Contacts of the helix formed by residues 736 - 751 (chain D) in PDB entry 6UZA
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 736 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376D LYS* 6.2 2.7 - - - -
734D ILE* 3.2 5.8 - - + +
735D GLU* 1.3 76.7 - - - +
737D ASP* 1.3 61.9 + - - +
738D ALA 3.3 2.4 + - - -
739D ASP* 3.7 9.7 + - - +
740D VAL* 3.4 23.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 737 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376D LYS* 5.3 9.6 - - - +
629D ARG* 6.1 0.2 - - - -
733D GLU* 6.4 0.7 - - + -
734D ILE* 3.6 19.5 + - + +
735D GLU 3.5 0.6 - - - -
736D ASP* 1.3 75.3 - - - +
738D ALA* 1.3 59.4 + - - +
739D ASP 3.2 0.9 - - - -
740D VAL* 3.6 10.2 - - + +
741D GLU* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 738 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622D PRO* 4.9 8.8 - - + +
625D ILE* 5.4 3.6 - - - +
629D ARG* 5.4 8.3 - - - +
734D ILE 4.0 6.1 + - - +
735D GLU* 4.1 13.9 + - - +
736D ASP 3.3 0.6 - - - -
737D ASP* 1.3 78.9 - - - +
739D ASP* 1.3 62.1 + - - +
741D GLU* 4.6 3.7 - - - +
742D TRP* 3.7 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 739 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622D PRO* 5.8 3.8 - - - +
735D GLU 4.6 8.5 - - - +
736D ASP* 3.7 10.0 + - - +
737D ASP 3.2 0.4 - - - -
738D ALA* 1.3 81.8 - - - +
740D VAL* 1.3 60.2 + - + +
742D TRP* 3.4 14.6 + - - -
743D LYS* 2.9 56.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 740 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375D LYS* 3.7 39.7 - - + +
376D LYS* 3.9 30.1 - - + +
379D ALA* 3.9 16.8 - - + +
736D ASP 3.4 15.9 - - - +
737D ASP* 3.3 12.6 + - + +
739D ASP* 1.3 79.5 - - + +
741D GLU* 1.3 57.9 + - - +
743D LYS 3.4 0.5 + - - -
744D PHE* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 741 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375D LYS* 4.8 18.6 - - + +
625D ILE* 4.5 21.8 - - + +
629D ARG* 4.6 9.0 - - - +
737D ASP 2.9 16.8 + - - +
738D ALA 4.6 2.2 - - - +
739D ASP 3.3 0.2 - - - -
740D VAL* 1.3 77.9 - - - +
742D TRP* 1.3 56.9 + - - +
744D PHE* 3.4 6.6 + - - +
745D ALA* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 742 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615D PRO* 3.9 15.4 + - + -
617D ASN 3.3 16.4 + - - -
618D GLU* 3.6 34.5 - - + -
621D GLY* 3.8 11.2 - - - -
622D PRO* 3.6 36.3 - - + +
625D ILE* 4.3 12.4 - - + +
738D ALA 3.7 14.2 + - - +
739D ASP* 3.4 18.7 + - - +
740D VAL 3.4 0.2 - - - -
741D GLU* 1.3 79.8 - - - +
743D LYS* 1.3 92.2 + - + +
745D ALA* 3.2 3.4 + - + +
746D ARG* 2.9 57.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 743 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379D ALA* 3.7 32.9 + - + +
384D GLN* 3.6 31.0 + - + +
739D ASP* 2.9 44.4 + - - +
741D GLU 3.4 0.2 - - - -
742D TRP* 1.3 105.7 - - + +
744D PHE* 1.3 57.4 + - - +
746D ARG* 3.4 14.4 + - - +
747D ALA* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 744 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369D ALA 4.2 2.5 - - - -
370D ILE* 3.7 49.4 - - + -
373D GLU* 4.1 27.6 - - + -
374D VAL 4.3 3.8 - - - -
375D LYS* 3.9 33.2 - - + +
378D VAL* 4.0 26.5 - - + -
379D ALA* 4.6 1.5 - - - +
740D VAL 2.9 18.3 + - - +
741D GLU* 3.7 5.8 - - - +
743D LYS* 1.3 77.4 - - - +
745D ALA* 1.3 58.6 + - - +
747D ALA* 3.4 2.5 + - - -
748D LYS* 2.9 55.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 745 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615D PRO* 4.9 16.0 - - + +
625D ILE* 4.2 19.5 - - + -
741D GLU 3.0 17.6 + - - +
742D TRP* 3.2 5.4 + - + +
744D PHE* 1.3 76.9 - - - +
746D ARG* 1.3 58.0 + - - +
748D LYS* 3.4 15.3 + - - +
749D LEU* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 746 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384D GLN* 3.1 30.5 - - - +
388D LEU* 5.6 4.0 - - - +
615D PRO 3.6 25.7 + - - +
616D ALA* 4.2 17.5 + - - -
618D GLU* 5.0 6.1 - - - +
742D TRP* 2.9 50.0 + - - +
743D LYS* 3.8 15.2 - - - +
745D ALA* 1.3 77.9 - - - +
747D ALA* 1.3 57.0 + - - +
749D LEU* 3.2 5.5 + - - +
750D TRP* 2.9 68.2 + - + +
1004D Y01 5.2 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 747 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370D ILE* 4.6 4.0 - - + -
378D VAL* 3.7 29.2 - - + -
384D GLN* 4.6 5.6 - - - +
387D LEU* 4.2 15.3 - - + -
743D LYS 2.9 17.6 + - - +
744D PHE 3.9 2.7 - - - +
746D ARG* 1.3 74.5 - - - +
748D LYS* 1.3 59.9 + - - +
750D TRP* 3.2 13.0 + - + +
751D PHE* 2.9 36.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 748 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370D ILE* 3.8 26.9 - - + +
744D PHE* 2.9 48.2 + - + +
745D ALA* 3.6 12.3 - - - +
746D ARG 3.3 0.2 - - - -
747D ALA* 1.3 75.2 - - - +
749D LEU* 1.3 61.7 + - - +
751D PHE* 3.8 6.6 + - - +
752D SER* 3.7 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 749 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391D TRP* 4.4 5.4 - - + -
443D PHE* 4.6 4.5 - - + -
612D TYR* 3.3 27.4 - - - +
613D ILE* 4.9 0.9 - - - -
615D PRO* 3.7 23.6 - - + -
616D ALA* 3.7 31.6 - - + +
745D ALA 2.9 14.6 + - - +
746D ARG* 3.2 8.5 + - - +
748D LYS* 1.3 76.0 - - - +
750D TRP* 1.3 76.5 + - + +
752D SER* 2.8 23.1 + - - +
753D TYR* 3.2 28.2 - - + -
1003D S9Y 6.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 750 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384D GLN* 4.3 16.8 - - - -
387D LEU* 3.8 36.1 - - + -
388D LEU* 3.6 35.9 - - + -
391D TRP* 3.6 38.8 - + + -
616D ALA* 5.3 0.4 - - - +
746D ARG* 2.9 62.6 + - + +
747D ALA* 3.2 17.9 + - - +
749D LEU* 1.3 84.3 - - + +
751D PHE* 1.3 56.9 + - + +
753D TYR* 3.0 20.3 + - - +
754D PHE* 3.4 26.7 + - + -
1004D Y01 3.7 21.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 751 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363D LEU* 4.2 19.7 - - + -
366D LEU* 4.0 25.4 - - + -
367D LYS* 3.6 39.3 - - + -
370D ILE* 3.6 24.5 - - + -
378D VAL* 5.5 0.2 - - + -
387D LEU* 3.7 41.1 - - + -
747D ALA 2.9 26.7 + - - +
748D LYS* 4.2 5.2 - - - +
749D LEU 3.3 0.6 - - - -
750D TRP* 1.3 76.4 - - + +
752D SER* 1.3 59.6 + - - +
753D TYR 3.3 0.6 + - - -
754D PHE* 3.7 25.4 + + + +
755D GLU* 3.9 15.2 - - - +
----------------------------------------------------------
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