Contacts of the helix formed by residues 604 - 613 (chain A) in PDB entry 3BJY
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 604 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A VAL* 5.5 0.4 - - - +
590A LYS 5.6 0.9 - - - +
593A MET* 6.3 1.3 - - + -
594A LYS* 3.1 41.0 + - + +
597A LEU* 3.7 19.7 - - + +
602A GLN 4.0 1.6 + - - -
603A ASP* 1.3 76.6 - - - +
605A GLU* 1.3 70.0 + - - +
606A GLU* 3.2 16.1 - - - +
607A SER* 2.3 42.5 + - - -
608A LEU* 3.3 16.3 + - - +
10T G 4.7 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 605 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A LEU* 5.2 0.6 - - - +
603A ASP 5.0 1.7 - - - +
604A ASP* 1.3 73.1 - - - +
606A GLU* 1.3 67.0 + - - +
608A LEU* 2.6 42.7 + - - +
609A LYS* 3.3 11.3 + - - +
612A TYR* 4.1 15.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 606 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A LYS* 5.6 3.2 + - + +
604A ASP* 3.2 13.7 + - - +
605A GLU* 1.3 77.0 - - - +
607A SER* 1.3 64.3 + - - +
608A LEU 3.1 0.2 + - - -
609A LYS* 3.2 54.8 + - - +
610A ILE 4.6 0.5 + - - -
617A VAL* 6.0 0.7 - - - +
9T G 3.3 47.1 + - - +
10T G 3.3 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 607 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A LEU* 3.6 16.8 - - - +
515A VAL* 6.3 0.9 - - - -
594A LYS* 2.8 19.2 + - - -
603A ASP* 4.7 6.5 - - - -
604A ASP* 2.3 36.3 + - - -
605A GLU 3.0 0.8 + - - -
606A GLU* 1.3 78.9 - - - +
608A LEU* 1.3 61.0 + - - +
609A LYS 3.6 0.2 + - - -
610A ILE* 3.5 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 608 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A TYR* 3.5 24.7 - - - +
514A LEU* 4.7 2.2 - - + -
603A ASP* 3.7 35.2 - - + +
604A ASP 3.5 13.9 - - - +
605A GLU* 2.6 42.1 + - - +
607A SER* 1.3 70.9 - - - +
609A LYS* 1.3 63.4 + - - -
610A ILE 3.0 3.1 - - - -
611A LEU* 2.8 29.8 + - + +
612A TYR* 3.2 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 609 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A GLU* 3.3 8.4 + - + +
606A GLU* 3.2 49.7 + - - +
608A LEU* 1.3 76.4 - - - +
610A ILE* 1.3 58.3 + - - +
612A TYR* 4.4 8.0 - - - +
613A ASP* 2.8 36.9 + - + +
617A VAL* 3.7 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 610 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A LEU* 3.7 39.7 - - + +
464A ILE* 4.4 16.4 - - + -
470A VAL* 5.9 1.6 - - + -
514A LEU* 4.3 10.3 - - + -
606A GLU 4.6 0.4 + - - -
607A SER 3.5 18.7 + - - +
608A LEU 3.0 1.4 + - - -
609A LYS* 1.3 78.1 - - - +
611A LEU* 1.3 68.7 + - + +
613A ASP 4.2 0.4 - - - -
614A PRO* 3.5 23.7 - - + +
617A VAL* 3.7 31.6 - - + +
618A LEU* 4.9 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 611 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A THR 4.7 0.3 - - - +
350A ILE* 3.0 40.2 + - + +
356A TYR* 4.0 25.1 - - + +
358A ILE* 4.5 1.8 - - + -
460A LEU* 5.1 2.3 - - + +
462A LEU* 4.0 16.2 - - + -
470A VAL* 5.0 0.2 - - + -
472A VAL* 3.8 28.5 - - + -
514A LEU* 4.0 27.1 - - + -
608A LEU* 2.8 32.7 + - + +
610A ILE* 1.3 86.2 - - + +
612A TYR* 1.3 66.6 + - + +
613A ASP 3.2 4.6 + - - -
614A PRO* 3.7 7.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 612 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LYS* 3.2 25.5 - - - +
350A ILE* 3.2 26.9 - - + +
351A THR* 3.7 23.1 + - - -
352A ASP* 3.8 25.4 + - - -
356A TYR* 4.3 17.1 + + - -
605A GLU* 4.1 19.5 - - - -
608A LEU* 3.2 34.4 + - + +
609A LYS* 4.2 6.1 - - - +
611A LEU* 1.3 86.4 - - + +
613A ASP* 1.3 64.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 613 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A THR* 5.2 0.7 - - - +
349A LYS* 3.6 36.0 + - - +
609A LYS* 2.8 18.1 + - + +
612A TYR* 1.3 81.1 - - + +
614A PRO* 1.3 71.4 - - - +
615A LYS* 4.0 9.0 + - - +
616A GLU* 3.5 30.0 + - + +
617A VAL* 3.4 17.6 + - + +
----------------------------------------------------------
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