Contacts of the helix formed by residues 413 - 434 (chain E) in PDB entry 2CEA
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 413 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411E LEU* 3.7 5.1 + - - -
412E ILE* 1.3 74.7 - - - +
414E PRO* 1.3 64.0 - - - +
415E ALA* 3.4 16.6 + - - +
416E GLU* 2.4 50.6 + - - -
417E LYS* 2.8 11.3 + - - -
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Residues in contact with PRO 414 (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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411E LEU* 5.4 4.0 - - + -
412E ILE 3.5 9.4 - - - +
413E SER* 1.3 82.1 - - - +
415E ALA* 1.3 62.3 + - - +
417E LYS* 3.3 15.4 + - + +
418E ARG* 3.0 27.6 + - - +
587E LEU* 5.5 0.2 - - - +
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Residues in contact with ALA 415 (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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413E SER* 2.8 14.5 + - - +
414E PRO* 1.3 76.4 - - - +
416E GLU* 1.3 63.4 + - - +
418E ARG* 3.0 25.6 + - - +
419E ILE* 3.2 12.7 + - + +
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Residues in contact with GLU 416 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412E ILE* 3.7 16.9 - - + +
413E SER* 2.4 45.1 + - - +
415E ALA* 1.3 71.2 - - - +
417E LYS* 1.3 61.9 + - - +
419E ILE* 2.9 20.4 + - + +
420E ILE* 3.0 21.6 + - + +
465F TYR* 3.6 26.5 - - + +
466F LEU* 3.5 42.7 + - + +
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Residues in contact with LYS 417 (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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360E LYS 5.7 3.4 + - - -
363E PRO* 5.7 15.4 - - + +
412E ILE* 3.7 29.8 - - + +
413E SER 2.8 10.0 + - - +
414E PRO* 3.4 18.1 - - + +
416E GLU* 1.3 73.5 - - - +
418E ARG* 1.3 63.3 + - - +
420E ILE* 3.2 9.9 + - + +
421E ALA* 2.8 24.9 + - - +
445E ILE* 4.8 22.4 - - + +
587E LEU* 3.9 37.6 + - + +
590E GLU* 5.6 7.2 + - - +
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Residues in contact with ARG 418 (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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414E PRO 3.0 18.2 + - - +
415E ALA* 3.0 13.9 - - - +
417E LYS* 1.3 76.4 - - - +
419E ILE* 1.3 58.3 + - + +
421E ALA* 3.2 4.0 + - - +
422E TYR* 3.0 55.8 + - - -
489E VAL* 5.3 3.8 - - - +
490E PHE* 3.9 28.7 - - + -
587E LEU* 4.1 29.0 - - + +
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Residues in contact with ILE 419 (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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415E ALA* 3.8 13.0 - - + +
416E GLU* 2.9 12.7 + - + +
418E ARG* 1.3 77.1 - - - +
420E ILE* 1.3 68.4 + - - +
422E TYR* 3.2 2.8 + - - +
423E HIS* 2.9 22.9 + - + +
486E GLU* 3.9 31.8 - - + +
490E PHE* 3.9 34.1 - - + -
494E THR* 4.2 18.2 - - + +
466F LEU* 4.3 17.7 - - + -
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Residues in contact with ILE 420 (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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412E ILE* 4.1 26.2 - - + -
416E GLU* 3.0 25.8 + - + +
417E LYS* 3.6 9.0 - - + +
419E ILE* 1.3 75.6 - - - +
421E ALA* 1.3 57.7 + - - +
423E HIS* 3.2 8.0 + - + +
424E GLU* 3.0 37.1 + - + +
444E SER 5.3 0.2 - - - +
445E ILE* 4.1 32.3 - - + +
466F LEU* 3.7 23.3 - - + -
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Residues in contact with ALA 421 (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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417E LYS 2.8 13.7 + - - +
418E ARG 3.3 9.2 - - - +
420E ILE* 1.3 75.0 - - - +
422E TYR* 1.3 64.1 + - - +
424E GLU 3.4 0.5 + - - -
425E ALA* 3.0 25.5 + - - +
445E ILE* 3.6 20.4 - - + +
583E VAL* 3.8 22.4 - - + -
586E LEU* 3.9 11.2 - - + +
587E LEU* 3.8 15.3 - - + -
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Residues in contact with TYR 422 (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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418E ARG* 3.0 50.0 + - - +
419E ILE 3.8 5.8 - - - +
421E ALA* 1.3 75.9 - - - +
423E HIS* 1.3 57.5 + - - +
425E ALA* 3.5 1.3 + - - +
426E GLY 2.8 23.6 + - - -
485E ALA* 3.4 19.8 - - + +
486E GLU* 5.3 1.1 - - - +
489E VAL* 3.7 29.4 - - + +
490E PHE* 4.1 21.5 - + + -
576E ARG* 5.0 0.7 + - - -
579E LEU* 3.7 23.3 - - + +
580E ASP* 2.8 36.1 + - - +
583E VAL* 3.7 35.1 - - + +
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Residues in contact with HIS 423 (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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419E ILE* 2.9 18.4 + - + +
420E ILE* 3.4 9.6 - - + +
421E ALA 3.2 0.2 - - - -
422E TYR* 1.3 77.6 - - - +
424E GLU* 1.3 76.6 + - - +
426E GLY 3.3 0.2 + - - -
427E HIS* 3.3 11.4 + - - -
482E GLY* 3.1 41.9 - - - +
486E GLU* 3.1 23.1 + - + +
496E GLY* 4.1 6.7 + - - -
497E ALA* 3.9 28.0 - - + -
500E ASP* 3.3 9.0 - - - -
1603E ZN 2.1 36.7 - - - -
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Residues in contact with GLU 424 (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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420E ILE* 3.0 26.8 + - + +
421E ALA 4.2 2.2 - - - +
423E HIS* 1.3 97.2 - - + +
425E ALA* 1.3 67.2 + - - +
427E HIS* 3.3 18.2 + - - +
428E ALA* 3.2 19.4 + - - +
443E ILE* 3.6 27.3 - - + +
444E SER 3.7 21.2 + - - +
445E ILE* 4.4 6.5 - - + -
1603E ZN 3.9 3.3 - - - -
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Residues in contact with ALA 425 (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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421E ALA 3.0 18.9 + - - +
422E TYR 3.8 1.8 - - - +
424E GLU* 1.3 76.2 - - - +
426E GLY* 1.3 65.6 + - - +
428E ALA* 2.9 9.1 + - - +
429E VAL* 2.8 25.5 + - + +
443E ILE* 4.7 2.9 - - - -
579E LEU* 3.7 19.7 - - + -
582E ILE* 3.7 29.4 - - + -
583E VAL* 4.0 9.6 - - + -
586E LEU* 4.5 2.1 - - + +
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Residues in contact with GLY 426 (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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422E TYR 2.8 18.3 + - - -
423E HIS 3.6 3.1 - - - -
424E GLU 3.1 0.4 - - - -
425E ALA* 1.3 78.2 - - - +
427E HIS* 1.3 65.8 + - - +
428E ALA 3.0 0.2 + - - -
429E VAL* 3.8 0.7 - - - +
430E VAL* 3.1 24.4 + - - +
481E GLY 4.1 10.1 - - - -
485E ALA* 4.1 5.8 - - - -
572E ILE* 4.0 11.9 - - - -
579E LEU* 3.7 11.8 - - - +
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Residues in contact with HIS 427 (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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423E HIS* 3.3 17.8 + - - -
424E GLU* 3.3 23.1 + - - +
426E GLY* 1.3 73.9 - - - +
428E ALA* 1.3 62.0 + - - +
430E VAL* 3.9 1.6 - - - +
431E SER* 2.8 31.6 + - - +
440E VAL* 5.4 0.9 - - + -
478E ALA* 2.9 26.9 + - + +
479E LEU* 3.0 26.2 - - + +
482E GLY 3.6 9.3 + - - +
500E ASP* 2.9 18.6 - - - -
1603E ZN 2.1 32.1 - - - -
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Residues in contact with ALA 428 (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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424E GLU 3.2 5.0 + - - +
425E ALA* 2.9 8.8 + - - +
427E HIS* 1.3 80.2 - - - +
429E VAL* 1.3 60.1 + - - +
431E SER* 3.3 2.6 + - - -
432E THR* 2.6 33.1 + - - -
440E VAL* 4.1 15.9 - - + -
443E ILE* 3.7 25.6 - - + -
597E LEU* 3.4 24.5 - - + -
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Residues in contact with VAL 429 (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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425E ALA 2.8 23.4 + - - +
426E GLY 3.8 3.1 - - - +
428E ALA* 1.3 70.6 - - - +
430E VAL* 1.3 66.2 + - - +
432E THR* 2.9 14.7 + - - -
433E VAL* 3.0 21.7 + - + +
571E ILE* 4.1 15.0 - - + +
572E ILE* 4.7 6.5 - - + -
575E TYR* 4.0 26.9 - - + +
579E LEU* 3.3 30.1 - - + +
582E ILE* 4.2 21.3 - - + -
597E LEU* 5.1 0.9 - - - -
601E LEU* 4.4 14.6 - - + -
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Residues in contact with VAL 430 (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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426E GLY 3.1 15.0 + - - +
427E HIS 3.9 2.0 - - - +
429E VAL* 1.3 78.8 - - - +
431E SER* 1.3 62.8 + - - +
433E VAL* 3.2 0.3 + - - +
434E VAL* 2.9 27.5 + - + +
477E THR* 3.5 18.8 - - + -
478E ALA* 3.4 34.1 - - + +
481E GLY* 4.0 15.9 - - - -
568E ALA* 4.3 15.5 - - + +
571E ILE* 4.0 27.3 - - + +
572E ILE* 4.4 8.3 - - + -
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Residues in contact with SER 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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427E HIS* 2.8 23.8 + - - +
428E ALA 3.6 5.2 - - - -
430E VAL* 1.3 76.9 - - - +
432E THR* 1.3 61.3 + - - +
434E VAL* 3.4 6.3 - - - +
437E GLY* 3.4 27.8 - - - +
438E GLU* 4.2 22.8 + - - +
440E VAL* 4.2 11.5 - - - +
478E ALA* 3.3 23.0 - - - +
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Residues in contact with THR 432 (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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428E ALA 2.6 22.3 + - - -
429E VAL 2.9 5.5 + - - -
431E SER* 1.3 80.2 - - - +
433E VAL* 1.3 60.5 + - - +
434E VAL 4.3 2.8 - - - +
440E VAL* 5.0 5.7 + - - +
597E LEU* 3.7 12.8 - - - +
598E ARG* 3.9 31.4 - - + +
601E LEU* 3.7 23.6 - - + -
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Residues in contact with VAL 433 (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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429E VAL* 3.0 19.4 + - + +
430E VAL 3.9 2.0 - - - +
432E THR* 1.3 76.8 - - - +
434E VAL* 1.3 65.1 + - - +
435E PRO* 3.3 8.0 - - - +
571E ILE* 4.1 22.4 - - + -
575E TYR* 3.5 47.3 - - + +
601E LEU* 4.4 8.7 - - + -
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Residues in contact with VAL 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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430E VAL* 2.9 19.4 + - + +
431E SER* 3.4 9.3 - - - +
432E THR 4.3 2.5 - - - +
433E VAL* 1.3 77.2 - - - +
435E PRO* 1.3 68.1 - - - +
437E GLY* 2.9 25.3 + - - +
474E ASP* 3.2 40.2 - - + +
477E THR* 4.5 11.7 - - + -
567E ARG* 3.6 36.3 - - - +
571E ILE* 4.6 7.0 - - + -
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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