Contacts of the strand formed by residues 530 - 546 (chain D) in PDB entry 1DQ8
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 VAL 530 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537C PRO* 5.1 4.0 - - + -
538C VAL 3.4 9.0 - - - +
539C GLY* 4.0 0.4 - - - -
492D VAL* 3.9 9.9 - - + +
495D ARG* 2.6 38.0 + - - +
519D TYR* 3.7 22.7 - - + -
522D VAL* 4.3 0.7 - - + -
523D MET* 3.4 28.5 - - + -
527D CYS* 3.8 33.2 - - + +
528D GLU* 3.9 6.1 - - - -
529D ASN* 1.3 76.3 - - - +
531D ILE* 1.3 61.7 + - - +
532D GLY 3.5 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 531 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538C VAL* 2.9 28.9 + - + +
539C GLY 4.7 2.0 - - - +
540C VAL* 4.1 13.2 - - + -
554C PRO* 5.0 0.4 - - + -
820C MET* 3.9 25.6 - - + -
492D VAL* 3.7 11.2 - - - -
495D ARG* 3.8 21.8 - - + -
496D ARG* 2.8 42.4 + - + +
499D LEU* 3.9 25.1 - - + -
509D LEU* 4.5 2.0 - - + -
512D LEU* 3.7 22.1 - - + +
529D ASN 4.0 5.8 - - - +
530D VAL* 1.3 77.1 - - - +
532D GLY* 1.3 57.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 532 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537C PRO* 3.8 1.7 - - - +
538C VAL* 3.0 25.0 + - - -
492D VAL* 4.0 1.2 - - - +
512D LEU* 4.5 2.7 - - - -
513D PRO 3.3 13.0 - - - -
514D TYR* 3.7 1.8 - - - -
519D TYR* 3.5 20.3 + - - -
530D VAL* 3.5 13.3 - - - +
531D ILE* 1.3 82.2 - - - +
533D TYR* 1.3 61.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 533 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533C TYR* 4.5 18.4 + + - -
535C PRO* 3.7 27.6 - - + -
536C ILE 3.2 16.8 - - - +
537C PRO* 4.4 2.0 - - + -
538C VAL* 3.9 5.8 - - - -
512D LEU* 3.2 16.7 - - - +
513D PRO* 3.1 39.8 + - + +
514D TYR* 3.7 15.3 - - - -
515D ARG 3.5 25.9 + - - -
516D ASP* 5.1 1.8 + - - +
517D TYR* 3.7 33.0 - + + -
519D TYR* 4.0 3.1 - - - -
532D GLY* 1.3 74.5 - - - +
534D MET* 1.3 59.6 - - - +
535D PRO* 4.1 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 534 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534C MET 3.1 5.4 - - - +
535C PRO* 4.2 0.9 - - - -
536C ILE* 2.7 39.5 + - + +
538C VAL* 3.7 13.5 - - + -
556C ALA* 4.5 6.5 - - + -
762C ILE* 3.6 19.7 - - + +
763C ALA* 3.2 24.7 - - - +
813C PRO* 3.5 21.1 - - - +
814C GLN* 3.4 32.8 - - - +
817C CYS* 3.5 21.8 - - - -
512D LEU* 4.2 9.6 - - + -
533D TYR* 1.3 72.4 - - - +
535D PRO* 1.3 62.4 - - - +
536D ILE* 3.5 14.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 535 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517C TYR* 3.6 33.3 + - + -
533C TYR* 3.7 21.1 - - + -
534C MET 3.6 5.4 - - - +
535C PRO* 4.4 0.9 - - + -
813C PRO* 3.8 21.8 - - + -
814C GLN* 3.7 14.0 + - - +
513D PRO* 4.0 18.2 - - + -
533D TYR* 3.5 20.2 - - + +
534D MET* 1.3 84.4 - - - +
536D ILE* 1.3 66.9 + - - +
537D PRO* 3.9 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 536 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533C TYR* 4.1 1.3 - - - -
534C MET* 2.8 43.8 + - + +
536C ILE* 4.0 14.4 - - + -
762C ILE* 4.0 16.8 - - + +
814C GLN* 4.1 9.6 - - - +
534D MET* 3.8 22.9 - - + +
535D PRO* 1.3 80.9 - - - +
537D PRO* 1.3 74.0 - - + +
538D VAL* 3.3 2.9 + - - +
556D ALA* 3.7 16.4 - - + +
557D THR* 3.6 29.2 - - - +
558D THR* 4.6 6.3 - - + -
762D ILE* 4.2 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 537 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517C TYR* 4.0 11.0 - - + +
519C TYR* 6.0 0.4 - - + -
522C VAL* 3.7 34.5 - - + -
526C CYS* 5.2 1.3 - - + -
527C CYS* 3.8 18.5 - - + -
530C VAL* 5.0 4.0 - - + -
532C GLY 3.8 7.9 - - - +
533C TYR* 4.3 3.8 - - + -
811C LEU* 4.3 5.2 - - + -
535D PRO 3.9 6.1 - - - +
536D ILE* 1.3 80.8 - - - +
538D VAL* 1.3 59.8 + - - +
555D MET 3.7 0.3 - - - +
556D ALA* 3.1 3.5 - - - -
557D THR 2.9 47.0 + - - +
558D THR* 3.8 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 538 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512C LEU* 4.6 7.4 - - + -
527C CYS* 4.1 3.1 - - - -
530C VAL* 3.4 3.6 - - - +
531C ILE* 2.9 49.1 + - + +
532C GLY 2.9 18.1 + - - +
533C TYR 3.8 3.4 - - - -
534C MET* 3.6 27.1 - - + +
536D ILE 3.5 14.4 - - - +
537D PRO* 1.3 73.0 - - - +
539D GLY* 1.3 65.6 + - - +
554D PRO* 4.3 9.6 - - + -
555D MET 3.3 13.0 - - - +
556D ALA* 4.1 7.9 - - + -
763D ALA* 4.7 3.8 - - + -
817D CYS* 4.4 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 539 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527C CYS* 3.6 7.3 - - - -
528C GLU 3.4 14.6 - - - -
529C ASN 3.2 12.1 - - - -
531C ILE* 4.7 2.2 - - - +
538D VAL* 1.3 75.5 - - - +
540D VAL* 1.3 61.4 + - - -
553D VAL 3.6 0.3 - - - +
554D PRO* 3.4 4.7 - - - +
555D MET* 2.8 36.4 + - - +
563D VAL* 4.2 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 540 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C ARG* 4.9 4.7 - - + -
499C LEU* 4.4 15.5 - - + -
529C ASN* 3.0 52.4 + - + +
531C ILE* 4.2 22.7 - - + -
539D GLY* 1.3 72.7 - - - +
541D ALA* 1.3 70.6 + - - +
552D GLN* 4.0 24.5 - - + +
553D VAL 3.3 19.3 - - - +
554D PRO* 4.7 0.9 - - + -
563D VAL* 3.5 7.8 - - - +
567D ASN* 4.3 0.7 - - - +
820D MET* 5.6 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 541 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540D VAL* 1.3 77.2 - - - +
542D GLY* 1.3 57.8 + - - +
552D GLN 3.8 0.5 - - - -
553D VAL* 2.8 39.8 + - + +
555D MET* 3.5 27.8 - - + +
566D THR* 4.0 11.2 - - + -
567D ASN* 3.5 27.6 - - + +
570D CYS* 4.4 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 542 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540D VAL 4.2 0.2 - - - -
541D ALA* 1.3 76.0 - - - +
543D PRO* 1.3 78.5 - - - +
544D LEU 3.7 1.6 - - - -
551D PHE 4.0 2.0 - - - -
552D GLN* 3.9 10.6 + - - +
567D ASN* 2.8 20.1 + - - +
570D CYS* 4.1 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 543 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502C LYS* 5.5 7.2 - - + +
542D GLY* 1.3 81.6 - - - +
544D LEU* 1.3 61.6 + - - +
545D CYS* 3.7 11.2 + - - -
550D GLU* 3.7 35.0 - - + +
551D PHE 3.4 6.5 - - - +
552D GLN* 3.4 22.4 - - - +
570D CYS* 3.5 19.2 - - - +
574D GLY* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 544 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542D GLY* 3.7 0.4 - - - -
543D PRO* 1.3 71.3 - - - +
545D CYS* 1.3 66.7 + - - +
546D LEU* 3.2 29.6 + - + -
549D LYS 3.4 1.4 - - - +
550D GLU* 4.3 0.4 - - - -
551D PHE* 2.8 40.2 + - + +
553D VAL* 4.3 11.0 - - + -
570D CYS* 4.1 24.0 - - + +
573D ILE* 4.4 18.8 - - + -
579D ALA* 5.4 1.8 - - + -
841D ILE* 3.9 10.1 - - + +
844D GLY* 4.0 18.4 - - - +
845D THR* 3.4 33.9 - - + +
848D ALA* 4.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 545 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543D PRO* 3.7 14.7 + - - -
544D LEU* 1.3 71.6 - - - +
546D LEU* 1.3 53.7 + - - +
548D GLU 5.4 0.9 - - - -
549D LYS 3.2 9.6 - - - +
550D GLU* 4.1 24.9 - - + -
570D CYS 5.4 0.4 + - - -
573D ILE* 3.8 6.4 - - - +
574D GLY* 3.8 24.9 - - - +
577D GLY 5.4 0.4 - - - -
578D GLY* 3.4 17.5 - - - +
579D ALA* 2.8 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 546 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544D LEU* 3.2 20.8 + - + -
545D CYS* 1.3 75.1 - - - +
547D ASP* 1.3 88.6 + - - +
548D GLU 3.3 1.1 - - - -
549D LYS* 2.9 24.0 + - - +
551D PHE* 3.9 21.5 - - + -
579D ALA* 3.4 15.0 - - + +
581D SER* 3.9 6.3 - - - +
708D CYS* 3.7 30.1 - - - -
837D GLN* 4.6 1.3 - - - +
840D ARG* 3.5 32.3 - - + +
841D ILE* 3.9 11.2 - - + +
844D GLY* 4.6 3.4 - - - -
----------------------------------------------------------
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