Contacts of the helix formed by residues 3408 - 3430 (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 GLY3408 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3319C ASN* 3.1 27.7 - - - +
3400C SER* 3.2 18.4 + - - -
3403C CYS* 4.7 0.6 - - - +
3407C ALA* 1.3 79.4 - - - +
3409C VAL* 1.3 66.3 + - - +
3410C ILE 3.4 1.8 - - - -
3411C ASP* 3.2 9.1 - - - +
3412C ALA* 2.9 23.6 + - - +
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Residues in contact with VAL3409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3400C SER* 3.1 31.2 + - - +
3401C TRP* 3.8 3.4 - - + +
3404C GLY 5.1 0.7 - - - +
3406C ALA* 4.1 26.0 - - - +
3407C ALA 4.6 0.4 - - - +
3408C GLY* 1.3 71.3 - - - +
3410C ILE* 1.3 72.2 + - + +
3413C TYR* 2.8 46.3 + - + +
3452C LYS* 3.5 52.0 - - + +
3453C ALA* 5.5 1.8 - - - +
3455C LYS* 6.3 0.4 - - + -
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Residues in contact with ILE3410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3406C ALA* 3.1 34.8 - - + +
3407C ALA 3.6 2.9 - - - +
3409C VAL* 1.3 77.1 - - + +
3411C ASP* 1.3 84.9 + - - +
3413C TYR* 4.9 0.7 - - - -
3414C MET* 2.9 60.2 + - + +
3453C ALA* 5.8 8.4 - - + +
3456C LEU* 3.6 32.1 - - + -
3458C SER* 4.1 6.1 - - - +
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Residues in contact with ASP3411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3319C ASN* 5.3 1.6 - - - +
3320C ILE* 3.3 25.0 - - + +
3323C PHE* 3.6 27.0 - - + -
3407C ALA 2.6 28.8 - - - +
3408C GLY* 3.2 7.3 - - - +
3409C VAL 3.1 0.8 - - - -
3410C ILE* 1.3 90.0 - - - +
3412C ALA* 1.3 56.7 + - - +
3415C THR* 2.0 38.1 + - - -
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Residues in contact with ALA3412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3319C ASN* 4.3 7.9 - - - +
3323C PHE* 4.4 4.2 - - + -
3326C GLN* 4.5 12.4 - - - +
3393C GLU* 5.0 9.1 - - + +
3396C ALA* 4.6 12.3 - - + +
3400C SER* 3.6 22.9 - - - +
3408C GLY 2.9 4.8 + - - +
3411C ASP* 1.3 78.6 - - - +
3413C TYR* 1.3 70.3 + - + +
3415C THR* 3.1 5.5 - - - +
3416C LEU* 2.9 29.8 + - - +
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Residues in contact with TYR3413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3393C GLU* 4.3 13.5 - - + -
3397C GLN* 2.8 49.1 + - + +
3400C SER* 3.0 14.0 - - - -
3409C VAL* 2.8 39.1 + - + +
3410C ILE* 4.9 0.4 - - - -
3412C ALA* 1.3 85.1 - - + +
3414C MET* 1.3 66.5 + - - +
3415C THR 2.9 0.8 + - - -
3416C LEU* 3.3 0.9 + - - -
3417C ALA* 2.9 25.4 + - - +
3446C VAL* 3.9 8.2 - - - +
3449C LYS* 3.4 52.0 - - + +
3452C LYS* 3.4 30.9 - - + -
3453C ALA* 5.9 1.3 - - + -
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Residues in contact with MET3414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3410C ILE* 2.9 44.7 + - + +
3413C TYR* 1.3 73.7 - - - +
3415C THR* 1.3 54.2 + - - +
3417C ALA* 3.1 7.4 - - - +
3418C ASP* 2.7 46.3 + - - +
3450C MET* 6.4 1.1 - - + -
3453C ALA* 5.8 6.3 - - + -
3458C SER* 2.7 48.7 - - - +
3460C GLU* 4.0 24.0 - - + +
3461C ALA* 5.7 2.0 - - + -
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Residues in contact with THR3415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3323C PHE* 3.6 16.8 - - + -
3326C GLN* 4.2 33.0 - - + +
3327C ASN 5.5 0.7 - - - +
3389C VAL* 5.5 1.6 - - + -
3411C ASP* 2.0 33.9 + - - -
3412C ALA* 3.1 7.4 - - - +
3413C TYR 2.9 0.2 - - - -
3414C MET* 1.3 75.8 - - - +
3416C LEU* 1.3 62.4 + - - +
3418C ASP* 2.7 29.5 + - - +
3419C PHE* 2.9 12.1 + - + +
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Residues in contact with LEU3416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3326C GLN* 5.5 0.7 - - - +
3389C VAL* 3.6 20.6 - - + -
3390C GLN* 3.6 39.9 - - + +
3393C GLU* 4.0 20.9 - - + -
3412C ALA 2.9 14.6 + - - +
3415C THR* 1.3 80.9 - - + +
3417C ALA* 1.3 63.4 + - - +
3419C PHE* 3.4 35.0 - - + -
3420C CYS* 2.9 39.3 + - - -
3442C TYR* 5.8 4.7 - - + -
3445C LEU* 5.8 4.5 - - + -
3446C VAL* 4.0 12.3 - - + -
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Residues in contact with ALA3417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3413C TYR 2.9 14.6 + - - +
3414C MET* 3.1 15.3 - - - +
3416C LEU* 1.3 78.0 - - - +
3418C ASP* 1.3 65.0 + - - +
3420C CYS* 3.0 3.8 + - - +
3421C ASP* 2.9 22.5 + - - +
3446C VAL* 3.4 32.7 - - + +
3460C GLU* 3.8 19.5 - - - +
3464C LYS* 5.3 3.7 - - + -
3465C PHE* 6.0 2.0 - - + -
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Residues in contact with ASP3418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3414C MET* 2.7 34.8 + - - +
3415C THR* 2.7 13.8 + - - +
3417C ALA* 1.3 70.0 - - - +
3419C PHE* 1.3 64.6 + - - +
3421C ASP* 3.8 5.3 - - - +
3422C GLN* 2.9 37.0 + - + +
3460C GLU* 3.4 29.6 - - - +
3994C ASP* 4.5 16.6 - - - +
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Residues in contact with PHE3419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3326C GLN 5.4 0.7 - - - -
3329C LEU 4.6 2.9 - - - -
3330C LEU* 4.9 17.7 - - + -
3333C THR* 4.1 18.4 - - + -
3385C LEU* 3.8 3.4 - - + -
3386C SER* 3.3 42.4 - - - -
3389C VAL* 4.0 21.3 - - + -
3415C THR* 2.9 12.1 + - + +
3416C LEU* 3.3 35.4 - - + +
3418C ASP* 1.3 77.7 - - - +
3420C CYS* 1.3 68.5 + - - +
3422C GLN* 3.5 6.6 - - - +
3423C GLN* 3.0 64.3 + - + +
3442C TYR* 6.5 2.2 - + - -
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Residues in contact with CYS3420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3416C LEU* 2.9 37.4 + - - -
3417C ALA* 3.0 8.5 + - - +
3419C PHE* 1.3 75.3 - - - +
3421C ASP* 1.3 55.6 + - - +
3423C GLN* 2.3 42.5 + - - +
3424C LEU 2.7 8.8 + - - -
3439C LEU* 4.4 13.7 - - + -
3442C TYR* 3.9 34.8 - - - -
3443C PRO* 5.0 13.0 - - + -
3446C VAL* 5.1 5.2 - - + -
3464C LYS* 6.0 2.5 - - - -
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Residues in contact with ASP3421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3417C ALA 2.9 13.6 + - - +
3418C ASP* 3.9 5.8 - - - +
3420C CYS* 1.3 75.6 - - - +
3422C GLN* 1.3 72.5 + - - +
3424C LEU* 3.0 17.3 - - + +
3425C ARG* 2.7 66.7 + - - +
3439C LEU* 5.3 0.2 - - - -
3460C GLU* 5.2 4.5 - - + +
3464C LYS* 4.7 21.1 - - + +
3467C ARG* 4.3 3.8 + - - -
3996C GLY* 4.9 2.9 - - - -
3999C THR* 4.5 3.1 - - - +
4000C ASN* 3.7 12.9 + - - +
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Residues in contact with GLN3422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3330C LEU* 5.9 7.2 - - + -
3334C TYR* 5.5 8.1 - - - -
3418C ASP* 2.9 28.6 + - + +
3419C PHE* 3.5 7.0 - - - +
3420C CYS 2.7 3.0 + - - -
3421C ASP* 1.3 84.3 - - - +
3423C GLN* 1.3 59.5 + - + +
3425C ARG* 2.8 29.0 + - - +
3426C LYS* 3.0 10.3 + - - +
3995C PRO* 3.1 35.3 - - + +
3996C GLY* 3.8 17.2 - - - -
3999C THR* 4.7 5.8 + - - +
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Residues in contact with GLN3423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3333C THR* 4.6 14.4 - - + +
3382C PHE* 4.6 16.7 + - + +
3385C LEU* 5.4 0.2 - - - +
3386C SER* 4.8 1.4 - - - -
3419C PHE* 3.0 64.0 - - - +
3420C CYS* 2.3 24.0 + - - +
3422C GLN* 1.3 71.1 - - + +
3424C LEU* 1.3 61.6 + - - +
3426C LYS* 3.1 25.3 - - + +
3427C GLU* 2.9 22.7 + - + +
3439C LEU* 4.1 8.7 - - + -
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Residues in contact with LEU3424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3420C CYS 2.7 9.7 + - - -
3421C ASP* 3.0 21.8 - - - +
3423C GLN* 1.3 69.9 - - - +
3425C ARG* 1.3 74.7 + - - +
3427C GLU* 2.4 29.5 + - + +
3428C GLU* 2.7 29.3 + - + +
3439C LEU* 3.4 36.5 - - + +
3440C GLN* 6.0 1.8 - - + +
3464C LYS* 6.4 0.7 - - - -
3467C ARG* 6.0 1.3 - - - +
3468C LEU* 5.6 10.5 - - + -
3471C ILE* 6.5 1.1 - - + -
3472C ILE* 5.9 7.4 - - + -
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Residues in contact with ARG3425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3421C ASP* 2.7 46.0 + - - +
3422C GLN* 2.8 17.5 + - - +
3424C LEU* 1.3 81.6 - - - +
3426C LYS* 1.3 65.5 + - - +
3428C GLU* 2.2 47.8 + - - -
3429C GLU* 3.0 18.2 + - - +
3467C ARG* 3.0 6.7 - - - +
3999C THR* 3.2 25.0 - - + +
4000C ASN* 2.9 23.4 + - - -
4003C ASP* 2.2 33.9 + - - +
4049C ARG* 3.0 38.9 + - - +
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Residues in contact with LYS3426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3382C PHE* 3.6 39.9 - - + -
3422C GLN 3.0 6.8 + - - +
3423C GLN* 3.1 32.3 - - + +
3425C ARG* 1.3 74.5 - - - +
3427C GLU* 1.3 81.0 + - - +
3429C GLU* 2.6 20.3 + - - +
3430C ASN* 2.6 56.4 + - - +
3432C SER* 4.5 0.2 + - - -
3435C ASP* 2.4 24.4 + - - -
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Residues in contact with GLU3427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3423C GLN* 2.9 11.8 + - + +
3424C LEU* 2.4 20.8 + - + +
3426C LYS* 1.3 104.9 + - - +
3428C GLU* 1.3 59.2 + - - +
3430C ASN* 2.7 42.6 + - - +
3431C ALA* 4.9 0.2 - - - -
3432C SER* 2.9 23.2 + - - +
3435C ASP* 2.9 27.1 - - + +
3436C SER* 5.3 3.4 - - - +
3439C LEU* 3.5 24.2 - - + -
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Residues in contact with GLU3428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3424C LEU* 2.7 35.5 + - + +
3425C ARG* 2.2 47.5 + - - +
3427C GLU* 1.3 74.9 - - - +
3429C GLU* 1.3 62.3 + - - +
4003C ASP* 4.9 2.3 - - - +
4045C CYS* 4.7 0.5 - - - -
4046C TYR* 3.0 21.5 + - - +
4049C ARG* 2.2 41.7 + - - +
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Residues in contact with GLU3429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3425C ARG 3.0 13.1 + - - +
3426C LYS* 2.6 17.4 + - - +
3428C GLU* 1.3 75.1 - - - +
3430C ASN* 1.3 61.2 + - + +
4046C TYR* 3.9 23.2 - - + +
4049C ARG* 3.7 30.3 - - - +
4050C LYS* 5.4 8.6 + - - +
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Residues in contact with ASN3430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3382C PHE* 5.7 0.8 - - - -
3426C LYS* 2.6 63.4 + - - +
3427C GLU* 2.7 50.5 + - - +
3429C GLU* 1.3 77.9 - - + +
3431C ALA* 1.3 55.6 + - - +
3432C SER* 4.4 7.0 + - - -
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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