Contacts of the helix formed by residues 372 - 385 (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 LYS 372 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324E SER* 3.7 23.5 + - - -
366E LEU* 3.5 27.4 - - - +
367E ALA* 4.7 9.2 - - - +
369E ASP* 3.0 14.1 + - + +
370E MET 3.0 1.2 - - - -
371E SER* 1.3 88.0 + - - +
373E HIS* 1.3 65.9 + - - +
374E MET 3.4 2.0 - - - -
375E ASN* 3.4 15.1 + - + +
376E LEU* 3.0 28.1 + - + +
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Residues in contact with HIS 373 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369E ASP 3.9 1.0 + - - -
370E MET* 3.1 31.9 + - + +
371E SER 3.4 0.6 - - - -
372E LYS* 1.3 76.7 - - - +
374E MET* 1.3 75.8 + - + +
376E LEU* 3.2 4.7 + - - +
377E LEU* 2.8 49.6 + - + +
412E HIS* 2.8 36.0 + + + +
472E TYR 4.5 2.2 + - - -
473E ILE* 3.6 45.0 + - + +
477E LEU* 3.9 24.2 - - + -
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Residues in contact with MET 374 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371E SER 5.1 3.2 + - - +
372E LYS 3.4 0.6 - - - -
373E HIS* 1.3 98.3 - - + +
375E ASN* 1.3 61.1 + - - +
377E LEU* 3.5 10.7 + - - +
378E ALA* 2.9 28.8 + - - +
472E TYR* 4.7 7.6 - - + +
473E ILE* 4.5 13.0 - - + -
387J LYS* 3.3 37.6 - - + +
388J LYS* 4.7 2.7 - - + -
389J VAL* 3.2 57.0 - - + +
390J THR 5.5 0.4 - - - +
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Residues in contact with ASN 375 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371E SER 4.6 4.8 + - - -
372E LYS* 3.4 20.6 + - + +
373E HIS 3.3 0.6 - - - -
374E MET* 1.3 76.2 - - - +
376E LEU* 1.3 67.4 + - - +
378E ALA* 3.1 8.8 + - - +
379E ASP* 2.9 32.3 + - - +
386J THR* 5.8 4.0 - - - -
388J LYS* 5.2 11.5 - - - +
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Residues in contact with LEU 376 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367E ALA* 3.6 36.8 - - + +
372E LYS* 3.0 21.7 + - + +
373E HIS* 3.5 4.5 - - - +
375E ASN* 1.3 78.0 - - - +
377E LEU* 1.3 56.6 + - - +
379E ASP* 3.3 7.7 + - - +
380E LEU* 3.0 22.0 + - - +
405E GLN* 5.2 3.4 - - + -
408E GLN* 4.1 26.0 - - + +
409E ASN* 3.3 45.8 + - - +
412E HIS* 4.0 28.0 - - + +
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Residues in contact with LEU 377 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373E HIS* 2.8 42.6 + - + +
374E MET* 3.8 11.7 - - - +
376E LEU* 1.3 73.4 - - - +
378E ALA* 1.3 61.4 + - - +
380E LEU* 3.2 4.9 + - + +
381E LYS* 2.9 47.2 + - - +
409E ASN* 4.3 2.9 + - - -
476E PRO* 3.8 27.1 - - + +
477E LEU* 3.9 16.4 - - + +
480E THR* 3.4 33.0 - - + +
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Residues in contact with ALA 378 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374E MET 2.9 19.3 + - - +
375E ASN* 3.1 9.2 + - - +
377E LEU* 1.3 74.2 - - - +
379E ASP* 1.3 67.6 + - - +
381E LYS* 3.2 12.1 + - - +
382E THR* 3.0 26.5 + - - -
385J GLU* 5.8 2.9 - - + -
386J THR* 4.8 17.9 - - - +
387J LYS 6.1 0.2 - - - +
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Residues in contact with ASP 379 (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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375E ASN* 2.9 23.8 + - - +
376E LEU* 3.8 10.6 - - + +
378E ALA* 1.3 78.3 - - - +
380E LEU* 1.3 63.7 + - - +
382E THR* 3.4 9.5 + - - -
383E MET* 3.0 22.9 + - - +
405E GLN* 3.7 35.0 + - + +
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Residues in contact with LEU 380 (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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376E LEU 3.0 13.7 + - - +
377E LEU* 3.4 9.9 - - + +
378E ALA 3.1 0.2 - - - -
379E ASP* 1.3 78.3 - - - +
381E LYS* 1.3 57.6 + - - +
383E MET* 3.1 14.2 + - + +
384E VAL* 2.9 32.5 + - + +
405E GLN* 5.1 2.2 - - + +
406E VAL* 5.4 2.5 - - - -
409E ASN* 3.6 39.9 - - + +
477E LEU* 4.5 12.3 - - + +
480E THR* 3.4 28.3 - - + -
481E TRP* 4.1 18.6 - - + +
484E LEU* 4.2 25.6 - - + -
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Residues in contact with LYS 381 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377E LEU* 2.9 38.4 + - + +
378E ALA* 3.6 11.0 - - - +
380E LEU* 1.3 74.1 - - - +
382E THR* 1.3 64.4 + - - +
384E VAL* 3.0 15.7 + - - +
385E GLU* 3.2 20.5 + - - +
476E PRO* 5.1 4.4 - - - +
480E THR* 3.8 30.1 - - + +
483J ASP* 5.8 1.6 + - - -
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Residues in contact with THR 382 (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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378E ALA 3.0 14.5 + - - -
379E ASP* 3.6 13.7 + - - -
381E LYS* 1.3 76.2 - - - +
383E MET* 1.3 57.9 + - - +
385E GLU* 3.0 31.0 + - - +
386E THR* 3.4 14.6 + - + +
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Residues in contact with MET 383 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379E ASP 3.0 12.3 + - - +
380E LEU* 3.4 15.5 - - + +
381E LYS 3.0 0.8 - - - -
382E THR* 1.3 74.9 - - - +
384E VAL* 1.3 56.4 + - - +
385E GLU 2.7 17.8 - - - +
386E THR* 4.0 5.0 + - - +
387E LYS* 3.7 14.6 - - + +
397E LEU* 4.4 8.5 - - + -
402E ASP* 3.2 47.8 - - + +
405E GLN* 3.1 27.4 - - - +
406E VAL* 3.8 26.0 - - - -
484E LEU* 4.3 13.9 - - + +
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Residues in contact with VAL 384 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380E LEU* 2.9 20.6 + - + +
381E LYS* 3.0 8.0 + - - +
383E MET* 1.3 73.1 - - - +
385E GLU* 1.3 63.4 + - + +
387E LYS* 3.0 28.9 - - - +
480E THR* 3.7 32.1 - - + +
483E ASP* 3.5 34.3 - - + +
484E LEU* 4.1 20.9 - - + +
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Residues in contact with GLU 385 (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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381B LYS* 5.1 20.1 - - + +
381E LYS* 3.2 13.7 + - - +
382E THR* 3.0 20.5 - - - +
383E MET 2.7 15.6 - - - +
384E VAL* 1.3 72.9 - - + +
386E THR* 1.3 79.7 + - + +
387E LYS 2.9 5.8 - - - -
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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