact with ARG 354 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344E ASP* 3.6 18.3 + - - -
346E PHE* 2.7 46.2 + - + +
347E GLN* 3.5 10.2 + - - +
349E LEU* 3.5 29.6 - - + +
350E THR 2.9 15.0 + - - +
351E LYS* 3.6 14.6 - - + +
353E GLN* 1.3 76.0 - - - +
355E GLN* 1.3 63.3 + - + +
357E LEU* 3.5 7.2 + - - +
358E ARG* 3.0 25.3 + - - +
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Residues in contact with GLN 355 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351E LYS* 3.1 44.7 + - + +
352E LYS* 3.5 14.4 + - - +
354E ARG* 1.3 77.9 - - + +
356E SER* 1.3 62.5 + - - +
358E ARG* 3.3 7.9 + - - +
359E LYS* 3.0 22.9 + - - +
311H ASN* 5.6 1.9 - - - +
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Residues in contact with SER 356 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285E LEU* 3.9 16.7 - - - +
352E LYS* 3.0 15.0 + - - +
353E GLN* 3.7 6.2 - - - -
355E GLN* 1.3 72.9 - - - +
357E LEU* 1.3 67.9 + - - +
359E LYS* 3.2 5.7 + - - +
360E MET* 2.9 38.1 + - - +
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Residues in contact with LEU 357 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285E LEU* 3.9 14.1 - - + +
288E LEU* 3.5 37.0 - - + -
289E ALA* 3.7 17.0 - - + +
292E PHE* 4.7 1.8 - - + -
335E PHE* 5.3 3.4 - - + -
346E PHE* 3.4 41.5 - - + -
349E LEU* 4.8 2.0 - - + -
353E GLN 2.8 17.3 + - - +
354E ARG* 3.8 6.7 - - - +
356E SER* 1.3 77.6 - - - +
358E ARG* 1.3 58.1 + - - +
360E MET* 3.8 8.8 - - - +
361E VAL* 2.8 48.6 + - + +
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Residues in contact with ARG 358 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335E PHE* 3.2 61.4 - - + +
354E ARG 3.0 19.0 + - - +
355E GLN* 3.7 6.1 - - - +
357E LEU* 1.3 77.1 - - - +
359E LYS* 1.3 61.9 + - - +
361E VAL* 3.4 0.9 + - - +
362E ILE* 3.0 40.4 + - + +
317H ALA 3.4 15.2 + - - -
318H LEU* 4.2 11.0 + - - +
321H ASN* 3.4 12.1 + - - +
322H ASP* 2.5 43.5 + - - +
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Residues in contact with LYS 359 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355E GLN 3.0 14.2 + - - +
356E SER* 3.6 9.6 - - - +
358E ARG* 1.3 79.1 - - - +
360E MET* 1.3 58.7 + - + +
362E ILE* 3.3 6.5 + - - +
363E ASP* 2.9 51.5 + - - +
400E TYR* 3.7 31.2 - - + +
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Residues in contact with MET 360 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285E LEU* 3.9 24.9 - - + +
286E GLU* 3.8 31.4 - - + +
289E ALA* 3.9 18.2 - - + -
356E SER* 2.9 36.3 + - - +
357E LEU* 3.8 10.3 - - - +
359E LYS* 1.3 75.3 - - + +
361E VAL* 1.3 58.2 + - - +
363E ASP* 3.2 1.6 + - - +
364E ILE* 2.8 38.7 + - + +
400E TYR* 3.8 30.1 - - + +
404E ILE* 3.9 18.4 - - + -
407E LEU* 5.0 3.8 - - - -
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Residues in contact with VAL 361 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289E ALA* 3.8 28.5 - - - +
292E PHE* 3.8 20.9 - - + -
293E ALA* 4.2 13.9 - - + -
296E ILE* 4.0 14.1 - - + -
331E LEU* 3.8 11.7 - - + -
335E PHE* 3.5 25.8 - - + -
357E LEU* 2.8 32.4 + - + +
360E MET* 1.3 72.5 - - - +
362E ILE* 1.3 62.4 + - - +
364E ILE* 3.8 0.8 - - - +
365E VAL* 3.0 25.7 + - + +
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Residues in contact with ILE 362 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331E LEU* 3.7 13.9 - - + +
335E PHE* 3.7 16.4 - - + -
358E ARG* 3.0 53.0 + - + +
359E LYS* 3.6 6.1 - - + +
361E VAL* 1.3 76.2 - - - +
363E ASP* 1.3 67.9 + - - +
366E LEU* 3.0 46.2 + - + +
321H ASN* 3.5 34.8 - - + +
322H ASP* 4.3 3.8 - - + +
323H SER* 4.8 3.6 - - - +
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Residues in contact with ASP 363 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359E LYS* 2.9 37.3 + - - +
360E MET 3.7 3.8 - - - +
362E ILE* 1.3 82.6 - - - +
364E ILE* 1.3 64.4 + - - +
366E LEU* 4.2 5.8 - - - +
367E ALA* 3.5 12.5 + - - +
400E TYR* 2.9 24.3 + - - -
404E ILE* 4.0 12.8 - - + +
408E GLN* 3.1 26.5 - - - +
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Residues in contact with ILE 364 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289E ALA 4.4 1.8 - - - -
290E ALA* 4.0 28.3 - - + +
293E ALA* 3.9 14.1 - - + -
360E MET* 2.8 27.5 + - + +
361E VAL 3.8 3.1 - - - +
363E ASP* 1.3 75.5 - - - +
365E VAL* 1.3 62.2 + - + +
367E ALA* 2.9 24.4 + - - +
368E THR* 3.5 6.9 + - - +
404E ILE* 4.1 11.9 - - + -
407E LEU* 4.0 29.4 - - + +
408E GLN* 4.0 14.0 - - + +
411E VAL* 3.5 37.0 - - + -
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Residues in contact with VAL 365 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293E ALA* 3.8 33.9 - - + +
296E ILE* 4.4 3.1 - - + -
297E HIS* 4.1 25.8 - - + +
327E GLU* 3.8 18.0 - - + +
330E HIS* 4.5 3.6 - - + -
331E LEU* 3.5 36.3 - - + +
361E VAL* 3.0 14.7 + - + +
364E ILE* 1.3 75.9 - - + +
366E LEU* 1.3 61.6 + - - +
368E THR* 2.6 32.3 + - - +
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Residues in contact with LEU 366 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324E SER* 4.3 7.6 + - - +
327E GLU* 4.1 7.2 - - + -
328E ASN* 3.9 39.3 - - - +
331E LEU* 3.7 17.5 - - + -
362E ILE* 3.0 38.0 + - + +
363E ASP* 4.3 6.7 - - - +
365E VAL* 1.3 77.0 - - - +
367E ALA* 1.3 58.2 + - - +
368E THR 3.2 1.0 + - - -
369E ASP* 3.5 11.7 - - - +
372E LYS* 3.5 26.1 - - - +
321H ASN* 5.7 0.9 - - + -
323H SER* 5.0 8.5 - - - +
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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