Contacts of the helix formed by residues 575 - 590 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C VAL* 3.9 15.8 - - + +
433C VAL* 3.6 34.5 - - + +
571C ILE* 2.8 31.2 + - + +
572C ILE 3.2 4.3 - - - -
574C LYS* 1.3 115.8 + - + +
576C ARG* 1.3 63.8 - - - +
577C LYS 3.2 2.7 - - - -
578C GLN* 3.2 24.5 + - + +
579C LEU* 3.0 20.7 + - - +
605C PHE* 3.4 33.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 576 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C TYR* 4.5 2.0 + - - -
488C VAL* 4.2 16.9 + - - +
489C VAL* 3.3 52.3 + - - +
572C ILE* 2.9 13.0 + - - +
573C ARG* 3.4 17.8 + - - +
574C LYS 3.5 1.6 + - - -
575C TYR* 1.3 76.7 - - - +
577C LYS* 1.3 61.4 + - + +
579C LEU* 3.1 12.4 + - - +
580C ASP* 2.8 55.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 577 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574C LYS 6.2 0.2 - - - +
575C TYR 3.2 0.6 - - - -
576C ARG* 1.3 81.2 - - + +
578C GLN* 1.3 70.1 + - - +
580C ASP* 3.1 11.0 + - - +
581C ASN* 2.9 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 578 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C VAL* 5.0 0.2 - - + -
574C LYS 5.3 1.2 + - - -
575C TYR* 3.2 34.5 - - + +
577C LYS* 1.3 85.2 + - - +
579C LEU* 1.3 68.2 + - - +
581C ASN* 3.1 3.6 + - - +
582C ILE* 2.9 31.7 + - + +
604C GLU* 3.4 49.4 + - + +
605C PHE* 3.9 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 579 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C TYR* 3.8 30.1 - - + +
425C ALA* 3.2 42.6 - - + -
426C GLY* 3.7 7.4 - - - +
429C VAL* 3.8 17.6 - - + +
485C ALA* 4.3 4.9 - - + -
489C VAL* 4.0 7.9 - - + -
572C ILE* 3.7 33.4 - - + +
575C TYR 3.0 12.6 + - - +
576C ARG* 3.1 12.8 + - - +
578C GLN* 1.3 77.4 - - - +
580C ASP* 1.3 63.0 + - - +
582C ILE* 3.2 2.7 + - - +
583C VAL* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 580 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C TYR* 2.8 29.9 + - - +
576C ARG* 2.8 47.0 + - - +
577C LYS* 3.4 11.3 - - - +
579C LEU* 1.3 74.9 - - - +
581C ASN* 1.3 66.0 + - - +
583C VAL* 3.4 3.4 + - - +
584C GLU* 3.1 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 581 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577C LYS* 2.9 21.9 + - - +
578C GLN 3.1 7.6 + - - +
580C ASP* 1.3 80.1 - - - +
582C ILE* 1.3 61.4 + - - +
584C GLU* 3.3 24.2 + - - +
585C ILE* 3.3 20.7 + - + +
604C GLU* 2.7 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 582 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C ALA* 4.1 10.5 - - + -
428C ALA* 4.9 6.7 - - + -
429C VAL* 4.0 23.6 - - + +
443C ILE* 3.8 27.6 - - + -
578C GLN* 2.9 22.2 + - - +
579C LEU 3.7 3.8 - - - +
581C ASN* 1.3 73.8 - - + +
583C VAL* 1.3 62.0 + - - +
585C ILE* 3.4 10.4 + - + +
586C LEU* 2.9 32.3 + - + +
592C ILE* 5.1 1.9 - - + +
600C ILE* 5.5 6.7 - - + -
601C LEU* 4.0 27.6 - - + -
604C GLU* 5.1 8.3 - - + +
605C PHE* 4.6 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 583 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C ARG* 4.7 2.5 - - - +
421C ALA* 3.5 24.2 - - + +
422C TYR* 3.7 47.8 - - + -
425C ALA* 3.8 17.9 - - + -
579C LEU 3.0 16.9 + - - +
580C ASP 3.5 5.8 - - - +
582C ILE* 1.3 77.2 - - - +
584C GLU* 1.3 56.0 + - - +
586C LEU* 2.9 9.5 + - - +
587C LEU* 2.7 47.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 584 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580C ASP* 3.1 14.6 + - - +
581C ASN* 3.3 20.2 + - - +
583C VAL* 1.3 81.6 - - - +
585C ILE* 1.3 64.3 + - + +
587C LEU* 3.6 10.5 + - + +
588C GLU* 3.4 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 585 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581C ASN* 3.3 15.8 + - + +
582C ILE* 3.7 9.6 - - - +
583C VAL 3.1 0.4 - - - -
584C GLU* 1.3 74.3 - - + +
586C LEU* 1.3 59.9 + - - +
588C GLU* 2.8 10.3 + - - +
589C LYS* 2.7 56.6 + - + -
592C ILE* 3.5 23.8 - - + -
600C ILE* 3.5 39.7 - - + -
604C GLU* 5.6 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 586 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C ALA* 4.0 20.6 - - + +
424C GLU* 4.3 2.5 - - + -
425C ALA* 4.2 7.4 - - - +
443C ILE* 3.4 51.1 - - + +
445C ILE* 3.6 37.2 - - + +
582C ILE* 2.9 23.6 + - + +
583C VAL* 2.9 6.5 + - - +
585C ILE* 1.3 76.9 - - - +
587C LEU* 1.3 65.6 + - - +
590C GLU* 2.8 33.7 + - - +
592C ILE* 3.6 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 587 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C LYS* 3.2 52.8 + - + +
418C ARG* 4.2 30.1 - - + +
421C ALA* 3.5 26.7 - - + -
445C ILE* 5.8 2.0 - - + -
583C VAL* 2.7 30.2 + - + +
584C GLU* 3.7 10.1 - - + +
586C LEU* 1.3 74.1 - - - +
588C GLU* 1.3 61.8 + - + +
590C GLU* 4.6 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 588 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584C GLU 3.4 10.2 + - - +
585C ILE* 2.8 12.7 + - - +
587C LEU* 1.3 82.6 - - - +
589C LYS* 1.3 84.6 + - + +
590C GLU* 4.8 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 589 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585C ILE* 2.7 37.8 + - + +
588C GLU* 1.3 92.3 + - + +
590C GLU* 1.3 66.0 + - - +
591C THR* 3.0 14.5 + - - +
592C ILE* 4.5 11.4 - - + -
596C GLU* 3.0 31.5 + - - +
600C ILE* 6.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 590 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C LYS* 5.5 9.2 - - - -
444C SER* 3.1 2.5 + - - -
445C ILE* 2.9 35.1 + - + +
446C ILE* 3.0 40.0 + - + +
447C PRO* 4.8 2.9 - - - +
586C LEU* 2.8 28.4 + - - +
587C LEU 5.1 5.8 - - - +
588C GLU 3.6 2.2 - - - +
589C LYS* 1.3 75.5 - - - +
591C THR* 1.3 64.9 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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