Contacts of the helix formed by residues 430 - 444 (chain E) in PDB entry 1I43
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 ASP 430 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316E GLN* 4.5 6.0 + - - +
429E GLU* 1.3 74.8 - - - +
431E PHE* 1.3 68.9 + - - +
432E ASP* 4.4 14.8 + - + +
433E ASP* 3.1 19.2 + - + +
434E LEU* 3.1 11.5 + - - +
56H SER* 2.6 31.7 + - - -
58H GLY* 4.8 6.5 + - - -
59H SER* 3.1 20.6 + - - +
311H HIS* 5.0 6.1 + - - -
315H GLN* 5.6 4.2 + - - -
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Residues in contact with PHE 431 (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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316E GLN* 4.5 6.2 - - - +
320E THR* 4.4 21.5 - - + +
323E ARG* 2.9 77.6 - - + +
324E MET* 3.9 13.5 - - + -
327E ILE* 3.9 17.7 - - + -
429E GLU 3.4 4.3 + - - -
430E ASP* 1.3 72.8 + - - +
432E ASP* 1.3 61.5 + - - +
434E LEU* 3.0 7.8 + - - +
435E LYS* 2.6 66.9 + - + -
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Residues in contact with ASP 432 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430E ASP* 3.3 12.6 + - + +
431E PHE* 1.3 87.6 - - - +
433E ASP* 1.3 59.5 + - - +
435E LYS* 3.8 16.2 + - - +
436E ALA* 2.9 34.7 + - - +
56H SER* 6.5 0.2 - - - -
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Residues in contact with ASP 433 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382E ILE* 3.4 12.0 - - + +
429E GLU* 5.3 0.4 - - + -
430E ASP* 3.1 11.4 + - - +
432E ASP* 1.3 78.4 - - - +
434E LEU* 1.3 63.5 + - + +
436E ALA* 3.8 4.5 - - - +
437E ASP* 3.1 23.0 + - - +
53H PHE 3.5 15.8 - - - +
54H LEU* 3.9 1.1 - - - -
55H ASN* 2.9 39.4 + - - +
56H SER* 3.1 24.3 + - - -
59H SER* 2.6 29.4 + - - +
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Residues in contact with LEU 434 (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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320E THR* 3.8 27.6 - - + -
324E MET* 5.5 0.4 - - + -
382E ILE* 4.0 24.0 - - + -
383E PRO* 5.3 0.2 - - + -
394E SER* 3.3 25.6 - - - +
424E PHE* 4.6 14.6 - - + -
426E PHE* 4.3 11.7 - - + -
427E GLY 4.8 3.8 - - - +
429E GLU* 3.6 40.2 - - + +
430E ASP 3.1 8.7 + - - +
431E PHE* 3.0 6.4 + - + +
433E ASP* 1.3 74.3 - - - +
435E LYS* 1.3 66.7 + - - +
437E ASP* 3.0 5.1 + - - +
438E ILE* 2.9 28.1 + - - +
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Residues in contact with LYS 435 (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 MET* 3.7 19.9 - - + -
327E ILE* 3.8 17.6 - - + +
431E PHE* 2.6 48.2 + - + +
432E ASP* 3.8 16.9 + - - +
434E LEU* 1.3 72.9 - - - +
436E ALA* 1.3 67.7 + - - +
437E ASP 3.1 0.2 + - - -
438E ILE* 3.2 2.1 + - - +
439E LEU* 2.9 50.3 + - + +
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Residues in contact with ALA 436 (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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432E ASP 2.9 21.4 + - - +
433E ASP* 3.8 5.2 - - - +
435E LYS* 1.3 77.7 - - - +
437E ASP* 1.3 57.5 + - - +
439E LEU* 3.8 7.1 - - - +
440E GLN* 2.9 32.1 + - - +
55H ASN* 6.1 3.1 - - - +
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Residues in contact with ASP 437 (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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380E LEU* 3.8 6.6 - - - +
381E LYS* 3.2 26.2 + - - +
382E ILE* 3.0 38.2 + - + +
383E PRO* 3.3 12.6 - - - +
424E PHE* 5.8 0.2 - - - -
433E ASP 3.1 14.4 + - - +
434E LEU* 3.0 11.0 + - + +
436E ALA* 1.3 74.2 - - - +
438E ILE* 1.3 61.1 + - + +
440E GLN* 2.9 33.4 - - - +
441E ALA* 2.9 16.1 + - - +
53H PHE* 5.4 4.6 - - + +
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Residues in contact with ILE 438 (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 MET* 3.5 24.0 - - + -
328E LEU* 3.9 17.5 - - + -
364E PHE* 5.3 1.1 - - + -
376E PHE* 3.7 10.5 - - + -
380E LEU* 3.9 9.6 - - + -
424E PHE* 4.0 24.2 - - + -
426E PHE* 3.4 35.9 - - + -
434E LEU* 2.9 17.0 + - + +
435E LYS 3.7 5.2 - - - +
437E ASP* 1.3 75.7 - - + +
439E LEU* 1.3 58.4 + - + +
441E ALA* 3.3 3.5 + - - +
442E LEU* 2.9 46.5 + - + +
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Residues in contact with LEU 439 (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 MET* 6.0 1.1 - - + -
327E ILE* 4.4 18.6 - - + -
328E LEU* 6.2 0.9 - - + -
331E HIS* 4.0 28.1 + - + +
435E LYS* 2.9 46.5 + - + +
436E ALA* 3.8 6.5 - - - +
438E ILE* 1.3 77.3 - - + +
440E GLN* 1.3 67.3 + - - +
442E LEU* 2.9 19.2 + - + +
443E ASP* 3.0 17.6 + - - +
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Residues in contact with GLN 440 (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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379E ALA* 3.7 20.1 + - - +
381E LYS* 4.0 23.4 + - - +
436E ALA 2.9 17.9 + - - +
437E ASP* 2.9 30.8 - - - +
439E LEU* 1.3 76.6 - - - +
441E ALA* 1.3 65.9 + - - +
443E ASP* 3.4 20.3 - - - +
444E SER* 3.1 19.6 + - - -
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Residues in contact with ALA 441 (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 PHE* 3.4 34.0 - - + +
379E ALA* 4.0 10.0 - - + +
380E LEU* 3.5 16.8 - - + +
437E ASP 2.9 18.2 + - - +
438E ILE 3.3 5.4 - - - +
440E GLN* 1.3 83.8 + - - +
442E LEU* 1.3 65.8 + - - +
444E SER* 3.1 22.4 + - - -
445E ILE 4.1 1.7 + - - -
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Residues in contact with LEU 442 (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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328E LEU* 3.8 18.2 - - + -
331E HIS* 4.1 23.3 - - + +
333E LYS* 3.5 41.0 + - + +
334E VAL* 4.0 13.7 - - + -
364E PHE* 5.5 0.4 - - + -
366E VAL* 4.8 7.2 - - + -
376E PHE* 3.6 18.4 - - + -
438E ILE* 2.9 38.7 + - + +
439E LEU* 2.9 8.5 + - + +
441E ALA* 1.3 73.1 - - - +
443E ASP* 1.3 65.8 + - - +
444E SER 3.3 0.2 - - - -
445E ILE* 3.3 31.6 + - + +
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Residues in contact with ASP 443 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331E HIS* 5.4 5.5 + - - -
333E LYS* 3.3 19.0 + - - +
439E LEU* 3.0 14.1 + - - +
440E GLN* 3.4 18.1 - - - +
441E ALA 3.1 0.2 - - - -
442E LEU* 1.3 79.2 - - - +
444E SER* 1.3 55.5 + - - +
445E ILE 2.8 13.9 + - - -
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Residues in contact with SER 444 (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 LYS* 3.9 23.9 - - - +
379E ALA* 4.0 15.1 - - - +
440E GLN* 3.1 19.4 + - - -
441E ALA* 3.1 12.9 + - - -
443E ASP* 1.3 74.5 - - - +
445E ILE* 1.3 60.3 + - - +
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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