Contacts of the helix formed by residues 575 - 590 (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 TYR 575 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429F VAL* 4.2 13.1 - - + +
433F VAL* 3.5 41.3 - - + +
571F ILE* 2.9 22.8 + - + +
572F ILE 3.2 4.4 - - - +
574F LYS* 1.3 116.6 + - + +
576F ARG* 1.3 61.4 + - - +
577F LYS 3.2 2.9 + - - -
578F GLN* 3.5 33.6 - - + +
579F LEU* 3.2 21.1 + - - +
605F PHE* 3.9 18.2 - + - -
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Residues in contact with ARG 576 (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* 5.5 0.4 + - - -
488F VAL* 3.7 28.1 + - - +
489F VAL* 3.5 34.2 + - - +
572F ILE* 2.8 15.3 + - - +
573F ARG* 3.6 13.6 + - - +
574F LYS 3.5 2.6 - - - -
575F TYR* 1.3 77.6 - - - +
577F LYS* 1.3 63.8 + - - +
579F LEU* 3.3 17.8 + - - +
580F ASP* 3.0 46.0 + - - +
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Residues in contact with LYS 577 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575F TYR 3.2 1.0 - - - -
576F ARG* 1.3 78.5 - - - +
578F GLN* 1.3 70.9 + - - +
580F ASP* 3.1 11.9 + - - +
581F ASN* 2.9 44.1 + - - +
604F GLU* 5.1 2.7 - - - +
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Residues in contact with GLN 578 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429F VAL* 4.9 0.7 - - + -
574F LYS 5.0 1.0 + - - -
575F TYR* 3.5 44.1 - - + +
577F LYS* 1.3 97.9 - - - +
579F LEU* 1.3 60.1 + - - +
581F ASN 3.7 0.2 - - - -
582F ILE* 2.8 38.0 + - + +
604F GLU* 3.2 56.0 - - + +
605F PHE* 4.0 17.9 - - + -
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Residues in contact with LEU 579 (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* 4.0 20.4 - - + +
425F ALA* 3.0 39.5 - - + +
426F GLY* 3.6 14.6 - - - +
429F VAL* 4.3 13.2 - - + +
485F ALA* 4.1 11.7 - - + -
489F VAL* 4.2 9.4 - - + -
572F ILE* 3.4 34.5 - - + +
575F TYR 3.2 14.8 + - - +
576F ARG* 3.4 13.2 - - - +
577F LYS 3.1 0.2 - - - -
578F GLN* 1.3 78.2 - - - +
580F ASP* 1.3 52.8 + - - +
582F ILE* 3.4 2.4 + - - +
583F VAL* 2.5 39.5 + - + +
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Residues in contact with ASP 580 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422F TYR* 2.9 30.9 + - - +
576F ARG* 3.0 40.9 + - - +
577F LYS* 3.1 11.3 + - - +
579F LEU* 1.3 73.6 - - - +
581F ASN* 1.3 66.9 + - - +
583F VAL* 3.1 7.4 + - - +
584F GLU* 3.0 23.2 + - - +
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Residues in contact with ASN 581 (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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577F LYS* 2.9 36.7 + - - +
578F GLN 3.7 2.9 - - - +
580F ASP* 1.3 78.2 - - - +
582F ILE* 1.3 62.6 + - - +
583F VAL 3.1 0.9 + - - -
584F GLU* 3.3 5.2 + - - +
585F ILE* 3.1 32.3 + - + +
604F GLU* 2.7 41.1 + - - +
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Residues in contact with ILE 582 (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* 4.4 11.2 - - + -
428F ALA* 5.0 7.0 - - + -
429F VAL* 3.9 23.8 - - + -
443F ILE* 3.6 29.2 - - + -
578F GLN* 2.8 28.3 + - + +
579F LEU 3.7 4.7 - - - +
581F ASN* 1.3 76.1 - - - +
583F VAL* 1.3 60.9 + - - +
585F ILE* 3.7 10.2 + - + +
586F LEU* 3.1 26.6 + - + +
592F ILE* 5.9 0.2 - - - +
600F ILE* 5.2 6.5 - - + -
601F LEU* 4.2 23.6 - - + -
604F GLU* 4.5 11.7 - - + +
605F PHE* 4.7 10.5 - - + -
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Residues in contact with VAL 583 (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* 6.0 0.4 - - - +
421F ALA* 3.4 29.8 - - + -
422F TYR* 3.5 45.3 - - + +
425F ALA* 3.9 12.6 - - + -
579F LEU 2.5 35.2 + - - +
580F ASP 3.5 4.5 - - - +
581F ASN 3.1 0.4 - - - -
582F ILE* 1.3 74.4 - - - +
584F GLU* 1.3 68.0 + - - +
585F ILE 3.0 1.6 - - - -
586F LEU* 3.0 7.4 + - - +
587F LEU* 2.9 32.9 + - + +
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Residues in contact with GLU 584 (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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580F ASP 3.0 15.0 + - - +
581F ASN* 4.0 5.6 - - - +
583F VAL* 1.3 75.4 - - - +
585F ILE* 1.3 64.3 + - + +
587F LEU* 3.4 15.9 + - + +
588F GLU* 3.4 29.5 + - - +
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Residues in contact with ILE 585 (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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581F ASN* 3.1 26.7 - - + +
582F ILE* 3.7 9.4 - - + +
584F GLU* 1.3 76.1 - - + +
586F LEU* 1.3 65.8 + - - +
588F GLU* 3.0 8.9 + - - +
589F LYS* 2.9 33.1 + - + +
592F ILE* 4.3 20.4 - - + -
596F GLU* 6.1 0.2 - - - +
600F ILE* 4.3 30.5 - - + -
604F GLU* 5.2 1.8 - - - +
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Residues in contact with LEU 586 (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* 4.2 16.8 - - + +
424F GLU* 4.4 7.0 - - + -
425F ALA* 4.5 1.8 - - + +
443F ILE* 3.6 41.3 - - + +
445F ILE* 2.9 35.5 - - + +
582F ILE* 3.1 18.5 + - + +
583F VAL* 3.0 5.8 + - - +
585F ILE* 1.3 78.4 - - - +
587F LEU* 1.3 57.8 + - - +
590F GLU 2.7 36.8 + - - +
592F ILE* 2.8 40.8 - - + -
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Residues in contact with LEU 587 (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* 3.7 68.0 + - + +
418F ARG* 4.3 30.7 - - + +
421F ALA* 4.4 11.4 - - + -
445F ILE* 3.8 5.6 - - + -
583F VAL* 2.9 30.7 + - + +
584F GLU* 3.5 16.6 - - + +
586F LEU* 1.3 76.9 - - - +
588F GLU* 1.3 60.8 + - - +
590F GLU* 4.5 6.2 - - - +
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Residues in contact with GLU 588 (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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584F GLU* 3.4 19.8 + - - +
585F ILE* 3.0 10.8 + - - +
587F LEU* 1.3 82.6 - - - +
589F LYS* 1.3 66.6 + - + +
590F GLU* 3.6 7.9 - - - +
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Residues in contact with LYS 589 (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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585F ILE* 2.9 28.8 + - + +
588F GLU* 1.3 84.9 - - + +
590F GLU* 1.3 63.3 + - - +
591F THR* 2.5 38.4 + - - +
592F ILE* 4.3 10.8 - - + +
596F GLU* 3.5 31.4 + - - +
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Residues in contact with GLU 590 (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* 4.7 12.0 - - - +
444F SER* 2.9 4.2 + - - -
445F ILE* 2.7 54.2 + - - +
446F ILE* 4.4 12.7 - - + +
586F LEU* 2.7 25.0 + - - +
587F LEU 4.5 10.9 - - - +
588F GLU 4.3 5.0 - - - +
589F LYS* 1.3 74.6 - - - +
591F THR* 1.3 64.0 + - - +
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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