Contacts of the helix formed by residues 614 - 626 (chain D) in PDB entry 4Z2C
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 614 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612D VAL* 6.1 0.2 - - - -
613D ASP* 1.3 78.4 + - + +
615D ALA* 1.3 60.6 + - - +
616D ALA* 3.1 5.2 - - + +
617D GLU* 3.0 36.1 + - + +
618D ALA* 3.1 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 615 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523D TYR* 3.4 16.1 + - + +
612D VAL* 5.9 3.8 - - + -
613D ASP 3.2 7.8 + - - +
614D ASP* 1.3 70.5 - - - +
616D ALA* 1.3 57.1 + - - +
618D ALA* 3.7 8.5 - - - -
619D ASP* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 616 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614D ASP* 3.1 5.1 - - + -
615D ALA* 1.3 79.0 - - - +
617D GLU* 1.3 57.0 + - - +
619D ASP* 3.5 5.5 + - - +
620D LYS* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 617 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A THR* 4.8 9.4 - - - -
614D ASP* 3.0 22.5 + - + +
616D ALA* 1.3 74.9 - - - +
618D ALA* 1.3 61.3 + - - +
620D LYS* 3.5 6.9 - - - +
621D ILE* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 618 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 5.0 9.6 - - + -
12A THR* 5.0 8.7 - - - +
523D TYR* 3.4 29.6 - - + +
612D VAL* 5.6 4.9 - - + -
613D ASP 6.2 0.4 - - - +
614D ASP 3.1 11.0 + - - +
615D ALA* 3.5 7.2 - - - +
617D GLU* 1.3 76.0 - - - +
619D ASP* 1.3 63.4 + - - +
621D ILE* 3.1 6.7 + - - +
622D PHE* 2.9 38.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 619 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463D GLU* 5.4 0.7 - - - +
523D TYR* 3.8 14.5 + - + +
615D ALA 2.9 19.1 + - - +
616D ALA* 3.8 5.8 - - - +
618D ALA* 1.3 75.0 - - - +
620D LYS* 1.3 57.0 + - - +
622D PHE* 3.9 3.2 - - - +
623D ASP* 2.9 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 620 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616D ALA 2.9 19.4 + - - +
617D GLU* 3.5 9.2 - - - +
618D ALA 3.1 0.2 - - - -
619D ASP* 1.3 76.1 - - - +
621D ILE* 1.3 57.4 + - - +
623D ASP* 3.2 7.2 + - - +
624D MET* 2.9 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 621 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A THR* 4.4 23.1 - - - +
15A MET* 5.6 2.5 - - + -
16A LYS* 6.3 0.9 - - + -
617D GLU 2.9 18.1 + - - +
618D ALA* 3.7 3.1 - - - +
620D LYS* 1.3 76.5 - - - +
622D PHE* 1.3 59.7 + - + +
624D MET* 3.6 8.7 - - - +
625D LEU* 2.9 47.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 622 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.6 23.3 - - + -
12A THR* 5.8 0.9 - - - -
15A MET* 3.9 31.2 - - + -
463D GLU* 4.0 19.9 - - + +
519D LEU 3.8 4.0 - - - -
520D THR* 3.5 47.1 - - + -
523D TYR* 3.4 44.4 - + + -
618D ALA* 2.9 31.9 + - + +
619D ASP* 3.9 5.4 - - - +
621D ILE* 1.3 78.7 - - + +
623D ASP* 1.3 62.0 + - - +
626D MET* 3.2 27.9 + - + +
627D GLY 3.5 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 623 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463D GLU* 4.1 14.7 + - - +
619D ASP 2.9 18.4 + - - +
620D LYS* 3.2 6.7 + - - +
622D PHE* 1.3 76.7 - - - +
624D MET* 1.3 57.8 + - - +
627D GLY* 3.2 19.6 - - - -
629D ARG* 5.4 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 624 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620D LYS* 2.9 21.1 + - + +
621D ILE* 3.6 8.1 - - - +
623D ASP* 1.3 78.9 - - - +
625D LEU* 1.3 73.5 + - + +
629D ARG 4.4 2.8 - - - +
632D PRO* 4.2 29.6 - - + +
633D ARG* 3.7 22.3 + - - +
636D PHE* 4.0 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 625 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A MET* 3.9 43.3 - - + +
16A LYS* 4.0 7.0 - - + +
19A PHE* 3.7 30.0 - - + -
621D ILE* 2.9 26.5 + - + +
624D MET* 1.3 82.1 - - + +
626D MET* 1.3 71.8 + - + +
627D GLY 3.4 1.1 - - - -
633D ARG* 2.4 32.6 + - + +
636D PHE* 3.6 42.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 626 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A MET* 4.2 18.6 - - + -
19A PHE* 4.2 21.3 - - - -
461D ASN* 3.4 40.4 + - - +
463D GLU* 3.2 22.0 - - + +
464D LYS* 4.3 1.7 - - - +
513D HIS* 5.2 3.6 - - + +
516D THR* 4.0 13.0 - - - +
517D LEU* 3.7 22.9 - - + +
520D THR* 3.5 32.8 - - + -
622D PHE* 3.2 15.8 + - + +
625D LEU* 1.3 85.9 - - + +
627D GLY* 1.3 65.5 + - - +
633D ARG* 3.9 0.7 - - - +
----------------------------------------------------------
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