Contacts of the helix formed by residues 413 - 434 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A ILE* 1.3 92.6 - - - +
414A PRO* 1.3 71.1 - - - +
415A ALA* 3.9 6.3 - - - -
416A GLU* 2.7 43.4 + - - +
417A LYS* 3.0 13.9 + - - +
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Residues in contact with PRO 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ILE 4.3 0.9 - - - +
413A SER* 1.3 85.8 - - - +
415A ALA* 1.3 69.1 + - + +
416A GLU 3.3 0.2 - - - -
417A LYS* 3.7 12.2 - - + +
418A ARG* 3.1 27.2 + - - +
587A LEU* 5.6 0.2 - - - +
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Residues in contact with ALA 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A SER* 4.5 6.5 - - - -
414A PRO* 1.3 82.7 - - + +
416A GLU* 1.3 60.0 + - - +
418A ARG* 3.2 21.9 - - - +
419A ILE* 3.3 18.1 - - + +
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Residues in contact with GLU 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ILE* 4.0 17.2 - - + +
413A SER* 2.7 38.3 + - - +
414A PRO 3.3 0.2 - - - -
415A ALA* 1.3 77.1 - - - +
417A LYS* 1.3 66.3 + - - +
419A ILE* 3.1 13.0 + - + +
420A ILE* 3.0 42.2 + - + +
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Residues in contact with LYS 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ILE* 4.0 16.1 - - + +
413A SER 3.0 19.0 + - - +
414A PRO* 3.7 11.2 - - + +
416A GLU* 1.3 76.8 - - - +
418A ARG* 1.3 64.5 + - - +
419A ILE 3.2 0.3 + - - -
420A ILE* 3.3 9.6 + - + +
421A ALA* 2.9 23.2 + - - +
445A ILE* 3.9 22.0 - - + +
587A LEU* 2.9 48.9 + - + +
588A GLU 5.4 0.2 + - - -
590A GLU* 4.4 15.4 + - - +
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Residues in contact with ARG 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A PRO 3.1 16.3 + - - +
415A ALA* 3.2 13.9 - - - +
417A LYS* 1.3 78.4 - - - +
419A ILE* 1.3 63.4 + - - +
421A ALA* 3.2 4.1 + - - +
422A TYR* 3.0 57.5 + - - -
489A VAL* 5.1 4.6 - - - +
490A PHE* 4.2 25.4 - - + -
583A VAL* 5.4 1.0 - - - +
587A LEU* 4.1 27.3 - - + +
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Residues in contact with ILE 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A ALA* 3.3 20.0 - - + +
416A GLU* 3.1 12.0 + - + +
418A ARG* 1.3 72.2 - - - +
420A ILE* 1.3 69.8 + - + +
422A TYR* 3.1 4.0 + - - +
423A HIS* 2.9 21.9 + - + +
486A GLU* 3.7 32.9 - - + +
490A PHE* 3.9 33.4 - - + -
494A THR* 4.3 20.6 - - + +
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Residues in contact with ILE 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A ILE* 3.7 27.1 - - + -
416A GLU* 3.0 37.5 + - + +
417A LYS* 3.6 7.2 - - + +
419A ILE* 1.3 75.8 - - + +
421A ALA* 1.3 58.1 + - - +
423A HIS* 3.2 7.8 + - - +
424A GLU* 2.9 36.2 + - + +
445A ILE* 3.9 35.0 - - + +
446A ILE 5.8 0.7 - - - +
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Residues in contact with ALA 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A LYS 2.9 13.7 + - - +
418A ARG 3.4 8.5 - - - +
419A ILE 3.1 0.4 - - - -
420A ILE* 1.3 77.4 - - - +
422A TYR* 1.3 57.8 + - - +
424A GLU* 3.4 1.6 + - - +
425A ALA* 2.8 30.3 + - - +
445A ILE* 4.1 19.0 - - + +
583A VAL* 3.6 22.7 - - + +
586A LEU* 4.0 11.1 - - + +
587A LEU* 4.0 16.2 - - + -
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Residues in contact with TYR 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A ARG* 3.0 53.2 + - - -
419A ILE 3.7 6.1 - - - +
421A ALA* 1.3 72.7 - - - +
423A HIS* 1.3 60.2 + - - +
425A ALA* 3.7 1.0 - - - +
426A GLY* 2.8 27.0 + - - -
485A ALA* 3.6 16.5 - - + +
486A GLU* 5.4 0.9 - - + +
489A VAL* 3.6 33.1 - - + +
490A PHE* 4.0 23.3 - + + -
576A ARG* 5.0 1.6 + - - -
579A LEU* 3.9 17.9 - - + +
580A ASP* 2.6 35.7 + - - +
583A VAL* 3.6 34.8 - - + +
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Residues in contact with HIS 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A ILE* 2.9 14.1 + - + +
420A ILE* 3.4 11.9 - - - +
422A TYR* 1.3 76.7 - - - +
424A GLU* 1.3 69.8 + - + +
426A GLY 3.1 1.7 + - - -
427A HIS* 3.0 27.2 + + - -
482A GLY* 3.1 32.8 - - - -
486A GLU* 2.7 25.5 + - + +
496A GLY* 4.2 5.8 - - - -
497A ALA* 3.6 29.6 - - + -
500A ASP* 3.6 6.7 - - - -
1603A ZN 2.1 36.7 - - - -
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Residues in contact with GLU 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A ILE* 2.9 29.5 + - + +
421A ALA* 3.9 3.4 - - - +
423A HIS* 1.3 82.9 - - + +
425A ALA* 1.3 65.7 + - - +
427A HIS* 3.1 32.2 + - - +
428A ALA* 3.1 12.5 + - - +
443A ILE* 3.7 29.5 - - + +
444A SER 3.9 20.0 + - - +
445A ILE* 4.7 0.9 - - + -
586A LEU* 4.6 4.3 - - + -
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Residues in contact with ALA 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A ALA 2.8 18.8 + - - +
422A TYR 3.7 0.9 - - - +
424A GLU* 1.3 76.1 - - - +
426A GLY* 1.3 57.6 + - - +
428A ALA* 3.1 7.8 + - - +
429A VAL* 2.8 33.8 + - - +
443A ILE* 4.6 3.1 - - - +
579A LEU* 3.2 26.7 - - + -
582A ILE* 3.8 21.1 - - + -
583A VAL* 3.8 11.7 - - + -
586A LEU* 4.7 2.4 - - + +
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Residues in contact with GLY 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A TYR 2.8 15.2 + - - -
423A HIS 3.4 5.6 - - - -
424A GLU 3.0 0.4 - - - -
425A ALA* 1.3 74.8 - - - +
427A HIS* 1.3 68.3 + - - +
428A ALA 3.0 0.5 + - - -
429A VAL* 4.0 0.2 - - - +
430A VAL* 3.1 25.8 + - - +
481A GLY 3.9 19.1 - - - -
485A ALA* 4.1 7.6 - - - -
572A ILE* 4.2 10.1 - - - -
579A LEU* 4.0 0.9 - - - +
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Residues in contact with HIS 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A HIS* 3.0 26.4 + + - -
424A GLU* 3.1 21.3 + - - +
426A GLY* 1.3 74.1 - - - +
428A ALA* 1.3 62.9 + - - +
430A VAL* 4.0 1.2 - - - +
431A SER* 3.0 28.3 + - - +
440A VAL* 5.5 0.2 - - - -
478A ALA* 2.9 26.8 + - + +
479A LEU* 3.1 24.7 - - + +
482A GLY 3.8 10.3 + - - +
500A ASP* 2.9 20.2 + - - -
1603A ZN 2.1 30.4 - - - -
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Residues in contact with ALA 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A GLU 3.1 6.3 + - - +
425A ALA 3.1 7.2 + - - +
426A GLY 3.0 0.8 - - - -
427A HIS* 1.3 76.1 - - - +
429A VAL* 1.3 64.6 + - - +
431A SER* 3.6 1.7 + - - -
432A THR* 2.9 30.2 + - - -
440A VAL* 4.1 14.8 - - + +
443A ILE* 3.3 37.2 - - + -
597A LEU* 3.9 15.9 - - + +
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Residues in contact with VAL 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425A ALA 2.8 23.0 + - - +
426A GLY 4.0 2.2 - - - +
428A ALA* 1.3 71.4 - - - +
430A VAL* 1.3 64.7 + - - +
432A THR* 3.1 4.3 + - - -
433A VAL* 3.0 32.9 + - + +
571A ILE* 3.9 20.6 - - + -
572A ILE* 4.7 11.0 - - + -
575A TYR* 4.1 18.4 - - + -
579A LEU* 4.2 17.5 - - + +
582A ILE* 3.7 29.6 - - + -
601A LEU* 4.4 17.0 - - + -
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Residues in contact with VAL 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A GLY 3.1 16.8 + - - +
427A HIS 4.1 2.0 - - - +
429A VAL* 1.3 74.9 - - - +
431A SER* 1.3 64.5 + - - +
433A VAL 2.9 1.2 + - - -
434A VAL* 2.8 29.6 + - + +
477A THR* 3.7 31.2 - - + -
478A ALA* 3.8 16.8 - - - +
481A GLY* 3.9 18.2 - - - -
568A ALA* 4.5 8.3 - - + -
571A ILE* 3.8 31.4 - - + -
572A ILE* 4.2 11.7 - - + -
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Residues in contact with SER 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A HIS* 3.0 19.9 + - - +
428A ALA 3.6 4.5 - - - -
430A VAL* 1.3 77.5 - - - +
432A THR* 1.3 62.4 + - - +
434A VAL* 3.4 13.9 - - - +
437A GLY* 3.5 17.3 - - - -
438A GLU* 3.8 27.5 + - - +
440A VAL* 4.1 12.2 - - - +
478A ALA* 3.6 21.5 - - - +
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Residues in contact with THR 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A ALA 2.9 17.1 + - - -
429A VAL 3.5 4.5 - - - -
430A VAL 3.1 1.0 - - - -
431A SER* 1.3 79.7 - - - +
433A VAL* 1.3 64.4 + - + +
434A VAL 3.7 3.8 - - - +
438A GLU 5.8 0.2 - - - -
439A PRO* 6.5 0.9 - - - -
440A VAL* 4.7 6.8 + - - +
597A LEU* 3.5 17.2 - - - +
598A ARG* 4.3 20.6 + - + +
601A LEU* 3.7 25.6 - - + -
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Residues in contact with VAL 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429A VAL* 3.1 20.2 - - + +
430A VAL 2.9 3.2 + - - +
432A THR* 1.3 78.5 - - + +
434A VAL* 1.3 68.9 + - - +
435A PRO* 3.3 6.4 - - - +
571A ILE* 3.9 28.5 - - + -
575A TYR* 3.7 42.2 - - + +
601A LEU* 4.9 5.4 - - + -
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Residues in contact with VAL 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A VAL* 2.8 31.9 + - + +
431A SER* 3.4 8.2 - - - +
432A THR 3.7 3.8 - - - +
433A VAL* 1.3 80.7 - - - +
435A PRO* 1.3 67.1 - - - +
436A ASN 3.1 0.2 + - - -
437A GLY* 3.2 22.7 + - - +
474A ASP* 2.9 42.8 - - + +
477A THR* 4.4 3.8 - - + -
567A ARG* 3.4 26.9 - - - +
571A ILE* 4.4 6.7 - - + -
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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
------------------------------------------------------------
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