Contacts of the helix formed by residues 579 - 590 (chain D) in PDB entry 1XMI
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 579 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A GLU* 2.5 31.7 - - - +
578D LEU* 1.3 76.2 - - - +
580D VAL* 1.3 65.2 + - - +
581D LEU 3.7 0.2 + - - -
582D THR* 2.5 30.3 + - - -
583D GLU* 3.0 20.9 + - - +
661D ILE* 3.8 20.3 - - + +
664D GLU* 3.2 20.4 - - - +
665D THR* 3.5 15.7 - - - +
668D ARG* 3.1 19.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 580 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ATP 5.8 1.6 - - - +
401A TRP* 4.2 19.1 - - + +
403A GLU* 6.5 0.4 - - - -
473A GLY 5.5 0.4 - - - +
474A GLU* 3.2 34.6 + - + +
579D ASP* 1.3 75.0 - - - +
581D LEU* 1.3 59.7 + - + +
583D GLU* 3.4 15.0 + - - +
584D LYS* 3.0 55.2 + - + +
606D LYS* 5.3 9.6 - - + +
661D ILE* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 581 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A MET 3.7 22.9 - - - +
473A GLY* 3.6 22.2 - - - +
474A GLU* 3.0 25.5 + - - +
476A GLU* 6.1 0.9 - - - +
579D ASP* 3.3 0.8 - - - +
580D VAL* 1.3 74.8 - - + +
582D THR* 1.3 60.4 + - - +
584D LYS* 3.3 19.1 + - + +
585D GLU* 3.0 34.3 + - - +
668D ARG* 3.6 34.5 - - - +
669D PHE* 5.3 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 582 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525D GLN* 3.7 9.2 - - - +
555D ARG* 4.8 2.0 - - - +
578D LEU* 3.9 10.3 - - + -
579D ASP* 2.5 29.4 + - - -
580D VAL 3.5 0.2 - - - -
581D LEU* 1.3 76.8 - - - +
583D GLU* 1.3 57.0 + - - +
585D GLU* 3.4 3.6 + - - +
586D ILE* 2.9 51.9 + - + +
664D GLU* 3.7 7.6 - - - +
667D ARG* 3.0 29.4 + - - +
668D ARG* 3.1 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 583 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575D PHE* 3.2 41.1 - - + +
578D LEU* 4.3 14.6 - - + +
579D ASP 3.0 18.5 + - - +
580D VAL* 3.5 13.1 - - - +
582D THR* 1.3 76.3 - - - +
584D LYS* 1.3 58.4 + - + +
586D ILE* 3.9 0.5 - - - +
587D PHE* 2.9 33.4 + - - +
606D LYS* 3.4 35.0 + - - +
609D HIS* 3.5 26.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 584 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A GLU* 4.4 19.8 + - - +
473A GLY 5.8 0.6 + - - -
474A GLU 5.4 0.2 + - - -
476A GLU* 4.2 23.7 + - - +
580D VAL* 3.0 41.3 + - + +
581D LEU* 3.3 21.6 + - + +
583D GLU* 1.3 77.2 - - + +
585D GLU* 1.3 63.5 - - + +
587D PHE* 3.5 5.4 + - - +
588D GLU* 3.1 24.4 + - - +
608D GLU* 3.4 36.7 - - - +
609D HIS* 5.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 585 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B SER* 6.5 1.1 - - - -
512B TYR* 3.3 38.9 - - + +
525D GLN* 3.0 25.9 + - - +
581D LEU* 3.0 18.0 + - - +
582D THR* 3.8 1.3 - - - +
583D GLU 3.3 0.2 - - - -
584D LYS* 1.3 77.7 - - + +
586D ILE* 1.3 57.1 + - - +
588D GLU* 3.3 5.9 + - - +
589D SER* 2.9 32.0 + - - -
668D ARG* 2.6 46.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 586 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523D ALA 4.1 10.8 - - - +
524D CYS* 3.8 22.0 - - + +
525D GLN* 3.8 16.8 - - + +
555D ARG* 3.9 16.6 - - + -
558D LEU* 3.6 30.3 - - + -
575D PHE* 3.6 12.1 - - + -
578D LEU* 4.1 7.9 - - + -
582D THR* 2.9 38.7 + - + +
585D GLU* 1.3 73.0 - - - +
587D PHE* 1.3 61.8 + - - +
589D SER* 3.5 4.7 - - - -
590D CYS* 2.8 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 587 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453D LEU* 4.3 6.5 - - + -
575D PHE* 4.0 13.3 - + + -
583D GLU 2.9 19.8 + - - +
584D LYS 3.7 3.6 - - - +
586D ILE* 1.3 77.6 - - - +
588D GLU* 1.3 60.8 + - + +
591D VAL* 3.3 27.3 + - + +
592D CYS* 3.0 48.9 + - - -
602D LEU* 3.6 27.8 - - + -
608D GLU* 3.9 18.2 - - + -
609D HIS* 3.6 50.9 - + - +
612D LYS* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 588 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584D LYS 3.1 18.6 + - - +
585D GLU* 3.6 5.2 - - - +
587D PHE* 1.3 79.8 - - + +
589D SER* 1.3 58.1 + - - +
592D CYS* 3.3 12.4 - - - +
593D LYS* 3.0 70.2 + - - +
608D GLU* 5.5 2.8 - - - +
612D LYS* 3.4 30.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 589 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B SER* 5.4 13.0 - - - -
523D ALA* 2.6 40.3 + - - +
525D GLN* 5.4 2.3 + - - +
585D GLU 2.9 22.1 + - - -
586D ILE* 3.5 4.0 - - - +
588D GLU* 1.3 74.8 - - - +
590D CYS* 1.3 58.5 + - - +
593D LYS* 3.4 13.8 - - - +
594D LEU* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 590 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523D ALA* 4.0 19.1 - - + +
524D CYS* 3.7 19.5 - - - -
558D LEU* 4.4 7.4 - - + -
562D VAL* 3.5 40.2 - - - -
586D ILE* 2.8 27.7 + - + +
589D SER* 1.3 72.4 + - - +
591D VAL* 1.3 67.9 + - + +
594D LEU* 3.3 5.3 + - - +
595D MET* 3.0 30.2 + - - +
----------------------------------------------------------
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