Contacts of the helix formed by residues 508 - 519 (chain C) in PDB entry 2A19
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 ASP 508 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506C ILE 4.3 0.4 + - - -
507C PHE* 1.3 80.3 - - - +
509C LYS* 1.3 55.7 + - - +
510C LYS* 2.9 25.6 + - + +
511C GLU* 2.8 53.1 + - - +
512C LYS 3.1 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 509 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508C ASP* 1.3 68.7 - - - +
510C LYS* 1.3 57.5 + - - +
511C GLU 3.4 0.2 - - - -
512C LYS* 3.9 12.8 - - + -
513C THR* 2.7 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 510 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508C ASP* 3.6 22.2 + - + +
509C LYS* 1.3 79.0 - - - +
511C GLU* 1.3 65.7 + - + +
513C THR* 3.5 9.3 + - - -
514C LEU* 3.9 5.4 + - - +
539C TRP* 3.3 58.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 511 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C LEU* 5.7 3.0 - - + +
478C LEU* 5.5 1.5 - - - +
482C LEU* 3.8 28.5 - - + +
507C PHE* 2.9 48.0 - - + +
508C ASP* 2.8 39.2 + - - +
510C LYS* 1.3 75.8 - - + +
512C LYS* 1.3 68.2 + - - +
514C LEU* 3.0 15.6 + - - +
515C LEU* 3.4 14.9 + - - +
539C TRP* 4.3 23.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 512 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503C ILE* 4.3 8.8 - - + +
504C SER 4.7 12.6 - - - +
505C ASP* 5.9 3.1 - - + -
507C PHE* 4.3 9.9 + - + +
508C ASP 3.1 4.4 + - - +
509C LYS* 4.0 17.5 - - + -
510C LYS 3.5 0.2 - - - -
511C GLU* 1.3 79.5 - - - +
513C THR* 1.3 66.4 + - + +
515C LEU* 3.2 14.4 + - - +
516C GLN* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 513 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509C LYS* 2.7 28.9 + - + +
510C LYS* 3.5 6.9 + - - -
511C GLU 3.2 0.2 + - - -
512C LYS* 1.3 81.5 - - + +
514C LEU* 1.3 59.7 + - - +
516C GLN* 3.8 9.6 - - + +
517C LYS* 3.5 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 514 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C PHE* 5.4 0.9 - - + -
478C LEU* 3.8 26.0 - - + -
510C LYS 3.9 8.4 + - - +
511C GLU* 3.0 9.8 + - - +
513C THR* 1.3 78.2 + - - +
515C LEU* 1.3 64.6 + - - +
517C LYS* 3.2 15.0 + - + +
518C LEU* 3.2 14.9 + - + +
527C PRO* 4.3 21.3 - - + -
531C GLU 5.9 0.2 - - - -
532C ILE* 4.7 23.3 - - + +
535C THR* 4.6 25.8 - - + +
536C LEU* 6.0 1.8 - - + +
539C TRP* 4.2 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 515 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C GLY* 3.4 26.7 - - - +
478C LEU* 3.9 20.4 - - + -
479C ALA* 3.8 24.9 - - + +
482C LEU* 5.0 0.9 - - + -
503C ILE* 4.2 20.6 - - + -
507C PHE* 3.6 36.3 - - + -
511C GLU 3.4 13.9 + - - +
512C LYS* 3.2 7.3 + - - +
514C LEU* 1.3 74.8 - - - +
516C GLN* 1.3 67.0 + - - +
517C LYS 3.1 0.9 + - - -
518C LEU* 3.2 5.4 + - - +
519C LEU* 3.2 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 516 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503C ILE* 4.4 26.1 - - + +
512C LYS 3.1 9.7 + - - +
513C THR* 3.8 13.9 - - + +
515C LEU* 1.3 78.5 - - - +
517C LYS* 1.3 63.8 + - - +
519C LEU* 3.9 7.7 - - - +
520C SER* 3.6 15.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 517 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513C THR 3.5 9.7 + - - +
514C LEU* 3.2 10.9 + - + +
515C LEU 3.1 1.0 - - - -
516C GLN* 1.3 77.1 - - - +
518C LEU* 1.3 61.5 + - - +
520C SER* 2.9 26.6 + - - -
525C ASP* 3.6 11.5 - - - +
526C ARG* 3.4 8.8 - - - -
527C PRO* 3.8 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 518 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471C LEU* 4.0 11.2 - - + +
472C TYR* 4.3 12.2 - - - +
475C GLY* 3.9 26.9 - - - +
514C LEU* 3.2 12.8 + - + +
515C LEU* 3.9 5.4 - - - +
517C LYS* 1.3 80.4 - - - +
519C LEU* 1.3 57.5 + - - +
520C SER 3.1 7.1 + - - +
526C ARG* 3.3 24.3 - - + +
527C PRO* 3.9 10.9 - - + +
532C ILE* 6.0 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 519 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C TYR* 4.8 9.0 - - + +
475C GLY 4.0 20.4 - - - +
476C LEU* 3.8 32.1 - - + +
479C ALA* 5.7 3.1 - - + -
501C GLY 5.5 12.8 - - - +
503C ILE* 4.1 23.0 - - + +
515C LEU* 3.2 32.2 + - + +
516C GLN* 3.9 4.6 - - - +
518C LEU* 1.3 72.1 - - + +
520C SER* 1.3 59.7 + - - +
----------------------------------------------------------
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