Contacts of the helix formed by residues 45 - 60 (chain 9) in PDB entry 2J28
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 LEU 45 (chain 9).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359 ARG* 5.4 5.2 - - + +
389 LEU* 5.8 0.4 - - + -
399 LEU* 2.3 75.1 - - + +
449 ALA* 1.3 75.4 - - - +
469 PRO* 1.3 82.1 - - + +
479 VAL 2.6 4.8 + - - -
489 VAL* 2.6 47.7 + - + +
499 ARG* 3.5 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 46 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449 ALA* 3.7 11.7 - - + -
459 LEU* 1.3 94.9 - - + +
479 VAL* 1.3 68.8 + - + +
499 ARG* 3.5 15.9 + - - +
2279 GLN* 5.5 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449 ALA* 5.1 13.2 - - + +
459 LEU* 2.6 5.1 + - - +
469 PRO* 1.3 81.5 - - + +
489 VAL* 1.3 57.6 + - + +
499 ARG 2.5 2.4 + - - -
509 GLU* 2.4 58.7 + - + +
519 PHE* 5.0 6.3 - - + +
859 ALA* 5.8 5.6 - - + +
2629 ILE* 6.4 0.9 - - + -
2659 ILE* 4.1 39.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 48 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359 ARG* 4.2 19.7 - - + +
389 LEU* 5.2 9.2 - - + -
439 VAL* 4.8 6.1 - - + -
449 ALA 3.2 11.4 - - - +
459 LEU* 2.6 48.9 + - + +
479 VAL* 1.3 79.2 - - + +
499 ARG* 1.3 68.0 + - - +
519 PHE* 2.5 22.8 + - + +
529 ILE* 2.7 36.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 49 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359 ARG* 5.5 7.1 - - - +
459 LEU 3.5 1.6 + - - +
469 PRO 3.5 15.0 - - - +
479 VAL 2.5 3.2 + - - -
489 VAL* 1.3 75.8 - - - +
509 GLU* 1.3 50.4 + - - +
529 ILE* 3.6 6.2 - - - +
539 ASN* 2.6 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 50 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469 PRO 4.3 0.2 + - - -
479 VAL* 2.4 47.9 + - + +
499 ARG* 1.3 67.3 - - - +
519 PHE* 1.3 70.5 + - - +
539 ASN* 2.7 11.1 + - - +
549 ARG* 2.7 54.0 + - - +
2659 ILE* 5.3 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 51 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319 LEU* 5.2 3.6 - - + -
349 VAL* 6.4 2.2 - - + -
389 LEU* 6.3 3.1 - - + -
479 VAL* 3.9 5.9 + - + +
489 VAL* 2.5 19.8 + - + +
509 GLU* 1.3 79.2 - - - +
529 ILE* 1.3 79.1 + - + +
539 ASN 2.4 14.0 + - - -
549 ARG* 2.8 13.5 + - - +
559 VAL* 2.8 26.7 + - + +
789 VAL* 4.1 5.2 - - - -
819 GLU* 2.9 54.7 - - + -
829 LEU* 3.3 28.0 - - + -
859 ALA* 3.8 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 52 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319 LEU* 3.3 39.4 - - + +
359 ARG* 3.5 50.5 - - + +
389 LEU* 5.6 2.0 - - + -
489 VAL* 2.7 36.8 + - + +
499 ARG* 3.7 5.4 - - - +
519 PHE* 1.3 83.2 - - + +
539 ASN* 1.3 66.3 + - - +
559 VAL* 2.9 19.6 - - - +
569 LYS* 3.1 14.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 53 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499 ARG* 2.6 23.1 + - + +
509 GLU* 2.7 18.5 + - - +
519 PHE 2.4 4.0 + - - -
529 ILE* 1.3 67.3 - - - +
549 ARG* 1.3 50.1 + - - +
559 VAL 2.4 4.3 + - - -
569 LYS* 2.3 39.7 + - - +
579 GLU* 2.2 53.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 54 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509 GLU* 2.7 44.3 + - + +
519 PHE* 3.6 7.9 - - - +
539 ASN* 1.3 71.9 - - - +
559 VAL* 1.3 68.2 + - - +
579 GLU* 2.9 32.5 + - + +
589 LYS* 3.1 14.6 + - + +
819 GLU* 3.4 36.1 + - + +
849 ALA* 4.5 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 55 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279 VAL* 6.5 0.7 - - + -
319 LEU* 4.3 17.9 - - + -
519 PHE* 2.8 56.7 + - + +
529 ILE* 2.9 12.6 - - - +
539 ASN 2.4 4.4 + - - -
549 ARG* 1.3 78.7 - - - +
569 LYS* 1.3 68.9 + - + +
589 LYS* 3.1 16.7 + - - +
599 ALA* 3.7 2.1 + - - +
749 PHE* 5.1 14.8 - - + -
779 ILE* 5.2 10.8 - - + +
789 VAL* 6.0 6.1 - - + -
819 GLU* 5.0 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 56 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279 VAL* 6.3 0.8 - - - +
289 LYS* 5.2 16.0 - - - +
319 LEU* 4.4 21.2 - - + +
529 ILE* 3.1 17.2 + - + +
539 ASN* 2.3 20.2 + - - +
559 VAL* 1.3 74.6 - - + +
579 GLU* 1.3 75.3 + - - +
599 ALA* 2.7 30.3 + - + +
609 VAL* 3.7 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 57 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539 ASN* 2.2 55.5 + - - +
549 ARG* 2.9 26.8 + - + +
569 LYS* 1.3 73.7 - - - +
589 LYS* 1.3 69.9 + - + +
609 VAL* 3.0 24.7 - - - +
619 GLY* 4.6 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 58 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549 ARG* 3.1 17.7 + - + +
559 VAL* 3.3 8.5 - - - +
569 LYS 2.8 1.6 + - - -
579 GLU* 1.3 77.9 - - + +
599 ALA* 1.3 63.6 + - - +
619 GLY* 2.5 17.7 + - - -
629 HIS* 2.2 39.3 + - + +
779 ILE* 4.2 22.4 - - + -
809 ASN* 5.1 7.3 - - - +
819 GLU* 4.5 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 59 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559 VAL 3.7 1.6 + - - +
569 LYS* 2.7 23.2 + - + +
589 LYS* 1.3 69.4 - - - +
609 VAL* 1.3 60.1 + - + +
619 GLY 2.6 14.2 + - - -
629 HIS* 2.0 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 60 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569 LYS* 4.2 3.4 - - + +
579 GLU* 3.0 21.9 - - - +
589 LYS 2.9 2.5 + - - -
599 ALA* 1.3 78.6 - - + +
619 GLY* 1.3 56.3 - - - +
----------------------------------------------------------
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