Contacts of the helix formed by residues 641 - 665 (chain D) in PDB entry 5DO7
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 TYR 641 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530D LEU* 6.3 0.2 - - - -
639D PRO* 2.8 26.1 + - + +
640D LEU* 1.3 80.0 - - + +
642D ALA* 1.3 72.9 + - + +
643D ILE 3.1 2.2 + - - -
644D TYR* 3.9 19.6 + - + +
645D LEU* 3.6 32.7 - - + +
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Residues in contact with ALA 642 (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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638D TYR* 4.6 5.2 - - + -
639D PRO* 2.8 37.6 + - + +
641D TYR* 1.3 91.3 - - + +
643D ILE* 1.3 56.9 + - - +
645D LEU* 2.8 31.1 + - - +
646D ILE* 3.1 21.8 + - + +
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Residues in contact with ILE 643 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534D LEU* 4.8 5.8 - - + -
598D TRP* 3.5 52.3 - - + +
601D GLU* 4.4 13.9 - - + +
602D GLY* 3.5 29.4 - - - +
605D LYS* 4.7 7.2 - - + -
606D ILE* 5.7 0.2 - - + -
638D TYR* 4.9 4.7 - - + +
639D PRO 3.8 20.2 - - - +
640D LEU 3.9 11.0 - - - +
641D TYR 3.1 1.2 - - - -
642D ALA* 1.3 78.1 - - + +
644D TYR* 1.3 56.1 + - + +
646D ILE* 2.8 35.3 + - + +
647D VAL* 2.8 20.7 + - + +
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Residues in contact with TYR 644 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530D LEU* 2.6 57.7 + - + +
533D LEU* 4.0 13.9 - - + -
534D LEU* 3.5 39.6 - - + +
537D LEU* 3.8 23.5 - - + +
602D GLY* 6.5 0.2 - - - -
606D ILE* 4.1 6.5 - - + +
640D LEU 3.7 23.1 - - - -
641D TYR* 4.0 17.7 - - + +
643D ILE* 1.3 79.3 - - + +
645D LEU* 1.3 63.9 + - + +
647D VAL* 3.4 9.3 + - - +
648D ILE* 2.8 33.1 + - - +
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Residues in contact with LEU 645 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641D TYR* 3.6 38.4 - - + +
642D ALA* 2.8 12.7 + - - +
644D TYR* 1.3 82.4 - - + +
646D ILE* 1.3 59.3 + - - +
648D ILE* 3.0 16.7 - - + +
649D GLY* 2.8 28.1 + - - -
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Residues in contact with ILE 646 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592D LYS* 4.1 10.5 - - + +
598D TRP* 3.1 64.4 - - + +
638D TYR* 4.8 9.6 - - + -
642D ALA* 3.1 16.7 + - + +
643D ILE* 2.8 27.3 + - + +
645D LEU* 1.3 78.3 - - + +
647D VAL* 1.3 56.8 + - - +
649D GLY* 3.6 0.9 - - - -
650D LEU* 2.8 30.8 + - + +
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Residues in contact with VAL 647 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534D LEU* 4.3 12.6 - - + -
537D LEU* 3.3 43.3 - - + +
538D VAL* 4.4 5.4 - - + +
541D CYS* 4.3 2.0 - - + +
595D PHE* 5.0 8.1 - - + -
598D TRP* 3.7 30.1 - - + -
643D ILE* 2.8 22.8 + - + +
644D TYR* 3.5 10.3 - - - +
646D ILE* 1.3 73.7 - - - +
648D ILE* 1.3 63.3 + - - +
649D GLY 3.0 1.6 - - - -
650D LEU* 3.3 12.7 - - + +
651D SER* 2.8 31.5 + - - -
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Residues in contact with ILE 648 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537D LEU* 4.1 22.0 - - + -
644D TYR 2.8 22.0 + - - +
645D LEU* 3.0 35.4 - - + +
647D VAL* 1.3 74.7 - - - +
649D GLY* 1.3 59.7 + - - +
651D SER* 3.4 20.7 - - - -
652D GLY* 3.4 5.4 + - - -
655D MET* 4.8 5.0 - - + +
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Residues in contact with GLY 649 (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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645D LEU 2.8 17.9 + - - -
646D ILE* 3.6 1.3 - - - -
648D ILE* 1.3 77.5 - - - +
650D LEU* 1.3 65.3 + - - +
652D GLY* 2.8 18.5 + - - -
653D GLY 3.3 3.6 + - - -
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Residues in contact with LEU 650 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541D CYS* 4.0 9.2 - - - -
592D LYS 5.0 0.9 - - - +
593D VAL* 3.2 42.6 - - + +
595D PHE* 3.8 32.8 - - + +
598D TRP* 3.8 23.3 - - + -
646D ILE* 2.8 20.9 + - + +
647D VAL* 3.3 13.9 - - - +
649D GLY* 1.3 70.0 - - - +
651D SER* 1.3 70.2 + - - +
653D GLY* 2.8 14.7 + - - +
654D PHE* 3.1 23.1 + - + -
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Residues in contact with SER 651 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537D LEU* 4.4 2.8 + - - +
540D PHE* 4.2 7.2 - - - -
541D CYS* 3.3 29.7 + - - +
544D ILE* 4.0 12.2 - - - +
647D VAL 2.8 16.3 + - - -
648D ILE* 3.4 18.5 - - - +
650D LEU* 1.3 76.1 - - - +
652D GLY* 1.3 66.1 + - - -
654D PHE* 2.8 5.9 + - - +
655D MET* 2.8 38.1 + - - +
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Residues in contact with GLY 652 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648D ILE 3.4 6.4 + - - -
649D GLY* 2.8 16.7 + - - -
651D SER* 1.3 73.5 - - - +
653D GLY* 1.3 51.9 + - - -
655D MET* 3.0 14.3 + - - +
656D VAL* 2.8 43.9 + - - +
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Residues in contact with GLY 653 (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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649D GLY 3.3 5.1 + - - -
650D LEU* 2.8 15.1 + - - -
652D GLY* 1.3 70.7 - - - +
654D PHE* 1.3 60.8 + - - -
656D VAL* 3.4 7.1 + - - +
657D LEU* 3.1 22.0 + - - +
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Residues in contact with PHE 654 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541D CYS* 3.7 25.1 - - - -
544D ILE* 3.6 18.2 - - + +
545D MET* 3.5 42.8 - - + +
548D ALA* 3.7 6.7 - - + +
566D LEU* 4.6 11.9 - - + -
570D PHE* 4.1 26.0 - + - -
593D VAL* 6.0 0.9 - - + -
595D PHE* 4.6 3.6 - + - -
650D LEU* 3.1 39.7 - - + -
651D SER* 2.8 7.7 + - - +
653D GLY* 1.3 71.2 - - - -
655D MET* 1.3 67.6 + - - +
657D LEU* 2.8 23.8 + - + +
658D TYR* 2.8 11.6 + - - +
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Residues in contact with MET 655 (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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493D PHE* 5.6 7.3 - - + +
497D ILE* 4.0 23.2 - - + +
540D PHE* 4.7 5.8 - - + -
544D ILE* 3.3 32.1 - - + +
648D ILE* 4.8 4.9 - - + +
651D SER* 2.8 33.5 + - - -
652D GLY* 3.2 19.7 - - - +
654D PHE* 1.3 75.2 - - - +
656D VAL* 1.3 58.1 + - + +
658D TYR* 3.2 5.7 + - - +
659D TYR* 2.8 30.2 + - - +
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Residues in contact with VAL 656 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652D GLY* 2.8 24.1 + - - +
653D GLY* 3.6 7.6 - - - +
655D MET* 1.3 74.6 - - + +
657D LEU* 1.3 63.0 + - + +
659D TYR* 4.0 6.4 - - + +
660D VAL* 2.8 33.5 + - + +
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Residues in contact with LEU 657 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548D ALA* 3.9 19.3 - - + -
549D ALA 5.0 0.9 - - - +
552D LEU* 3.1 34.8 - - + -
562D PHE* 5.5 7.6 - - + -
653D GLY 3.1 13.4 + - - +
654D PHE* 2.8 17.4 + - + +
656D VAL* 1.3 78.2 - - + +
658D TYR* 1.3 53.8 + - - +
660D VAL* 2.9 10.2 - - + +
661D SER* 2.6 38.3 + - - +
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Residues in contact with TYR 658 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471D CYS* 4.2 6.2 - - - -
477D MET* 4.8 0.7 - - - +
492D TYR* 4.4 7.3 - - - -
493D PHE* 3.8 23.8 - - - -
496D LYS* 3.2 31.3 + - + -
497D ILE* 4.1 12.6 - - + -
544D ILE* 4.9 2.9 - - + -
547D LEU* 3.2 56.3 - - + -
548D ALA* 3.5 10.0 - - + +
551D ALA* 3.4 21.1 - - + -
654D PHE 2.8 14.7 + - - +
655D MET* 3.4 11.4 - - - +
657D LEU* 1.3 70.6 - - - +
659D TYR* 1.3 60.4 + - - +
661D SER* 3.1 1.5 + - - -
662D LEU* 2.8 61.4 + - + +
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Residues in contact with TYR 659 (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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488D THR* 4.4 6.5 - - - -
489D THR* 3.8 24.4 + - - +
493D PHE* 3.2 65.3 - + + +
655D MET 2.8 19.4 + - - +
656D VAL* 4.0 7.2 - - + +
658D TYR* 1.3 74.1 - - - +
660D VAL* 1.3 57.6 + - - +
662D LEU* 2.9 19.4 - - - +
663D ARG* 3.6 35.1 + - + +
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Residues in contact with VAL 660 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656D VAL* 2.8 26.1 + - + +
657D LEU* 2.9 29.6 - - + +
659D TYR* 1.3 69.4 - - - +
661D SER* 1.3 71.6 + - - +
662D LEU 2.2 24.8 - - - +
664D PHE* 3.2 40.4 + - + +
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Residues in contact with SER 661 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548D ALA 4.5 0.6 + - - -
551D ALA* 3.9 7.6 - - - +
552D LEU* 3.2 51.8 - - - +
657D LEU 2.6 28.9 + - - -
658D TYR* 3.1 3.3 + - - -
660D VAL* 1.3 76.9 - - - +
662D LEU* 1.3 51.2 + - - +
664D PHE 5.4 0.2 - - - -
665D ILE* 2.5 48.4 + - - +
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Residues in contact with LEU 662 (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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477D MET* 4.8 17.7 - - + -
488D THR* 3.9 11.2 - - + -
492D TYR* 4.1 15.3 - - + -
493D PHE* 4.1 21.8 - - + +
551D ALA* 3.7 22.4 - - + -
658D TYR* 2.8 58.0 + - + +
659D TYR* 2.9 6.9 - - - +
660D VAL 2.2 28.1 - - - +
661D SER* 1.3 71.7 - - - +
663D ARG* 1.3 58.8 + - - +
664D PHE 2.5 8.8 + - - -
665D ILE 3.7 4.7 - - - +
666D LYS 5.8 0.9 - - - +
667D GLN* 4.9 4.7 - - + +
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Residues in contact with ARG 663 (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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487D TYR* 3.9 29.9 + - + +
488D THR* 3.1 36.5 + - + +
489D THR* 3.6 25.0 + - - +
659D TYR* 3.6 31.6 + - - +
662D LEU* 1.3 75.2 - - - +
664D PHE* 1.3 98.2 + - + +
665D ILE* 3.5 5.6 + - - -
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Residues in contact with PHE 664 (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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660D VAL* 3.2 33.4 - - + +
662D LEU 2.5 9.7 + - - -
663D ARG* 1.3 124.9 - - + +
665D ILE* 1.3 69.8 + - - +
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Residues in contact with ILE 665 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551D ALA 3.9 11.9 - - - +
552D LEU* 4.2 13.0 - - - +
553D LEU 5.9 0.2 - - - +
661D SER* 2.5 41.9 + - - +
662D LEU* 3.7 10.2 - - - +
663D ARG 3.9 3.3 + - - -
664D PHE* 1.3 88.0 - - - +
666D LYS* 1.3 101.4 + - + +
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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
------------------------------------------------------------
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