Contacts of the helix formed by residues 3317 - 3335 (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 SER3317 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3315C TYR* 3.4 15.7 - - - -
3316C LEU* 1.3 85.1 + - - +
3318C LYS* 1.3 54.6 + - - +
3319C ASN* 2.7 16.5 - - - +
3320C ILE* 2.4 45.5 + - - +
3321C LEU* 2.9 10.6 + - - +
3399C PRO* 4.3 0.6 - - - +
3403C CYS* 3.9 18.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS3318 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3309C GLU* 2.2 56.3 + - + +
3312C VAL* 3.3 9.9 - - - +
3314C SER* 2.9 39.5 + - - +
3315C TYR* 3.1 18.8 + - - +
3317C SER* 1.3 73.7 - - - +
3319C ASN* 1.3 62.2 + - - +
3322C ALA* 2.9 30.4 + - + +
3395C GLU* 3.5 31.0 - - + +
3399C PRO* 4.9 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN3319 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3316C LEU* 5.2 0.2 - - + -
3317C SER* 3.7 7.2 - - - -
3318C LYS* 1.3 74.9 - - - +
3320C ILE* 1.3 71.6 + - - +
3323C PHE* 2.8 32.3 + - - +
3396C ALA* 3.3 33.1 - - - +
3399C PRO* 3.3 36.7 + - + +
3400C SER* 3.3 12.6 + - - -
3403C CYS* 4.5 5.1 - - - +
3408C GLY* 3.1 35.1 - - - +
3411C ASP* 5.3 0.3 - - - +
3412C ALA* 4.3 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE3320 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3277C VAL* 4.9 7.4 - - + -
3315C TYR* 5.9 0.2 - - - +
3317C SER* 2.4 41.1 + - - +
3319C ASN* 1.3 90.9 - - - +
3321C LEU* 1.3 56.8 + - + +
3323C PHE* 3.0 24.1 - - + +
3324C ARG* 2.9 46.1 + - + +
3403C CYS* 5.4 4.7 - - - -
3407C ALA* 4.9 2.7 - - + +
3408C GLY* 4.7 1.3 - - - -
3411C ASP* 3.3 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3321 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3273C LEU* 3.6 21.8 - - + +
3277C VAL* 3.4 29.6 - - + -
3280C TYR* 3.4 12.8 - - + -
3308C ASP* 3.1 36.1 - - - +
3309C GLU* 3.0 29.8 - - + +
3312C VAL* 3.8 1.3 - - + -
3315C TYR* 3.3 29.6 - - + +
3317C SER 2.9 6.7 + - - +
3320C ILE* 1.3 74.8 - - + +
3322C ALA* 1.3 57.4 + - - +
3323C PHE 3.0 0.9 - - - -
3324C ARG* 2.4 27.4 + - + +
3325C ASP* 2.8 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3322 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3309C GLU* 4.5 3.3 + - + +
3318C LYS* 2.9 23.1 + - + +
3319C ASN 3.9 1.6 - - - +
3321C LEU* 1.3 71.3 - - - +
3323C PHE* 1.3 60.7 + - - +
3325C ASP* 2.9 14.5 - - - +
3326C GLN* 3.0 5.2 + - - +
3392C ALA* 2.9 47.5 - - + +
3395C GLU* 3.1 28.0 - - + +
3396C ALA* 3.9 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE3323 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3319C ASN* 2.8 24.7 + - - +
3320C ILE* 3.0 33.9 - - + +
3322C ALA* 1.3 71.8 - - - +
3324C ARG* 1.3 76.3 + - + -
3326C GLN* 2.5 42.5 + - - +
3327C ASN* 2.8 18.6 + - + -
3396C ALA* 4.5 2.3 - - + +
3411C ASP* 3.6 35.7 - - + -
3412C ALA* 4.4 2.7 - - - +
3415C THR* 3.6 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG3324 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3247C ARG* 2.9 41.8 - - - +
3277C VAL* 2.6 36.5 + - - +
3280C TYR* 3.2 36.8 - - + -
3281C CYS* 3.1 27.1 - - - +
3320C ILE* 2.9 38.6 + - - +
3321C LEU* 2.4 30.1 + - + +
3323C PHE* 1.3 79.2 - - - +
3325C ASP* 1.3 59.5 + - - +
3327C ASN* 3.0 14.9 + - - +
3328C ILE* 2.9 26.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP3325 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3304C VAL* 5.0 8.6 - - + +
3321C LEU 2.8 9.4 + - - +
3322C ALA* 2.9 13.7 - - - +
3324C ARG* 1.3 70.9 - - - +
3326C GLN* 1.3 63.8 + - - +
3328C ILE* 2.5 39.8 + - + +
3329C LEU* 2.9 33.3 + - - +
3359C ILE* 4.8 4.9 - - - +
3388C ALA* 2.6 31.9 - - - +
3389C VAL* 3.1 8.0 - - - -
3392C ALA* 3.0 11.0 - - + +
3395C GLU* 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN3326 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3322C ALA 3.2 12.6 - - - +
3323C PHE* 2.5 28.1 + - - +
3325C ASP* 1.3 73.8 - - - +
3327C ASN* 1.3 58.8 + - - +
3329C LEU 3.5 0.2 + - - -
3330C LEU* 2.9 24.1 + - - +
3389C VAL* 2.3 66.0 + - + +
3392C ALA* 3.8 2.3 - - - +
3393C GLU* 2.8 33.0 - - - +
3396C ALA* 5.2 0.5 - - - +
3412C ALA* 4.5 12.5 - - - +
3415C THR* 4.2 25.3 - - + +
3416C LEU* 5.5 1.7 - - - +
3419C PHE* 5.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN3327 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3280C TYR* 3.4 31.1 + - - +
3281C CYS* 4.2 3.6 - - - +
3283C LEU* 5.5 0.6 - - - +
3284C SER* 2.6 17.1 + - - -
3287C ARG* 2.2 62.8 + - - +
3323C PHE* 2.8 17.5 + - + +
3324C ARG* 3.0 25.9 + - - +
3326C GLN* 1.3 74.2 - - - +
3328C ILE* 1.3 57.9 + - - +
3330C LEU* 2.9 15.5 - - - +
3415C THR* 5.5 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE3328 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3280C TYR* 5.2 16.2 - - + -
3283C LEU* 6.0 6.7 - - + -
3287C ARG* 3.6 4.7 - - - +
3297C VAL 5.2 0.4 - - - +
3300C VAL* 6.4 2.2 - - + -
3301C LEU* 3.5 37.2 - - + -
3303C THR 5.0 4.3 - - - +
3304C VAL* 4.1 28.9 - - + +
3324C ARG* 2.9 21.4 + - + +
3325C ASP* 2.5 26.7 + - - +
3327C ASN* 1.3 74.4 - - + +
3329C LEU* 1.3 61.1 + - + +
3331C GLY* 2.2 31.9 + - - -
3332C THR* 2.8 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3329 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3301C LEU* 5.5 4.0 - - + -
3304C VAL* 6.3 1.1 - - + -
3325C ASP* 2.9 26.8 + - - +
3328C ILE* 1.3 80.3 - - + +
3330C LEU* 1.3 50.6 + - - +
3331C GLY 3.2 0.2 - - - -
3332C THR* 4.2 5.6 - - + +
3333C THR* 2.0 44.6 + - - -
3359C ILE* 5.4 6.3 - - + +
3384C HIS* 4.6 2.2 - - + +
3385C LEU* 3.0 52.7 - - + +
3388C ALA* 3.3 13.0 - - + -
3389C VAL* 3.1 35.4 - - + +
3419C PHE* 4.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3330 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3287C ARG* 3.1 26.9 - - - +
3326C GLN 2.9 15.5 + - - +
3327C ASN* 2.9 13.9 - - - +
3329C LEU* 1.3 75.7 - - - +
3331C GLY* 1.3 54.8 + - - -
3333C THR* 3.6 4.1 - - + -
3334C TYR* 2.9 43.8 + - + +
3389C VAL* 4.7 1.4 - - - +
3419C PHE* 4.9 17.0 - - + -
3422C GLN* 5.9 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY3331 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3283C LEU* 5.0 4.3 - - - -
3287C ARG* 2.8 33.7 - - - +
3297C VAL* 4.8 4.9 - - - -
3328C ILE 2.2 18.7 + - - -
3330C LEU* 1.3 65.6 - - - +
3332C THR* 1.3 57.7 + - - +
3334C TYR* 2.7 24.3 + - - +
3335C ARG* 3.1 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR3332 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3297C VAL* 3.2 24.5 - - + +
3301C LEU* 3.1 29.9 - - + +
3328C ILE* 2.8 19.7 + - - +
3329C LEU* 4.3 3.6 - - + -
3331C GLY* 1.3 69.7 - - - -
3333C THR* 1.3 64.3 + - - +
3336C ILE* 4.2 3.1 - - - +
3341C LEU* 3.1 27.6 - - + +
3352C GLU* 4.7 10.1 - - + +
3377C LEU* 5.7 7.6 - - + -
3381C ALA* 6.1 1.4 - - + +
3385C LEU* 3.6 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR3333 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3329C LEU 2.0 28.4 + - - -
3330C LEU* 3.6 6.3 - - + -
3332C THR* 1.3 79.7 - - - +
3334C TYR* 1.3 69.0 + - - +
3335C ARG 2.9 2.1 + - - -
3336C ILE* 3.0 22.7 + - - +
3382C PHE* 4.0 19.2 - - + -
3385C LEU* 3.0 38.1 - - + +
3419C PHE* 4.1 5.4 - - + -
3423C GLN* 4.6 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR3334 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3287C ARG* 5.4 15.3 - - + -
3330C LEU* 2.9 27.7 + - + +
3331C GLY* 2.7 13.7 + - - +
3333C THR* 1.3 72.6 - - - +
3335C ARG* 1.3 60.8 + - - +
3336C ILE 2.7 32.3 + - - +
3337C ILE* 3.1 44.9 + - + +
3422C GLN* 5.5 9.9 - - - -
3992C ARG* 5.2 19.0 + - - +
3995C PRO* 5.5 10.1 - - + +
4053C GLY* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG3335 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3286C CYS 4.9 3.2 + - - -
3287C ARG* 4.9 8.1 + - - +
3289C ARG 4.1 8.5 + - - -
3290C SER* 2.7 40.6 + - - +
3291C GLN 4.2 1.2 + - - -
3292C GLY 3.4 16.0 + - - -
3293C CYS* 2.5 35.7 + - - +
3297C VAL* 5.9 1.8 - - + -
3331C GLY 3.1 9.2 + - - +
3332C THR* 5.5 0.2 - - - -
3333C THR 2.9 1.2 + - - -
3334C TYR* 1.3 83.6 - - - +
3336C ILE* 1.3 59.4 + - - +
3337C ILE* 3.5 4.8 + - - +
3338C ALA* 4.1 2.8 - - - +
3340C ALA* 3.3 32.6 + - + +
3341C LEU* 3.5 33.7 - - + +
3992C ARG* 4.7 4.6 - - - +
4098C LEU* 5.2 4.9 - - - +
----------------------------------------------------------
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