Contacts of the helix formed by residues 3295 - 3320 (chain D) in PDB entry 1DDX
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 VAL3295 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3200D PHE* 3.4 27.1 - - + -
3203D GLN* 4.2 7.2 - - - +
3291D VAL 5.7 0.4 - - - +
3292D PHE 3.8 1.8 + - - -
3293D GLY 3.1 4.2 + - - -
3294D LEU* 1.3 91.5 - - + +
3296D PRO* 1.3 56.9 - - + +
3297D GLY 2.6 16.9 + - - +
3298D LEU* 2.6 58.3 + - + +
3299D MET 3.0 10.4 + - - -
3407D PHE* 5.3 3.6 - - + -
3408D LEU* 4.6 10.8 - - + -
3411D ASN* 4.0 2.2 - - - -
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Residues in contact with PRO3296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3294D LEU 4.0 2.5 - - - +
3295D VAL* 1.3 83.7 - - + +
3297D GLY* 1.3 60.8 + - - +
3299D MET* 4.1 4.7 - - + -
3300D MET* 3.1 23.7 + - - +
3407D PHE* 3.4 49.8 - - + +
3410D ASN 3.2 28.0 - - - +
3411D ASN* 3.4 24.7 - - - +
3414D LEU* 3.9 8.3 - - + +
3422D PHE* 3.9 17.5 - - + -
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Residues in contact with GLY3297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3200D PHE* 3.6 42.4 - - - -
3295D VAL* 2.6 9.5 + - - +
3296D PRO* 1.3 76.6 - - - +
3298D LEU* 1.3 63.0 + - - +
3300D MET* 3.3 19.8 - - - +
3301D TYR* 3.4 9.7 + - - -
3407D PHE* 4.5 1.8 - - - -
3426D PHE* 4.2 7.6 - - - -
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Residues in contact with LEU3298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3200D PHE* 3.9 6.7 - - + +
3203D GLN* 3.1 40.8 - - + +
3204D HIS* 3.7 23.7 - - + +
3207D HIS* 5.1 4.9 - - + +
3291D VAL* 5.5 2.2 - - + +
3292D PHE* 3.6 46.9 - - + +
3295D VAL* 2.6 39.9 + - + +
3297D GLY* 1.3 68.4 - - - +
3299D MET* 1.3 69.4 + - - +
3301D TYR* 2.7 18.5 + - - +
3302D ALA* 3.0 10.5 + - - -
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Residues in contact with MET3299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3263D PRO* 4.3 2.7 - - - -
3273D MET* 5.1 1.1 - - + -
3275D TYR* 3.9 5.2 - - - +
3285D PHE* 3.3 37.7 - - + -
3287D VAL* 4.2 17.0 - - + -
3292D PHE* 2.9 31.6 + - + +
3293D GLY* 3.2 20.2 - - - -
3295D VAL 3.0 9.2 + - - +
3296D PRO* 4.0 4.3 - - + +
3298D LEU* 1.3 78.4 - - - +
3300D MET* 1.3 57.5 + - - +
3302D ALA* 3.1 7.0 - - - +
3303D THR* 2.7 35.8 + - - +
3411D ASN* 3.5 15.9 - - - +
3414D LEU* 3.6 20.0 - - + -
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Residues in contact with MET3300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3197D MET* 3.3 40.2 - - + +
3200D PHE* 5.5 1.1 - - - -
3296D PRO 3.1 18.4 + - - +
3297D GLY 3.3 10.5 - - - +
3298D LEU 2.8 3.8 + - - -
3299D MET* 1.3 75.9 - - - +
3301D TYR* 1.3 71.4 + - - +
3303D THR* 3.3 5.5 - - - -
3304D ILE* 3.0 33.3 + - + +
3414D LEU* 3.5 17.7 - - + +
3419D LEU* 3.4 20.6 - - + +
3422D PHE* 3.9 13.2 - - + +
3423D VAL* 3.5 30.1 - - + +
3426D PHE* 4.0 15.9 - - + -
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Residues in contact with TYR3301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3197D MET* 3.2 35.1 + - - +
3200D PHE* 3.2 28.9 - - + -
3201D PHE* 2.9 55.1 - + + +
3204D HIS* 3.5 22.4 - + + +
3297D GLY 3.4 6.6 + - - -
3298D LEU 2.7 12.4 + - - +
3300D MET* 1.3 76.8 - - - +
3302D ALA* 1.3 73.1 + - - +
3304D ILE* 2.6 34.1 + - + +
3305D TRP* 2.8 21.9 + - - -
3564D ILE* 4.1 12.9 - - + +
3567D LEU* 5.4 2.7 - - + -
3568D ILE* 4.9 4.7 - - + -
3580D PHE* 3.6 6.6 - - - -
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Residues in contact with ALA3302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3204D HIS* 3.7 13.9 + - - +
3233D ILE* 6.2 1.8 - - - -
3263D PRO* 4.8 0.9 - - + -
3287D VAL* 4.5 28.9 - - + -
3292D PHE* 4.9 4.3 - - + -
3298D LEU 3.0 7.6 + - - +
3299D MET* 3.1 19.5 - - + +
3301D TYR* 1.3 81.5 - - - +
3303D THR* 1.3 64.1 + - - +
3304D ILE 2.6 0.7 + - - -
3305D TRP* 2.6 15.1 + - - -
3306D LEU* 2.7 14.6 + - + -
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Residues in contact with THR3303 (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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3261D VAL 3.1 27.8 - - - +
3262D TYR* 3.6 14.5 - - + -
3263D PRO* 3.2 33.3 - - + +
3299D MET* 2.7 25.2 + - - +
3300D MET* 3.3 10.5 - - - -
3302D ALA* 1.3 75.7 - - - +
3304D ILE* 1.3 61.2 + - - +
3306D LEU* 3.7 4.2 - - + +
3307D ARG* 2.9 44.4 + - + +
3414D LEU* 4.5 1.4 - - - +
3419D LEU* 4.6 4.7 - - + -
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Residues in contact with ILE3304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3300D MET* 3.0 25.0 + - + +
3301D TYR* 2.6 50.6 + - + +
3302D ALA 2.6 4.2 + - - -
3303D THR* 1.3 70.2 - - - +
3305D TRP* 1.3 54.0 + - + +
3307D ARG* 2.7 29.5 + - - +
3419D LEU* 3.6 16.8 - - + +
3567D LEU* 3.5 25.4 - - + +
3568D ILE* 4.8 10.1 - - + -
3571D ASN* 2.6 44.1 + - + +
3572D VAL* 4.7 8.5 - - + -
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Residues in contact with TRP3305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3201D PHE* 4.8 15.8 - + - -
3204D HIS* 3.4 33.0 + + - -
3232D HIS* 5.2 1.8 - + - -
3233D ILE* 4.4 27.1 - - + -
3301D TYR* 2.8 18.5 + + + -
3302D ALA* 2.6 10.4 + - - +
3304D ILE* 1.3 75.7 - - + +
3306D LEU* 1.3 55.5 + - - +
3308D GLU* 2.6 39.9 + - + +
3309D HIS* 2.8 14.1 + - - +
3336D LEU* 4.1 16.2 - - + +
3339D GLU* 3.7 22.0 - - + -
3340D THR* 3.2 43.1 - - + -
3343D ILE* 4.3 9.4 - - + -
3567D LEU* 3.5 32.8 - - + +
3571D ASN* 4.1 0.4 - - - +
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Residues in contact with LEU3306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3233D ILE* 4.9 8.3 - - + +
3252D LEU* 4.7 20.4 - - + -
3253D LYS 3.9 17.5 - - - +
3254D TYR* 4.2 9.4 - - + -
3261D VAL* 4.0 22.7 - - + -
3262D TYR 5.1 2.5 - - - -
3263D PRO* 3.6 35.7 - - + -
3264D PRO* 4.4 2.2 - - + -
3287D VAL* 6.1 0.9 - - + -
3302D ALA* 2.7 20.2 + - + +
3303D THR* 3.7 6.1 - - + +
3305D TRP* 1.3 73.5 - - - +
3307D ARG* 1.3 74.1 + - + +
3309D HIS* 3.3 15.2 + - - +
3310D ASN* 3.4 18.8 + - - +
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Residues in contact with ARG3307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3260D GLU* 3.3 27.4 + - - +
3261D VAL* 2.5 74.6 + - + +
3262D TYR* 4.6 4.8 - - - -
3303D THR* 2.9 35.5 + - - +
3304D ILE* 2.7 18.5 + - - +
3306D LEU* 1.3 77.6 - - + +
3308D GLU* 1.3 59.2 + - - -
3310D ASN* 3.6 3.8 + - - +
3311D ARG* 2.9 24.1 + - - +
3419D LEU* 4.2 17.2 - - - +
3571D ASN* 3.3 34.9 + - + +
3572D VAL* 5.9 0.9 - - - -
3573D LYS 6.1 0.4 - - - +
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Residues in contact with GLU3308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3304D ILE 2.7 5.5 + - - -
3305D TRP* 2.6 33.0 + - + +
3307D ARG* 1.3 70.3 - - - +
3309D HIS* 1.3 60.4 + - - -
3311D ARG* 2.8 39.6 + - - +
3312D VAL* 2.8 20.4 + - - +
3336D LEU* 3.2 23.1 - - + +
3339D GLU* 2.5 39.4 - - - +
3567D LEU* 4.2 8.6 - - + +
3570D ASN* 5.1 1.3 - - - +
3571D ASN* 2.8 23.2 + - - +
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Residues in contact with HIS3309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3233D ILE* 5.6 0.2 - - + -
3234D TYR* 2.8 36.1 + + - -
3250D GLY 2.8 22.8 + - - -
3252D LEU* 3.4 22.4 + - + +
3305D TRP 2.8 9.7 + - - +
3306D LEU* 3.4 9.9 - - - +
3308D GLU* 1.3 71.6 - - - +
3310D ASN* 1.3 82.0 + - - +
3312D VAL* 2.6 28.6 + - - +
3313D CYS* 2.8 18.0 + - - -
3329D PHE* 3.7 16.5 - + - -
3332D SER* 3.4 24.4 - - - -
3336D LEU* 3.5 20.1 - - + +
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Residues in contact with ASN3310 (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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3251D LYS* 3.6 23.0 - - + +
3252D LEU* 2.9 36.8 + - - +
3254D TYR* 3.4 26.8 - - + +
3306D LEU* 3.4 15.4 + - + +
3307D ARG* 4.1 4.3 - - - +
3309D HIS* 1.3 94.4 - - - +
3311D ARG* 1.3 62.9 + - - +
3313D CYS* 3.2 9.1 + - - +
3314D ASP* 3.1 27.8 + - - +
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Residues in contact with ARG3311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3307D ARG 2.9 15.4 + - - +
3308D GLU* 2.8 47.6 + - - +
3310D ASN* 1.3 77.4 - - - +
3312D VAL* 1.3 65.9 - - - +
3314D ASP* 3.2 15.3 + - - +
3315D ILE* 3.1 38.2 + - + +
3339D GLU* 3.9 5.9 + - - -
3558D ILE* 4.1 12.5 - - - +
3570D ASN* 3.9 43.0 + - - +
3571D ASN* 4.1 5.6 - - - +
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Residues in contact with VAL3312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3308D GLU* 2.8 17.3 + - - +
3309D HIS 2.6 15.7 + - - +
3311D ARG* 1.3 69.7 - - - +
3313D CYS* 1.3 66.9 + - - +
3315D ILE* 2.8 22.9 + - + +
3316D LEU* 2.9 22.0 + - + -
3332D SER* 3.2 32.5 - - - +
3335D ILE* 3.9 15.7 - - + -
3336D LEU* 3.8 20.6 - - + -
3558D ILE* 3.8 25.6 - - + -
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Residues in contact with CYS3313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3249D ASP* 3.2 21.5 - - + +
3250D GLY* 3.0 31.2 - - - -
3251D LYS* 3.8 11.4 - - + -
3309D HIS* 2.8 22.8 + - - -
3310D ASN 3.2 9.6 - - - +
3312D VAL* 1.3 77.6 - - - +
3314D ASP* 1.3 64.7 + - - +
3316D LEU* 3.1 5.8 + - - +
3317D LYS* 2.8 25.2 + - - +
3328D LEU* 4.0 5.3 - - - +
3332D SER* 3.1 22.4 - - - -
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Residues in contact with ASP3314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3249D ASP* 5.4 1.2 - - - +
3251D LYS* 2.8 38.4 + - - -
3310D ASN 3.1 10.5 + - - +
3311D ARG* 3.4 11.0 - - - +
3312D VAL 3.1 0.2 - - - -
3313D CYS* 1.3 75.6 - - - +
3315D ILE* 1.3 63.8 + - + +
3317D LYS* 3.2 10.0 + - - +
3318D GLN* 3.0 24.3 + - - +
----------------------------------------------------------
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Residues in contact with ILE3315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3311D ARG* 3.1 32.5 - - + +
3312D VAL* 2.8 31.7 + - - +
3314D ASP* 1.3 72.9 - - + +
3316D LEU* 1.3 65.2 + - + +
3318D GLN* 3.1 20.7 - - + +
3319D GLU* 3.1 11.6 + - - +
3554D VAL* 4.0 22.8 - - + +
3558D ILE* 3.5 26.7 - - + -
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Residues in contact with LEU3316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3312D VAL* 2.9 17.4 + - + +
3313D CYS 3.4 4.3 - - - +
3315D ILE* 1.3 74.3 - - + +
3317D LYS* 1.3 50.7 + - - +
3318D GLN 2.6 5.5 + - - -
3319D GLU* 2.5 31.0 + - + +
3320D HIS* 2.7 22.9 + - + +
3323D TRP* 4.4 3.6 - - + -
3328D LEU* 3.4 23.6 - - + +
3331D THR* 3.4 34.8 - - + +
3332D SER* 3.8 20.6 - - - +
3335D ILE* 3.8 9.4 - - + -
3550D PHE 4.0 18.6 - - - +
3551D GLY* 4.5 9.4 - - - +
3554D VAL* 5.6 0.9 - - + -
3555D GLY* 4.6 12.1 - - - +
3558D ILE* 6.4 0.7 - - + -
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Residues in contact with LYS3317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3249D ASP* 2.7 35.9 + - + +
3251D LYS* 5.7 2.6 - - - +
3313D CYS 2.8 19.0 + - - +
3314D ASP* 3.6 11.4 + - - +
3316D LEU* 1.3 70.3 - - - +
3318D GLN* 1.3 61.4 - - - +
3320D HIS 4.0 8.7 - - - +
3321D PRO* 3.5 22.3 - - + +
3328D LEU* 3.5 19.3 - - + +
----------------------------------------------------------
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Residues in contact with GLN3318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3314D ASP 3.0 11.5 + - - +
3315D ILE* 3.1 16.4 - - + +
3316D LEU 2.6 4.8 + - - -
3317D LYS* 1.3 80.1 - - - +
3319D GLU* 1.3 70.3 + - - +
3321D PRO* 3.6 9.0 - - - +
----------------------------------------------------------
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Residues in contact with GLU3319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2048C MET* 5.8 0.9 - - + -
2050C THR 4.9 2.8 - - - -
2051C GLY* 4.8 3.3 + - - -
3315D ILE* 3.1 9.9 + - - +
3316D LEU* 2.5 17.8 + - + +
3318D GLN* 1.3 83.3 - - - +
3320D HIS* 1.3 78.3 + - + +
3321D PRO* 3.3 8.3 - - - +
3322D GLU* 3.9 2.1 - - - +
3551D GLY 4.5 10.8 - - - +
3554D VAL* 3.1 44.4 - - + +
----------------------------------------------------------
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Residues in contact with HIS3320 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2048C MET* 3.3 31.2 - - + -
2049C SER 3.2 16.9 + - - -
2050C THR* 4.5 3.7 - - - -
3316D LEU* 2.7 18.2 + - + +
3317D LYS* 3.7 12.8 - - - +
3319D GLU* 1.3 92.8 + - + +
3321D PRO* 1.3 59.7 - - - +
3322D GLU* 2.8 17.8 + - - +
3323D TRP* 3.0 73.6 + + + +
3328D LEU* 5.7 0.2 - - - +
3551D GLY* 3.2 21.7 + - - -
----------------------------------------------------------
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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