Contacts of the helix formed by residues 3268 - 3289 (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 THR3268 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3232C ARG* 3.1 28.9 - - - +
3236C PHE* 5.9 2.3 - - - -
3266C SER* 2.8 8.3 + - - +
3267C LYS* 1.3 81.5 - - - +
3269C ARG* 1.3 66.5 + - - +
3270C ASP* 3.4 6.0 + - - +
3271C ASP* 2.6 39.5 + - - +
3272C TRP* 3.9 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG3269 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3268C THR* 1.3 75.5 - - - +
3270C ASP* 1.3 84.8 + - - +
3272C TRP* 4.1 5.4 + - - +
3273C LEU* 4.0 13.7 + - - +
3311C ASN* 3.1 46.4 + - - +
3312C VAL* 3.3 4.2 - - - +
3313C SER* 3.1 41.7 + - - +
3315C TYR* 4.2 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP3270 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3236C PHE* 5.7 7.6 - - + -
3268C THR* 3.2 5.9 + - - +
3269C ARG* 1.3 108.1 + - - +
3271C ASP* 1.3 65.8 + - - +
3272C TRP 3.2 2.0 - - - -
3273C LEU* 3.1 33.1 - - + +
3274C VAL* 2.9 33.3 + - + +
3315C TYR* 4.4 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP3271 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3240C MET* 6.1 0.9 - - - -
3262C LEU* 2.6 48.4 - - - +
3263C HIS* 3.3 11.7 - - - -
3266C SER* 3.3 8.3 - - - -
3267C LYS* 3.0 18.5 + - - +
3268C THR* 2.6 39.7 + - - +
3270C ASP* 1.3 72.4 - - - +
3272C TRP* 1.3 90.7 + - - +
3274C VAL* 5.3 0.4 - - - -
3275C SER* 2.8 22.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP3272 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3263C HIS* 3.3 24.9 + + + +
3267C LYS* 5.2 5.0 - - + +
3268C THR 3.9 7.7 + - - -
3269C ARG* 4.3 5.2 - - - +
3270C ASP 3.2 0.2 - - - -
3271C ASP* 1.3 105.1 + - + +
3273C LEU* 1.3 54.2 + - - +
3275C SER* 2.2 36.4 + - - -
3276C TRP* 2.7 31.6 + + - +
3307C LEU* 4.0 20.0 - - + -
3311C ASN* 3.8 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3273 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3269C ARG 4.0 1.1 - - - +
3270C ASP* 3.1 38.0 + - + +
3272C TRP* 1.3 75.5 - - - +
3274C VAL* 1.3 58.7 + - + +
3276C TRP* 3.2 9.0 - - + +
3277C VAL* 2.9 34.6 + - - +
3308C ASP* 3.1 35.0 - - - +
3311C ASN* 3.2 27.8 - - + +
3312C VAL* 3.6 4.7 - - + -
3315C TYR* 3.4 32.8 - - + +
3321C LEU* 3.6 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL3274 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3236C PHE* 4.9 4.5 - - + -
3240C MET* 3.6 22.9 - - + -
3243C ILE* 3.4 42.6 - - + -
3244C ASP* 5.0 2.5 - - - +
3262C LEU* 4.0 3.4 - - + -
3270C ASP* 2.9 23.5 + - + +
3271C ASP 3.9 3.4 - - - +
3272C TRP 2.6 3.0 + - - -
3273C LEU* 1.3 72.1 - - + +
3275C SER* 1.3 65.4 + - - +
3277C VAL* 2.9 14.8 - - + +
3278C GLN* 2.9 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER3275 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3259C LEU* 3.3 14.7 + - - +
3262C LEU* 3.1 20.3 - - - +
3263C HIS* 3.1 43.7 + - - -
3271C ASP 2.8 18.0 + - - -
3272C TRP 2.2 21.6 + - - -
3274C VAL* 1.3 69.5 - - - +
3276C TRP* 1.3 49.8 + - - -
3278C GLN* 4.7 0.4 - - - -
3279C SER* 2.8 40.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP3276 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3263C HIS* 6.4 1.1 - + - -
3272C TRP* 2.7 54.6 + + + +
3273C LEU* 3.2 17.3 - - + +
3275C SER* 1.3 68.0 - - - +
3277C VAL* 1.3 69.6 + - - +
3279C SER* 2.8 19.3 + - - -
3280C TYR* 2.8 62.9 + + + +
3303C THR* 3.1 44.4 - - + -
3307C LEU* 3.1 48.9 - - + -
3308C ASP* 3.7 3.8 - - - +
3311C ASN* 3.4 10.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL3277 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3244C ASP* 5.1 1.1 - - - +
3247C ARG* 3.2 14.6 - - - +
3273C LEU 2.9 22.2 + - - +
3274C VAL* 2.9 37.0 - - + +
3276C TRP* 1.3 71.9 - - - +
3278C GLN* 1.3 62.5 + - - +
3280C TYR* 3.1 10.4 + - - +
3281C CYS 3.0 4.7 + - - -
3315C TYR* 5.1 3.4 - - - +
3320C ILE* 4.9 7.9 - - + -
3321C LEU* 3.4 28.7 - - + -
3324C ARG* 2.6 44.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN3278 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3243C ILE* 2.5 47.6 + - + +
3246C ALA* 4.9 3.8 - - + -
3247C ARG* 3.1 51.0 + - - +
3255C ALA* 5.5 1.8 - - + -
3259C LEU* 3.7 29.6 - - + -
3274C VAL 2.9 15.9 + - - +
3275C SER* 3.7 2.9 - - - +
3276C TRP 2.9 0.6 + - - -
3277C VAL* 1.3 78.3 - - - +
3279C SER* 1.3 64.1 + - - +
3281C CYS* 2.9 9.0 + - - +
3282C ARG* 2.7 32.8 + - + +
3285C HIS* 4.1 1.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER3279 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3256C MET* 4.8 1.6 - - - +
3259C LEU* 3.1 13.3 - - - +
3263C HIS* 5.8 0.7 + - - -
3275C SER* 2.8 18.0 + - - -
3276C TRP* 2.8 16.4 + - - -
3278C GLN* 1.3 71.3 - - - +
3280C TYR* 1.3 68.5 + - - +
3282C ARG* 3.0 24.9 + - - +
3283C LEU* 2.9 21.5 + - - +
3300C VAL* 4.2 23.2 - - - +
3303C THR* 6.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR3280 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3276C TRP* 2.8 54.3 + + + +
3277C VAL* 3.1 19.5 - - - +
3279C SER* 1.3 83.0 - - - +
3281C CYS* 1.3 63.9 + - - +
3283C LEU* 3.1 19.5 + - - +
3284C SER 3.4 0.5 + - - -
3300C VAL* 5.1 8.1 - - + -
3303C THR* 4.3 16.2 - - - -
3304C VAL 4.6 2.8 + - - -
3308C ASP* 2.2 33.8 + - - +
3321C LEU* 3.4 22.9 - - + -
3324C ARG* 3.2 34.5 - - + +
3327C ASN* 3.4 17.6 + - - +
3328C ILE* 5.2 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS3281 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3247C ARG* 3.3 24.9 - - - +
3250C ASN* 4.4 0.2 - - - -
3277C VAL 3.0 2.2 + - - -
3278C GLN* 2.9 16.0 + - - +
3280C TYR* 1.3 78.8 - - - +
3282C ARG* 1.3 55.4 + - - +
3284C SER* 2.7 26.9 + - - +
3285C HIS* 2.6 49.3 + - - -
3324C ARG* 3.1 18.5 - - - +
3327C ASN* 4.4 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG3282 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3251C ASN 5.8 0.2 - - - +
3252C PHE* 3.9 15.4 + - + +
3255C ALA* 4.6 10.7 - - + +
3256C MET* 2.6 58.2 - - - +
3259C LEU* 3.2 26.0 - - - +
3278C GLN* 2.7 30.7 + - + +
3279C SER* 3.0 31.2 + - - +
3281C CYS* 1.3 69.4 - - - +
3283C LEU* 1.3 68.9 + - - +
3285C HIS* 3.1 21.8 + - + +
3286C CYS* 3.0 19.9 + - - -
3296C GLN* 5.7 0.2 - - - -
3300C VAL* 5.9 4.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3283 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3279C SER 2.9 7.7 + - - -
3280C TYR 3.3 10.8 - - - +
3282C ARG* 1.3 73.2 - - - +
3284C SER* 1.3 56.5 + - - +
3285C HIS 2.5 0.9 + - - -
3286C CYS* 2.0 34.8 + - - -
3287C ARG* 2.7 47.6 + - + +
3296C GLN* 3.1 54.6 - - + +
3297C VAL* 3.5 14.6 - - - +
3300C VAL* 3.5 21.4 - - + +
3301C LEU* 4.9 0.7 - - + +
3327C ASN* 5.5 0.2 - - - +
3328C ILE* 6.1 7.0 - - + -
3331C GLY* 5.0 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER3284 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3280C TYR 3.4 0.6 + - - -
3281C CYS* 2.7 19.5 + - - -
3283C LEU* 1.3 72.5 - - - +
3285C HIS* 1.3 53.3 + - - +
3286C CYS 3.3 0.2 - - - -
3287C ARG* 3.0 31.2 + - - +
3288C SER* 2.7 31.9 + - - -
3327C ASN* 2.6 35.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS3285 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3246C ALA 4.0 1.6 - - - -
3247C ARG* 3.8 14.4 - - - -
3250C ASN* 2.5 58.8 + - + +
3251C ASN 4.1 3.2 + - - -
3252C PHE* 3.1 29.0 - - + -
3278C GLN* 4.1 5.6 - - - -
3281C CYS* 2.6 44.1 + - - -
3282C ARG* 3.1 21.7 - - + +
3283C LEU 2.5 4.0 + - - -
3284C SER* 1.3 76.7 - - - +
3286C CYS* 1.3 55.4 + - - -
3288C SER* 3.0 25.2 - - - -
3289C ARG* 4.1 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS3286 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3252C PHE* 3.6 28.7 - - - -
3282C ARG 3.0 13.0 + - - -
3283C LEU 2.0 24.3 + - - +
3285C HIS* 1.3 64.5 - - - +
3287C ARG* 1.3 59.8 + - - +
3288C SER 2.9 6.0 + - - -
3289C ARG* 3.0 38.6 + - - +
3291C GLN 3.8 7.5 - - - +
3292C GLY* 5.9 0.7 - - - -
3296C GLN* 3.6 44.6 - - + -
3335C ARG* 4.9 1.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG3287 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3283C LEU* 2.7 25.5 + - + +
3284C SER* 3.0 28.2 + - - +
3286C CYS* 1.3 70.6 - - - +
3288C SER* 1.3 65.2 + - - +
3289C ARG 3.1 7.0 - - - +
3296C GLN* 5.5 0.2 - - - +
3327C ASN* 2.2 60.1 + - - +
3328C ILE* 3.3 5.9 + - - +
3330C LEU* 3.1 26.2 - - - +
3331C GLY* 2.8 31.7 - - - +
3334C TYR* 5.4 16.9 - - + -
3335C ARG* 4.9 8.8 + - - +
3992C ARG* 4.6 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER3288 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3250C ASN* 5.3 4.5 + - - +
3284C SER 2.7 21.5 + - - -
3285C HIS* 3.0 23.9 + - - -
3286C CYS 2.9 0.2 - - - -
3287C ARG* 1.3 80.4 - - - +
3289C ARG* 1.3 60.7 + - - -
3989C ARG* 6.0 4.9 - - - -
3992C ARG* 3.1 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG3289 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2958C LEU* 4.8 25.5 - - + +
2964C ASP* 5.9 1.4 + - - -
3252C PHE* 3.6 34.6 - - + -
3285C HIS 4.5 2.5 - - - +
3286C CYS* 3.0 33.6 + - - +
3287C ARG* 3.1 8.3 - - - +
3288C SER* 1.3 81.5 - - - +
3290C SER* 1.3 60.7 + - - +
3291C GLN* 3.3 56.3 + - + +
3292C GLY* 5.2 2.8 - - - +
3335C ARG* 4.1 4.7 + - - -
3989C ARG* 6.3 0.9 - - - +
3992C ARG* 3.4 8.2 + - - +
4100C GLU* 4.9 3.6 - - - +
----------------------------------------------------------
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