Contacts of the helix formed by residues 3374 - 3403 (chain C) in PDB entry 5Y3R
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 ILE3374 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3341C LEU 3.2 25.4 - - - +
3342C SER* 3.1 26.4 - - - +
3343C SER* 4.2 3.8 - - - +
3344C GLU 3.5 15.7 - - - +
3345C PRO* 3.6 34.0 - - + +
3349C ALA* 4.7 0.4 - - + -
3373C VAL* 1.3 77.9 - - + +
3375C ALA* 1.3 57.1 + - + +
3376C GLY 3.5 1.6 - - - -
3377C LEU* 3.5 12.9 - - + +
3378C TYR* 2.6 37.1 + - + +
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Residues in contact with ALA3375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3373C VAL* 3.2 15.9 - - + +
3374C ILE* 1.3 80.7 - - + +
3376C GLY* 1.3 59.7 + - - +
3378C TYR* 3.0 26.3 - - - +
3379C GLN* 3.8 3.8 + - - +
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Residues in contact with GLY3376 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3353C GLU* 3.9 16.4 + - - +
3357C ARG* 4.4 0.9 - - - +
3373C VAL* 4.1 0.8 - - - +
3375C ALA* 1.3 74.6 - - - +
3377C LEU* 1.3 58.1 + - - +
3378C TYR 3.0 1.8 - - - -
3380C ARG* 2.6 66.8 + - - +
3381C ALA 3.1 4.8 + - - -
3384C HIS* 4.6 4.3 - - - -
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Residues in contact with LEU3377 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3332C THR* 5.7 8.3 - - + -
3336C ILE* 5.8 0.9 - - - +
3341C LEU* 5.5 7.6 - - + +
3342C SER* 4.3 11.6 + - - +
3349C ALA* 3.5 16.2 - - + +
3352C GLU* 4.1 15.9 - - + +
3353C GLU* 3.4 17.2 - - + +
3356C ALA* 3.6 29.6 - - + -
3373C VAL 3.1 20.2 - - - +
3374C ILE* 3.4 18.5 + - + +
3375C ALA 3.3 0.2 - - - -
3376C GLY* 1.3 74.0 - - - +
3378C TYR* 1.3 66.3 + - - +
3381C ALA* 3.0 35.9 + - + +
3382C PHE* 5.5 1.7 - - - -
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Residues in contact with TYR3378 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3339C ASN* 4.9 15.7 - - - +
3342C SER* 4.5 22.4 + - - +
3374C ILE* 2.6 17.9 + - + +
3375C ALA* 3.0 17.5 - - - +
3376C GLY 3.0 1.0 - - - -
3377C LEU* 1.3 78.0 - - - +
3379C GLN* 1.3 96.8 + - + +
3382C PHE* 5.1 10.0 - - - -
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Residues in contact with GLN3379 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3375C ALA 3.8 2.5 + - - +
3376C GLY 3.6 1.4 + - - -
3378C TYR* 1.3 109.7 - - + +
3380C ARG* 1.3 80.7 + - + +
3381C ALA 3.4 2.0 + - - -
3382C PHE* 3.9 19.9 + - - +
3383C GLN* 4.8 1.7 + - - +
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Residues in contact with ARG3380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3357C ARG* 3.1 56.1 - - - +
3376C GLY* 2.6 33.9 + - - +
3379C GLN* 1.3 88.5 + - + +
3381C ALA* 1.3 63.4 + - - -
3382C PHE 3.3 1.6 - - - -
3383C GLN* 3.2 39.3 + - - +
3384C HIS* 3.0 26.2 + - - +
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Residues in contact with ALA3381 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3332C THR* 6.1 1.1 - - + +
3336C ILE* 6.1 4.5 - - + -
3376C GLY 3.1 6.5 + - - -
3377C LEU* 3.0 41.1 + - + +
3379C GLN 3.4 0.2 - - - -
3380C ARG* 1.3 74.2 - - - +
3382C PHE* 1.3 60.5 + - + +
3384C HIS* 2.5 37.8 + - - +
3385C LEU* 2.8 28.4 + - + +
----------------------------------------------------------
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Residues in contact with PHE3382 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3333C THR* 4.0 28.5 - - + -
3336C ILE* 4.5 27.8 - - + -
3377C LEU 5.5 2.2 - - - -
3378C TYR 5.1 7.6 - - - -
3379C GLN 3.9 14.3 + - - +
3380C ARG 3.3 0.2 - - - -
3381C ALA* 1.3 79.7 - - + +
3383C GLN* 1.3 57.9 + - + +
3385C LEU* 3.5 18.9 - - + +
3386C SER* 2.8 31.9 + - - -
3423C GLN* 4.6 11.7 + - + +
3426C LYS* 3.6 42.4 - - + -
3430C ASN* 5.7 0.7 - - - -
3435C ASP* 5.1 6.5 - - - +
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Residues in contact with GLN3383 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3379C GLN 5.1 1.3 - - - +
3380C ARG* 3.2 45.6 + - - +
3381C ALA 3.0 0.2 - - - -
3382C PHE* 1.3 77.0 - - + +
3384C HIS* 1.3 64.4 + - + +
3386C SER* 2.3 26.3 + - - -
3387C GLU* 2.9 29.1 + - - +
3434C ILE* 5.8 8.7 - - - +
3435C ASP* 6.1 1.3 - - - +
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Residues in contact with HIS3384 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3329C LEU* 4.6 2.9 - - + -
3353C GLU 5.1 0.2 - - - -
3356C ALA* 3.0 45.4 - - + +
3357C ARG* 3.3 41.6 - - + +
3359C ILE 3.1 13.6 - - - +
3376C GLY* 4.3 7.0 - - - -
3380C ARG* 3.0 41.6 + - + +
3381C ALA* 2.5 17.6 + - - +
3383C GLN* 1.3 76.8 + - + +
3385C LEU* 1.3 67.3 + - + +
3387C GLU* 5.4 0.7 - - - -
3388C ALA* 2.9 23.9 + - - +
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Residues in contact with LEU3385 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3329C LEU* 3.0 31.8 - - + +
3332C THR* 3.6 15.3 - - + +
3333C THR* 3.0 55.0 - - + +
3381C ALA* 2.8 36.3 + - + +
3382C PHE* 3.5 18.8 - - + +
3384C HIS* 1.3 71.9 - - + +
3386C SER* 1.3 62.9 + - - +
3389C VAL* 2.9 30.0 + - - +
3419C PHE* 3.8 6.7 - - + -
----------------------------------------------------------
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Residues in contact with SER3386 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3382C PHE 2.8 20.1 + - - -
3383C GLN* 2.3 31.0 + - - -
3385C LEU* 1.3 78.5 - - - +
3387C GLU* 1.3 68.1 + - - +
3389C VAL* 3.3 2.9 - - - +
3390C GLN* 2.8 31.8 + - - +
3419C PHE* 3.3 25.0 - - - -
3423C GLN* 4.8 1.8 - - - -
3438C GLU* 4.8 7.9 + - - -
3442C TYR* 5.7 7.0 - - - -
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Residues in contact with GLU3387 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3359C ILE 5.3 2.2 - - - +
3383C GLN* 2.9 21.4 + - - +
3384C HIS* 4.6 0.7 - - - +
3386C SER* 1.3 87.0 + - - +
3388C ALA* 1.3 54.1 + - - +
3390C GLN* 4.3 7.0 - - - +
3391C ALA* 2.5 37.2 + - - +
3438C GLU* 3.6 24.7 - - - +
3442C TYR* 4.8 6.4 + - + +
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Residues in contact with ALA3388 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3325C ASP* 2.6 21.4 - - - +
3329C LEU* 3.3 18.2 - - + -
3359C ILE* 3.1 46.8 + - + +
3384C HIS 2.9 5.6 + - - +
3387C GLU* 1.3 77.2 - - - +
3389C VAL* 1.3 56.5 + - - +
3391C ALA* 3.5 6.1 - - - +
3392C ALA* 2.9 19.6 + - - +
3395C GLU* 5.3 0.3 - - - +
----------------------------------------------------------
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Residues in contact with VAL3389 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3325C ASP* 3.1 6.5 - - - -
3326C GLN* 2.3 61.8 + - + +
3329C LEU* 3.1 24.6 - - + +
3385C LEU 2.9 26.0 + - - +
3386C SER 3.3 4.0 - - - +
3388C ALA* 1.3 73.9 - - - +
3390C GLN* 1.3 52.9 + - - +
3392C ALA* 2.7 16.8 + - - +
3415C THR* 5.5 1.1 - - + -
3416C LEU* 3.6 29.4 - - + -
3419C PHE* 4.0 18.2 - - + -
----------------------------------------------------------
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Residues in contact with GLN3390 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3386C SER* 2.8 21.6 + - - +
3387C GLU* 4.6 5.2 - - - +
3389C VAL* 1.3 72.5 - - - +
3391C ALA* 1.3 59.2 + - - +
3393C GLU* 2.7 35.5 + - - +
3394C GLU* 2.9 16.3 + - + +
3416C LEU* 3.6 26.3 - - + +
3442C TYR* 3.2 52.4 + - - -
3445C LEU* 4.3 17.2 - - - +
----------------------------------------------------------
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Residues in contact with ALA3391 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3387C GLU* 2.5 26.0 + - - +
3388C ALA* 3.5 9.4 - - - +
3390C GLN* 1.3 77.3 - - - +
3392C ALA* 1.3 57.7 + - - +
3393C GLU 3.1 0.3 + - - -
3394C GLU* 3.2 5.2 + - - +
3395C GLU* 3.0 37.5 + - - +
----------------------------------------------------------
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Residues in contact with ALA3392 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3322C ALA* 2.9 43.8 - - - +
3325C ASP* 3.0 16.6 - - + +
3326C GLN* 3.1 3.3 + - - +
3388C ALA 2.9 6.3 + - - +
3389C VAL 2.7 15.7 + - - +
3391C ALA* 1.3 72.7 - - - +
3393C GLU* 1.3 56.5 + - - +
3395C GLU* 3.1 19.9 - - - +
3396C ALA* 2.9 24.9 + - - +
----------------------------------------------------------
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Residues in contact with GLU3393 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3326C GLN* 2.8 20.2 - - - +
3390C GLN* 2.7 33.1 + - + +
3392C ALA* 1.3 78.7 - - - +
3394C GLU* 1.3 87.8 + - - +
3396C ALA* 3.3 4.5 + - - +
3397C GLN* 2.9 37.9 + - - +
3412C ALA* 5.0 14.4 - - + +
3413C TYR* 4.3 10.6 - - + -
3416C LEU* 4.0 22.0 - - + -
3445C LEU* 5.5 6.6 - - - +
3449C LYS* 5.6 3.3 + - - -
----------------------------------------------------------
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Residues in contact with GLU3394 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3390C GLN* 2.9 12.3 + - + +
3391C ALA* 3.2 6.3 + - - +
3393C GLU* 1.3 94.8 - - - +
3395C GLU* 1.3 64.5 + - - +
3396C ALA 3.2 0.8 + - - -
3397C GLN* 2.7 36.8 + - - +
3398C PRO* 4.2 8.5 - - - +
3445C LEU* 5.6 4.5 - - - +
----------------------------------------------------------
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Residues in contact with GLU3395 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3309C GLU* 5.6 4.3 - - - +
3318C LYS* 3.5 31.5 - - + +
3322C ALA* 3.1 25.3 - - + +
3325C ASP* 5.6 0.3 - - - +
3388C ALA 5.3 0.3 - - - +
3391C ALA* 3.0 20.2 + - - +
3392C ALA* 3.1 21.4 + - - +
3394C GLU* 1.3 77.1 - - - +
3396C ALA* 1.3 58.2 + - - +
3397C GLN 3.6 0.4 + - - -
3398C PRO* 5.0 0.5 - - - +
3399C PRO* 4.1 8.8 - - - +
----------------------------------------------------------
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Residues in contact with ALA3396 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3319C ASN* 3.3 42.7 - - - +
3322C ALA* 3.9 2.9 - - + -
3323C PHE* 4.5 2.5 - - - +
3326C GLN* 5.2 0.7 - - - +
3392C ALA 2.9 17.1 + - - +
3393C GLU* 3.6 5.4 - - - +
3394C GLU 3.2 0.4 - - - -
3395C GLU* 1.3 77.9 - - - +
3397C GLN* 1.3 62.5 + - - +
3399C PRO* 3.2 7.0 - - - +
3400C SER* 3.1 22.3 + - - -
3412C ALA* 4.6 9.0 - - + -
----------------------------------------------------------
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Residues in contact with GLN3397 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3393C GLU* 2.9 24.8 + - - +
3394C GLU* 2.7 42.7 + - - +
3395C GLU 3.6 0.2 - - - -
3396C ALA* 1.3 75.5 - - - +
3398C PRO* 1.3 75.5 - - + +
3400C SER* 3.1 10.1 + - - -
3401C TRP* 3.6 2.6 + - - +
3413C TYR* 2.8 39.8 + - + +
3449C LYS* 5.9 5.0 - - - +
3452C LYS* 5.2 4.9 + - - +
----------------------------------------------------------
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Residues in contact with PRO3398 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3394C GLU* 4.2 11.2 - - - +
3395C GLU 5.0 0.7 - - - +
3396C ALA 4.0 0.2 - - - -
3397C GLN* 1.3 96.1 - - + +
3399C PRO* 1.3 65.8 - - + +
3401C TRP* 2.8 27.3 + - + +
3402C SER* 2.9 16.0 + - - +
----------------------------------------------------------
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Residues in contact with PRO3399 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3315C TYR 5.4 0.4 - - - +
3316C LEU* 3.7 17.5 - - + -
3317C SER 4.3 0.9 - - - +
3318C LYS* 4.9 7.0 - - + -
3319C ASN* 3.3 35.7 + - + +
3395C GLU 4.1 7.6 - - - +
3396C ALA* 3.2 13.7 - - - +
3398C PRO* 1.3 98.3 - - + +
3400C SER* 1.3 59.0 + - - +
3402C SER* 3.4 12.3 - - - +
3403C CYS* 2.9 28.1 + - - +
----------------------------------------------------------
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Residues in contact with SER3400 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3319C ASN* 3.3 6.8 + - - +
3396C ALA 3.1 15.7 + - - -
3397C GLN 3.1 0.9 - - - -
3398C PRO 3.1 0.2 - - - -
3399C PRO* 1.3 77.0 - - - +
3401C TRP* 1.3 60.0 + - - +
3403C CYS 4.2 2.6 + - - -
3404C GLY 4.5 5.4 - - - +
3408C GLY 3.2 21.2 + - - -
3409C VAL* 3.1 30.0 + - - +
3412C ALA* 3.6 5.7 - - - +
3413C TYR* 3.0 43.9 + - - -
----------------------------------------------------------
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Residues in contact with TRP3401 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3397C GLN 3.6 2.5 + - - +
3398C PRO* 2.8 15.5 + - + +
3400C SER* 1.3 76.6 - - - +
3402C SER* 1.3 67.7 + - - +
3404C GLY 5.1 2.3 + - - +
3409C VAL* 3.8 3.7 - - + +
3452C LYS* 3.1 41.0 - - + +
----------------------------------------------------------
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Residues in contact with SER3402 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3316C LEU* 3.7 14.0 - - - +
3398C PRO* 2.9 17.3 + - - +
3399C PRO* 3.1 14.6 + - - +
3401C TRP* 1.3 85.5 - - - +
3403C CYS* 1.3 68.4 + - - +
3404C GLY* 3.6 1.5 - - - -
----------------------------------------------------------
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Residues in contact with CYS3403 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3316C LEU* 3.5 28.8 - - + +
3317C SER* 3.9 20.0 - - - +
3319C ASN* 4.5 9.0 - - - +
3320C ILE* 5.4 4.5 - - - -
3399C PRO 2.9 15.9 + - - +
3400C SER 4.2 0.8 + - - -
3401C TRP 3.7 0.6 - - - -
3402C SER* 1.3 79.5 - - - +
3404C GLY* 1.3 59.0 + - - +
3407C ALA* 3.8 19.1 - - + -
3408C GLY 4.7 0.4 - - - +
----------------------------------------------------------
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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