Contacts of the helix formed by residues 549 - 570 (chain D) in PDB entry 5HIE
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 GLU 549 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547D LYS 4.0 1.7 + - - +
548D PHE* 1.3 75.6 - - - +
550D MET* 1.3 66.5 + - - +
551D ILE* 3.2 26.5 - - + +
552D LYS* 2.9 18.3 + - + +
553D LEU* 3.0 10.7 + - - +
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Residues in contact with MET 550 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548D PHE 3.9 1.2 + - - -
549D GLU* 1.3 70.6 - - - +
551D ILE* 1.3 55.4 - - - +
553D LEU* 3.1 24.5 + - + +
554D ILE* 2.9 52.8 + - + +
650D MET* 3.6 29.2 - - - +
682D ARG* 4.6 9.9 - - + +
684D ASN* 3.4 54.2 - - + +
685D CYS* 3.8 16.8 - - + +
686D PRO* 4.2 7.6 - - + -
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Residues in contact with ILE 551 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549D GLU* 3.5 29.6 - - + +
550D MET* 1.3 76.4 - - - +
552D LYS* 1.4 59.6 + - + +
554D ILE* 3.6 12.8 + - + +
555D ASP* 3.1 26.4 + - + +
718D ALA* 4.7 11.0 - - + +
721D LEU* 3.8 38.1 - - + -
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Residues in contact with LYS 552 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548D PHE* 3.7 37.5 - - + -
549D GLU* 2.9 17.3 + - + +
551D ILE* 1.4 79.3 - - + +
553D LEU* 1.4 54.3 + - - +
555D ASP* 3.1 19.0 + - - +
556D ILE* 2.8 41.6 + - + +
584D LEU* 4.6 4.4 - - - +
587D ASP 3.2 28.2 + - - -
588D LEU* 3.8 29.7 + - + +
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Residues in contact with LEU 553 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541D LEU* 4.4 5.4 - - + -
548D PHE* 3.8 40.4 - - + +
549D GLU 3.0 11.3 + - - +
550D MET* 3.5 34.8 - - + +
552D LYS* 1.4 74.6 - - - +
554D ILE* 1.4 61.5 + - - +
556D ILE* 3.4 4.7 + - - +
557D ALA* 3.2 21.7 + - - +
649D LEU* 3.4 53.6 - - + +
650D MET* 3.8 15.3 - - + +
682D ARG* 4.6 13.7 - - - +
684D ASN* 5.7 0.4 - - - +
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Residues in contact with ILE 554 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550D MET* 2.9 49.0 + - + +
551D ILE* 3.8 11.7 - - + +
553D LEU* 1.4 70.4 - - - +
555D ASP* 1.3 55.1 + - - +
557D ALA* 3.3 8.3 + - - +
558D ARG* 2.8 32.9 + - + +
650D MET* 4.7 2.9 - - + -
686D PRO* 4.1 8.3 - - + -
689D MET* 4.6 10.1 - - + -
714D ILE* 3.8 15.5 - - + +
717D LEU* 3.7 36.6 - - + +
718D ALA* 4.5 20.6 - - + -
720D SER 6.2 0.4 - - - +
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Residues in contact with ASP 555 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551D ILE* 3.1 16.3 + - + +
552D LYS* 3.1 21.9 + - - +
554D ILE* 1.3 74.6 - - - +
556D ILE* 1.4 55.4 + - - +
558D ARG* 2.8 36.2 + - - +
559D GLN* 2.8 56.8 + - - +
588D LEU 4.2 3.1 - - - +
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Residues in contact with ILE 556 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537D LEU* 3.7 31.2 - - + -
548D PHE* 4.3 14.8 - - + -
552D LYS* 2.8 44.8 + - + +
553D LEU* 3.8 5.8 - - - +
554D ILE 3.3 0.4 - - - -
555D ASP* 1.4 71.9 - - - +
557D ALA* 1.3 54.5 + - - +
559D GLN* 3.4 4.1 + - - +
560D THR* 2.7 40.5 + - - +
582D ILE* 4.6 0.9 - - + -
584D LEU* 3.9 35.9 - - + -
590D VAL* 3.8 18.5 - - + +
645D VAL* 5.9 0.2 - - + -
649D LEU* 3.8 15.7 - - + -
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Residues in contact with ALA 557 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553D LEU 3.2 13.6 + - - +
554D ILE* 3.4 11.2 - - - +
556D ILE* 1.3 73.2 - - - +
558D ARG* 1.4 58.8 + - - +
560D THR* 3.2 3.8 + - - -
561D ALA* 2.9 32.7 + - - +
642D PHE* 3.5 7.8 - - - -
646D LEU* 3.6 30.3 - - + -
649D LEU* 4.1 8.7 - - + +
650D MET* 5.4 1.1 - - + -
689D MET* 5.2 3.6 - - - -
714D ILE* 4.2 12.6 - - + -
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Residues in contact with ARG 558 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512D ASN* 4.7 6.9 + - - -
554D ILE* 2.8 21.7 + - + +
555D ASP* 2.8 37.5 + - - +
557D ALA* 1.4 72.2 - - - +
559D GLN* 1.3 83.6 + - - +
561D ALA* 4.7 0.7 - - - -
562D GLN* 3.0 45.4 + - - +
711D LEU* 3.4 10.8 - - + +
714D ILE* 3.7 23.3 - - + +
715D GLU* 4.2 29.4 + - + +
718D ALA* 5.6 7.2 - - + -
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Residues in contact with GLN 559 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512D ASN* 3.2 29.9 + - - +
555D ASP* 2.8 45.5 + - - +
556D ILE* 3.7 2.8 - - - +
558D ARG* 1.3 93.1 - - - +
560D THR* 1.3 63.7 + - - +
562D GLN* 3.3 5.7 + - - -
563D GLY 3.2 17.3 + - - -
588D LEU 2.8 20.2 + - - -
589D THR* 3.3 9.8 - - - +
590D VAL* 2.8 38.7 + - + +
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Residues in contact with THR 560 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556D ILE* 2.7 24.6 + - - +
557D ALA* 3.2 5.5 + - - -
559D GLN* 1.3 74.8 - - - +
561D ALA* 1.4 57.1 + - - +
563D GLY 3.2 2.3 + - - -
564D MET* 3.0 36.2 + - + +
577D LEU* 4.8 4.7 - - + -
582D ILE* 3.9 36.7 - - + +
590D VAL* 3.5 18.2 - - - +
592D ILE* 3.4 12.2 - - + +
642D PHE* 3.7 24.0 - - + -
645D VAL* 5.1 3.3 - - + +
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Residues in contact with ALA 561 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557D ALA 2.9 17.7 + - - +
558D ARG 3.9 3.8 - - - +
560D THR* 1.4 75.2 - - - +
562D GLN* 1.3 56.1 + - - +
565D ASP* 3.0 31.2 + - - +
642D PHE* 3.6 15.8 - - + -
707D PHE* 3.8 16.3 - - + +
710D ILE* 3.9 13.5 - - + -
711D LEU* 3.9 13.0 - - + +
714D ILE* 3.9 13.7 - - + -
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Residues in contact with GLN 562 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510D HIS* 3.9 14.8 + - + +
512D ASN* 3.6 15.5 - - - +
558D ARG* 3.0 31.5 + - - +
559D GLN* 3.4 9.2 - - - +
560D THR 3.2 0.2 - - - -
561D ALA* 1.3 78.0 - - - +
563D GLY* 1.3 61.8 - - - +
565D ASP* 3.6 5.9 + - - +
566D TYR* 3.3 21.0 + - - +
711D LEU* 3.3 31.6 - - - +
715D GLU* 3.7 15.6 + - - -
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Residues in contact with GLY 563 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510D HIS* 4.3 4.7 - - - -
512D ASN* 3.8 15.8 - - - +
513D ILE* 3.4 22.4 - - - +
559D GLN 3.2 7.3 + - - -
560D THR 3.2 2.4 + - - -
562D GLN* 1.3 77.3 - - - +
564D MET* 1.3 57.3 + - - +
566D TYR* 3.4 4.9 - - - +
567D LEU* 3.1 31.1 + - - +
592D ILE* 3.9 4.3 - - - -
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Residues in contact with MET 564 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560D THR* 3.0 23.6 + - + +
562D GLN 3.4 0.2 - - - -
563D GLY* 1.3 73.7 - - - +
565D ASP* 1.4 59.1 + - - +
567D LEU* 3.3 18.8 + - + +
568D HIS* 2.9 45.7 + - + +
574D HIS* 4.3 7.9 - - + -
577D LEU* 4.0 29.8 - - + -
592D ILE* 4.0 13.0 - - + -
638D ASP* 3.5 39.0 - - + +
707D PHE* 3.6 37.2 - - + -
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Residues in contact with ASP 565 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561D ALA 3.0 18.6 + - - +
562D GLN* 3.8 8.7 - - - +
563D GLY 3.4 0.2 - - - -
564D MET* 1.4 75.0 - - - +
566D TYR* 1.4 57.3 + - - +
568D HIS* 3.6 3.4 + - - +
569D ALA* 2.9 31.0 + - - +
707D PHE* 3.7 14.7 - - + +
708D PRO* 3.4 39.2 - - - +
711D LEU* 4.0 18.5 - - + +
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Residues in contact with TYR 566 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507D LYS 3.0 18.0 + - - -
508D THR* 3.6 25.1 - - + -
509D ARG* 3.3 16.4 + - - +
510D HIS* 3.5 46.9 - + + +
513D ILE* 4.0 9.6 - - + -
562D GLN 3.3 11.1 + - - +
563D GLY 3.4 8.7 - - - +
564D MET 3.2 0.4 - - - -
565D ASP* 1.4 75.5 - - - +
567D LEU* 1.4 68.6 + - - +
569D ALA* 3.1 11.2 + - + +
570D LYS* 3.1 49.6 + - + +
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Residues in contact with LEU 567 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504D VAL* 4.5 0.2 - - + -
508D THR* 4.1 22.2 - - + -
513D ILE* 3.8 18.4 - - + -
563D GLY 3.1 16.9 + - - +
564D MET* 3.3 30.3 + - + +
566D TYR* 1.4 77.1 - - + +
568D HIS* 1.3 55.6 + - + +
570D LYS* 3.0 18.3 + - - +
571D SER 3.1 0.2 + - - -
572D ILE* 2.8 50.3 + - + +
574D HIS* 4.6 2.7 - - + -
592D ILE* 4.4 3.4 - - + -
595D PHE* 3.6 43.5 - - + -
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Residues in contact with HIS 568 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564D MET* 2.9 24.0 + - + +
565D ASP* 3.9 6.5 - - - +
567D LEU* 1.3 78.6 - - + +
569D ALA* 1.3 57.8 + - - +
571D SER* 3.0 20.8 + - - -
572D ILE 3.3 16.2 - - - -
635D PHE* 3.4 71.3 - + + +
638D ASP* 3.1 23.8 + - + +
706D LEU* 5.3 1.6 - - - +
707D PHE* 3.5 34.0 + + + +
708D PRO* 6.2 1.8 - - + -
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Residues in contact with ALA 569 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565D ASP* 2.9 22.4 + - - +
566D TYR* 3.1 8.9 + - + +
568D HIS* 1.3 75.0 - - - +
570D LYS* 1.4 59.4 + - + +
571D SER* 3.2 4.7 + - - -
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Residues in contact with LYS 570 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506D ARG 5.4 0.2 + - - -
507D LYS* 3.1 64.5 + - + +
566D TYR* 3.1 43.8 + - + +
567D LEU* 3.0 10.6 + - - +
569D ALA* 1.4 75.7 - - + +
571D SER* 1.4 66.4 + - - +
572D ILE* 3.3 18.5 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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