Contacts of the helix formed by residues 413 - 434 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412F ILE* 1.3 81.2 - - - +
414F PRO* 1.3 55.0 - - - -
415F ALA* 3.0 8.7 - - - +
416F GLU* 1.6 84.0 + - - +
417F LYS* 2.9 9.9 + - - +
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Residues in contact with PRO 414 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412F ILE 3.8 6.7 - - - +
413F SER* 1.3 79.5 - - - +
415F ALA* 1.3 65.6 + - - +
416F GLU 3.2 0.2 - - - -
417F LYS* 3.5 29.0 - - + +
418F ARG* 3.1 24.9 + - - +
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Residues in contact with ALA 415 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413F SER* 2.7 10.7 + - - +
414F PRO* 1.3 78.1 - - - +
416F GLU* 1.3 66.2 + - + +
418F ARG* 3.3 18.4 - - - +
419F ILE* 3.8 10.2 + - - +
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Residues in contact with GLU 416 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412F ILE* 4.1 9.1 + - - +
413F SER* 1.6 65.2 + - - +
415F ALA* 1.3 68.7 - - + +
417F LYS* 1.3 67.9 + - - +
418F ARG 2.9 1.6 - - - -
419F ILE* 2.6 28.6 + - + +
420F ILE* 3.1 22.8 + - + +
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Residues in contact with LYS 417 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412F ILE 5.4 1.5 - - - +
413F SER 2.9 7.7 + - - +
414F PRO* 3.5 34.2 - - + +
416F GLU* 1.3 74.7 - - - +
418F ARG* 1.3 64.3 + - - +
420F ILE* 3.3 13.7 + - + +
421F ALA* 3.0 22.3 + - - +
445F ILE* 5.2 12.5 - - + +
587F LEU* 3.7 44.6 + - + +
590F GLU* 4.7 15.6 + - - +
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Residues in contact with ARG 418 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414F PRO 3.1 18.6 - - - +
415F ALA* 3.3 11.7 - - - +
416F GLU 2.7 3.6 + - - -
417F LYS* 1.3 76.6 - - - +
419F ILE* 1.3 65.5 + - + +
421F ALA* 3.3 7.2 - - - +
422F TYR* 3.1 58.1 + - - -
489F VAL* 5.8 1.4 - - - +
490F PHE* 4.4 18.0 - - + -
583F VAL* 6.0 0.2 - - - +
587F LEU* 4.3 27.2 - - + +
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Residues in contact with ILE 419 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415F ALA 3.9 13.5 - - - +
416F GLU* 2.6 22.1 + - + +
418F ARG* 1.3 70.7 - - - +
420F ILE* 1.3 68.6 + - + +
422F TYR* 2.8 15.2 + - - +
423F HIS* 2.8 12.1 + - + +
486F GLU* 3.9 33.3 - - + +
490F PHE* 3.9 27.8 - - + -
494F THR* 3.9 23.6 - - + +
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Residues in contact with ILE 420 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412F ILE 5.1 8.7 - - - +
416F GLU* 3.1 29.3 + - + +
417F LYS* 3.9 10.3 - - + +
419F ILE* 1.3 78.3 - - + +
421F ALA* 1.3 62.4 + - - +
423F HIS* 3.3 9.3 + - + +
424F GLU* 3.0 40.0 + - + +
445F ILE* 4.2 21.3 - - + +
447F PRO* 6.4 2.5 - - + -
450F TYR* 4.3 23.1 - - + +
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Residues in contact with ALA 421 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417F LYS 3.0 13.2 + - - +
418F ARG* 3.3 12.8 - - - +
420F ILE* 1.3 78.0 - - - +
422F TYR* 1.3 58.5 + - - +
424F GLU* 3.3 1.7 + - - +
425F ALA* 2.8 29.3 + - - +
445F ILE* 3.6 21.9 - - + +
583F VAL* 3.4 24.9 - - + +
586F LEU* 4.2 5.5 - - + +
587F LEU* 4.4 13.0 - - + -
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Residues in contact with TYR 422 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418F ARG* 3.1 52.2 + - - -
419F ILE 2.8 10.6 + - - +
421F ALA* 1.3 72.7 - - - +
423F HIS* 1.3 66.4 + - - +
425F ALA* 3.6 4.0 - - - +
426F GLY 2.9 18.9 + - - -
485F ALA* 3.4 20.4 - - + +
486F GLU* 5.3 0.7 - - - +
489F VAL* 3.9 30.0 - - + +
490F PHE* 3.5 28.9 - + + -
576F ARG* 5.5 0.7 + - - -
579F LEU* 4.0 13.0 - - + -
580F ASP* 2.9 31.4 + - - -
583F VAL* 3.5 33.2 - - + +
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Residues in contact with HIS 423 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419F ILE* 2.8 12.0 + - + +
420F ILE* 3.4 15.5 - - + +
422F TYR* 1.3 75.5 - - - +
424F GLU* 1.3 74.2 + - - +
426F GLY 3.0 10.2 + - - -
427F HIS* 2.9 32.2 + + - -
482F GLY* 3.2 28.8 - - - +
483F ARG 4.2 3.4 - - - -
486F GLU* 3.3 27.4 + - + +
496F GLY* 4.2 9.4 - - - -
497F ALA* 4.1 17.5 - - - -
500F ASP* 3.4 7.4 - - - -
1606F ZN 2.1 37.5 - - - -
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Residues in contact with GLU 424 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420F ILE* 3.0 25.7 + - + +
421F ALA 3.8 3.1 - - - +
423F HIS* 1.3 84.6 - - - +
425F ALA* 1.3 69.2 + - - +
427F HIS* 3.1 22.5 + - - +
428F ALA* 2.9 22.1 + - - +
443F ILE* 4.6 11.2 - - + +
444F SER 3.6 23.1 - - - +
445F ILE* 4.3 5.8 - - + -
450F TYR* 3.4 31.1 - - - -
451F LYS* 4.0 19.4 - - + +
586F LEU* 4.4 13.2 - - + -
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Residues in contact with ALA 425 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421F ALA 2.8 17.4 + - - +
422F TYR 3.6 2.5 - - - +
424F GLU* 1.3 76.5 - - - +
426F GLY* 1.3 51.4 + - - +
428F ALA* 2.9 10.4 + - - +
429F VAL* 2.7 37.0 + - + +
579F LEU* 3.0 30.5 - - + +
582F ILE* 4.4 16.8 - - + -
583F VAL* 3.9 14.8 - - + -
586F LEU* 4.5 3.9 - - + +
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Residues in contact with GLY 426 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422F TYR 2.9 15.6 + - - -
423F HIS 3.0 4.9 + - - -
425F ALA* 1.3 73.3 - - - +
427F HIS* 1.3 65.1 + - - +
429F VAL* 4.5 0.4 - - - -
430F VAL* 3.1 30.0 + - - +
481F GLY 3.7 20.4 - - - -
485F ALA* 4.0 2.0 - - - -
572F ILE* 3.9 14.8 - - - -
579F LEU* 3.6 2.8 - - - +
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Residues in contact with HIS 427 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423F HIS* 2.9 29.8 + + - -
424F GLU* 3.5 20.6 - - - +
426F GLY* 1.3 74.2 - - - +
428F ALA* 1.3 65.2 + - - +
430F VAL* 4.0 0.5 - - - +
431F SER* 2.9 32.0 + - - +
451F LYS* 4.3 24.2 - - + +
478F ALA 3.0 24.6 + - - +
479F LEU* 3.1 23.3 - - + -
482F GLY 3.8 8.7 + - - +
500F ASP* 3.1 13.5 - - - -
1606F ZN 2.1 36.5 - - - -
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Residues in contact with ALA 428 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424F GLU 2.9 10.7 + - - +
425F ALA* 2.9 13.3 + - - +
427F HIS* 1.3 76.8 - - - +
429F VAL* 1.3 65.6 + - + +
431F SER* 3.4 2.6 + - - -
432F THR* 3.0 28.4 + - - +
440F VAL* 4.2 7.4 - - + +
443F ILE* 3.8 28.3 - - + -
451F LYS* 4.0 10.5 - - - +
582F ILE* 5.0 7.4 - - + -
601F LEU* 5.7 6.5 - - + -
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Residues in contact with VAL 429 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425F ALA 2.7 25.5 + - - +
426F GLY* 4.1 4.7 - - - +
428F ALA* 1.3 70.6 - - - +
430F VAL* 1.3 67.5 + - - +
432F THR* 3.0 3.8 + - - -
433F VAL* 2.9 24.6 + - + +
571F ILE* 4.2 13.0 - - + +
572F ILE* 4.9 9.4 - - + -
575F TYR* 4.2 26.9 - - + +
579F LEU* 4.3 20.4 - - + +
582F ILE* 3.9 24.5 - - + -
605F PHE* 4.2 16.6 - - + -
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Residues in contact with VAL 430 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426F GLY 3.1 17.5 + - - +
427F HIS 4.1 1.3 - - - +
429F VAL* 1.3 74.2 - - - +
431F SER* 1.3 63.8 + - - +
433F VAL 3.2 0.2 + - - -
434F VAL* 2.9 27.4 + - + +
477F THR* 3.3 39.9 - - + +
478F ALA* 3.7 11.9 - - + +
481F GLY* 3.8 16.4 - - - -
568F ALA* 4.2 13.5 - - + +
571F ILE* 3.8 21.3 - - + -
572F ILE* 4.0 16.6 - - + -
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Residues in contact with SER 431 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427F HIS* 2.9 25.8 + - - +
428F ALA 3.6 3.8 - - - -
430F VAL* 1.3 78.4 - - - +
432F THR* 1.3 61.6 + - - +
434F VAL* 3.4 18.9 - - - +
437F GLY* 3.5 14.8 - - - -
438F GLU* 4.2 14.6 + - - +
440F VAL* 3.9 20.4 - - - -
451F LYS* 4.4 8.4 + - - -
478F ALA* 3.5 20.7 - - - +
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Residues in contact with THR 432 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428F ALA 3.0 16.3 + - - -
429F VAL 3.0 5.4 + - - -
431F SER* 1.3 78.4 - - - +
433F VAL* 1.3 63.8 + - - +
434F VAL 3.8 3.8 - - - +
435F PRO* 5.6 0.2 - - - +
440F VAL* 4.1 11.9 - - - +
601F LEU* 4.3 19.3 - - + +
605F PHE* 4.4 34.2 - - + -
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Residues in contact with VAL 433 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429F VAL* 2.9 19.8 + - + +
430F VAL 4.0 0.7 - - - +
432F THR* 1.3 76.0 - - - +
434F VAL* 1.3 67.7 + - - +
435F PRO* 3.5 7.1 - - - +
571F ILE* 4.0 26.2 - - + -
575F TYR* 3.5 40.8 - - + +
605F PHE* 3.5 28.9 - - + -
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Residues in contact with VAL 434 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430F VAL* 2.9 21.9 + - + +
431F SER* 3.4 11.4 - - - +
432F THR 3.8 3.8 - - - +
433F VAL* 1.3 79.9 - - - +
435F PRO* 1.3 67.2 - - + +
437F GLY* 3.2 29.4 + - - +
474F ASP* 3.5 30.1 - - + +
477F THR* 4.7 8.1 - - + -
478F ALA* 5.3 1.1 - - + -
567F ARG* 3.0 39.7 - - - +
571F ILE* 4.9 4.5 - - + +
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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
------------------------------------------------------------
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