Contacts of the helix formed by residues 561 - 576 (chain D) in PDB entry 1DQA
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 CYS 561 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528C GLU* 2.7 24.5 + - - -
104D COA 4.0 11.2 - - - +
560D GLY* 1.3 73.7 - - - +
562D LEU* 1.3 57.1 + - - +
564D ALA* 3.8 4.4 - - - +
565D SER* 2.8 32.7 + - - -
865D SER* 3.1 45.3 - - - -
866D HIS* 3.7 27.4 - - + +
869D HIS* 3.6 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 562 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D COA 3.5 20.3 - - - -
555D MET* 3.9 7.2 - - + -
557D THR* 3.7 28.7 - - + +
559D GLU* 3.3 22.5 + - + +
560D GLY 3.3 2.2 + - - -
561D CYS* 1.3 77.4 - - - +
563D VAL* 1.3 60.0 + - - +
565D SER* 3.8 0.6 - - - -
566D THR* 2.8 45.9 + - - +
752D HIS* 4.1 6.5 - - + -
755D ASN* 3.6 47.1 - - + +
756D ILE* 3.9 9.9 - - + -
759D ALA* 4.1 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 563 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527C CYS* 3.9 26.7 - - - -
528C GLU* 3.4 31.6 + - + +
529C ASN* 4.1 2.9 - - + -
104D COA 5.5 0.2 - - + -
539D GLY* 4.1 6.7 - - - -
540D VAL 3.5 31.6 - - - +
541D ALA* 4.2 3.5 - - + +
555D MET* 4.2 18.6 - - + -
557D THR* 4.1 13.9 - - + -
559D GLU 4.8 0.6 + - - -
562D LEU* 1.3 74.6 - - + +
564D ALA* 1.3 59.7 + - - +
566D THR* 3.3 5.8 + - - -
567D ASN* 2.8 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 564 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528C GLU* 2.9 23.8 + - + +
104D COA 3.6 61.3 + - + +
561D CYS* 3.8 7.2 - - - +
563D VAL* 1.3 77.3 - - - +
565D SER* 1.3 56.2 + - - +
567D ASN* 3.4 2.6 + - - +
568D ARG* 3.0 28.1 + - - +
869D HIS* 5.2 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 565 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D COA 2.6 46.1 + - - +
561D CYS 2.8 22.6 + - - -
562D LEU* 3.8 3.8 - - - -
564D ALA* 1.3 69.3 - - - +
566D THR* 1.3 66.5 + - - +
568D ARG 3.2 1.2 + - - -
569D GLY 3.0 8.7 + - - -
752D HIS* 4.8 2.8 - - - -
849D GLY* 4.4 3.0 + - - -
852D SER* 2.7 48.0 + - - -
853D LEU 3.8 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 566 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541D ALA* 3.9 8.3 - - + -
555D MET* 3.6 18.5 - - - +
562D LEU* 2.8 21.0 + - - +
563D VAL 3.7 2.7 - - - -
565D SER* 1.3 76.5 - - - +
567D ASN* 1.3 57.5 + - - +
569D GLY* 3.3 1.9 + - - -
570D CYS* 3.0 28.5 + - - -
752D HIS* 5.4 0.2 - - - -
756D ILE* 3.0 25.2 - - + +
845D THR* 3.4 37.7 - - + +
848D ALA* 3.8 3.0 - - + +
849D GLY* 4.3 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 567 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C TYR* 4.0 10.1 - - - -
529C ASN* 4.8 6.5 + - - +
104D COA 3.1 47.2 + - + +
540D VAL 4.5 4.8 - - - +
541D ALA* 3.7 13.0 - - + +
542D GLY 2.8 38.4 + - - +
563D VAL 2.8 17.5 + - - +
564D ALA 3.6 4.9 - - - +
566D THR* 1.3 72.4 - - - +
568D ARG* 1.3 60.6 + - - +
570D CYS* 3.2 5.7 + - - +
571D ARG* 2.9 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 568 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D COA 3.0 92.2 + - + +
564D ALA 3.0 11.8 + - - +
565D SER 3.2 5.4 + - - +
567D ASN* 1.3 78.5 - - - +
569D GLY* 1.3 55.7 + - - +
571D ARG* 3.2 3.5 + - - +
572D ALA* 2.9 27.7 + - - +
720D VAL* 3.5 18.3 + - + +
721D LEU* 3.5 27.1 + - + +
722D LYS* 3.6 9.7 - - - +
852D SER* 2.8 48.5 + - - -
855D ALA* 4.1 4.4 - - - +
856D ALA* 4.0 10.7 - - - +
861D HIS* 4.7 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 569 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565D SER 3.0 11.5 + - - -
566D THR 3.3 1.3 + - - -
568D ARG* 1.3 76.2 - - - +
570D CYS* 1.3 62.2 + - - +
572D ALA* 3.4 7.1 + - - +
573D ILE* 3.0 28.4 + - - +
721D LEU* 5.1 0.7 - - - -
848D ALA* 3.3 30.5 - - - -
851D LEU* 3.9 6.4 - - - +
852D SER* 3.9 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 570 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541D ALA* 4.5 6.5 - - - -
542D GLY* 4.2 20.2 - - - -
543D PRO 3.7 18.8 - - - +
544D LEU* 4.0 28.8 - - - -
545D CYS 5.5 0.2 + - - -
553D VAL* 5.5 0.7 - - - -
566D THR* 3.0 22.1 + - - +
567D ASN 3.4 9.6 - - - +
569D GLY* 1.3 76.1 - - - +
571D ARG* 1.3 55.9 + - - +
573D ILE* 3.2 6.7 + - - +
574D GLY* 2.8 28.2 + - - -
845D THR* 5.2 3.8 - - - -
848D ALA* 3.5 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 571 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C HIS* 4.7 19.7 - - - -
104D COA 3.3 48.8 + - + +
542D GLY 6.1 0.2 - - - -
543D PRO 5.6 0.4 - - - -
567D ASN 2.9 13.8 + - - +
568D ARG* 3.4 9.6 - - - +
570D CYS* 1.3 75.6 - - - +
572D ALA* 1.3 63.3 + - - +
574D GLY* 3.3 3.4 + - - -
575D LEU* 3.1 66.9 + - + +
720D VAL* 4.5 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 572 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568D ARG 2.9 13.1 + - - +
569D GLY 3.6 8.1 - - - +
571D ARG* 1.3 77.6 - - - +
573D ILE* 1.3 61.5 + - - +
575D LEU* 3.4 4.2 + - - +
576D GLY* 3.1 17.2 + - - -
712D ILE* 3.8 10.7 - - + +
716D VAL* 3.8 27.0 - - + +
720D VAL* 4.3 4.0 - - + +
721D LEU* 4.2 21.1 - - + -
851D LEU* 4.1 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 573 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544D LEU* 4.5 9.6 - - + -
545D CYS* 3.9 8.7 - - + +
569D GLY 3.0 18.6 + - - +
570D CYS* 3.6 7.6 - - - +
572D ALA* 1.3 75.0 - - - +
574D GLY* 1.3 61.7 + - - +
576D GLY* 3.0 9.2 + - - -
577D GLY 3.3 0.2 + - - -
578D GLY* 2.9 26.4 + - - +
579D ALA* 3.6 29.8 - - + +
710D ALA* 4.4 7.4 - - + -
712D ILE* 3.8 11.0 - - + -
844D GLY 4.3 3.8 - - - +
847D MET* 3.8 22.0 - - + -
848D ALA* 3.7 29.8 - - + +
851D LEU* 3.7 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 574 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543D PRO 5.5 0.4 - - - -
545D CYS* 4.0 29.5 - - - +
570D CYS 2.8 19.6 + - - -
571D ARG* 3.3 3.6 + - - -
573D ILE* 1.3 72.6 - - - +
575D LEU* 1.3 59.5 + - - +
577D GLY* 3.0 18.2 + - - -
578D GLY 4.0 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 575 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571D ARG* 3.1 61.0 + - + +
572D ALA 3.9 2.0 - - - +
574D GLY* 1.3 76.3 - - - +
576D GLY* 1.3 56.7 + - - +
577D GLY 3.2 1.8 + - - -
713D PRO* 3.9 12.3 - - - +
716D VAL* 3.8 20.7 - - + +
720D VAL* 3.8 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 576 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572D ALA 3.1 8.2 + - - -
573D ILE* 3.0 8.7 + - - -
575D LEU* 1.3 78.0 - - - +
577D GLY* 1.3 58.0 + - - +
578D GLY 3.5 5.9 + - - +
711D VAL* 3.3 19.1 + - - +
713D PRO* 3.4 27.7 - - - +
----------------------------------------------------------
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