Contacts of the helix formed by residues 3975 - 3992 (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 LYS3975 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2901C LEU* 5.9 1.8 - - - +
2904C GLU* 2.7 24.0 + - - +
2905C LEU 6.2 0.2 - - - -
2936C TYR* 5.2 1.1 - - + -
2937C ASP* 2.6 49.5 + - - +
2938C VAL* 3.2 9.9 - - - +
2940C ARG* 3.1 37.3 - - + +
2941C GLY* 2.9 26.9 - - - +
3968C ILE* 4.1 2.4 - - - +
3973C PRO 5.3 0.2 - - - -
3974C MET* 1.3 83.4 + - - -
3976C GLU* 1.3 54.3 + - - +
3977C THR* 2.7 23.3 + - - +
3978C GLY* 2.9 19.2 + - - +
3979C LEU* 3.0 10.8 + - + +
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Residues in contact with GLU3976 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3901C ARG* 3.8 5.9 + - - -
3968C ILE* 3.7 12.8 - - + -
3971C MET* 2.8 48.8 - - + +
3972C LEU* 3.0 15.7 - - - +
3974C MET* 2.8 29.9 - - + +
3975C LYS* 1.3 73.1 - - - +
3977C THR* 1.3 67.9 + - - +
3979C LEU* 3.0 30.6 - - - +
3980C MET* 2.8 31.8 + - + +
3981C TYR 3.5 0.9 + - - -
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Residues in contact with THR3977 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2904C GLU* 5.1 0.2 + - - -
2940C ARG* 4.2 21.3 + - - +
3968C ILE* 4.6 5.8 - - - +
3975C LYS* 2.7 19.8 + - - +
3976C GLU* 1.3 76.7 - - - +
3978C GLY* 1.3 52.5 + - - +
3981C TYR* 2.4 36.8 + - + +
4108C MET* 5.5 9.8 - - + +
4109C ASP* 4.6 18.0 + - - +
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Residues in contact with GLY3978 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2932C SER 6.0 1.1 - - - -
2940C ARG* 4.9 3.2 - - - +
3975C LYS* 2.9 8.3 + - - -
3977C THR* 1.3 82.6 - - - +
3979C LEU* 1.3 61.1 + - - -
3980C MET 3.1 0.5 - - - -
3981C TYR* 2.3 39.1 + - - +
3982C SER* 3.2 8.7 + - - -
3983C ILE* 4.6 0.3 - - - +
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Residues in contact with LEU3979 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2929C LEU* 4.1 11.4 - - + +
2932C SER* 4.8 3.1 + - - +
2933C ILE* 3.5 52.9 - - + +
2937C ASP* 3.6 18.8 - - - +
3972C LEU* 4.6 4.0 - - + -
3974C MET* 3.4 20.4 - - + -
3975C LYS* 3.0 13.9 + - + +
3976C GLU* 2.9 43.1 + - - +
3978C GLY* 1.3 77.7 - - - +
3980C MET* 1.3 56.9 + - - +
3983C ILE* 2.9 20.0 - - - +
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Residues in contact with MET3980 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3905C ALA* 3.6 25.4 - - + +
3908C HIS* 3.8 24.7 - - + -
3909C ALA* 3.4 34.5 - - + -
3963C LEU* 5.1 2.2 - - + -
3971C MET* 4.9 11.9 - - - +
3976C GLU* 2.8 20.4 + - + +
3978C GLY 3.1 0.9 - - - -
3979C LEU* 1.3 75.3 - - - +
3981C TYR* 1.3 69.2 + - - +
3982C SER 3.5 0.7 - - - -
3983C ILE* 3.0 14.3 - - + +
3984C MET* 2.9 39.7 + - + +
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Residues in contact with TYR3981 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2957C LEU* 5.4 6.3 - - + -
3977C THR* 2.4 36.0 + - + +
3978C GLY* 2.3 27.8 + - - +
3980C MET* 1.3 66.3 - - - +
3982C SER* 1.3 79.8 + - - +
3984C MET* 2.5 42.1 + - - +
3985C VAL* 3.0 13.7 + - + -
4101C GLU* 2.8 31.7 + - + +
4104C VAL* 3.3 23.1 - - + +
4105C LYS* 3.0 47.9 - - + -
4108C MET* 4.4 7.9 - - + -
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Residues in contact with SER3982 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2932C SER* 4.6 10.7 - - - -
2935C GLU* 4.7 1.2 + - - -
2957C LEU* 3.3 35.0 - - - +
3978C GLY* 3.2 6.3 + - - -
3981C TYR* 1.3 96.4 - - - +
3983C ILE* 1.3 52.4 + - - +
3985C VAL* 2.7 30.0 + - - +
3986C HIS* 2.5 34.6 + - - -
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Residues in contact with ILE3983 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2929C LEU* 3.5 33.4 - - + -
2932C SER* 4.7 6.5 - - - +
3784C ARG* 5.2 8.7 - - - -
3786C LEU* 5.8 8.5 - - + -
3906C SER* 5.7 4.3 - - - -
3909C ALA* 3.9 24.0 - - + -
3913C ILE* 6.0 0.7 - - + -
3978C GLY 4.6 0.2 - - - +
3979C LEU 2.9 31.2 - - - +
3980C MET* 3.0 14.8 - - + +
3981C TYR 2.8 0.2 + - - -
3982C SER* 1.3 77.8 - - - +
3984C MET* 1.3 63.2 + - - +
3986C HIS* 2.7 34.5 + - + +
3987C ALA* 3.0 9.2 + - - +
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Residues in contact with MET3984 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3908C HIS* 5.5 0.2 - - + -
3909C ALA* 3.4 31.4 - - - +
3912C CYS* 4.6 11.9 - - + -
3913C ILE* 3.5 26.5 - - + -
3980C MET* 2.9 38.7 + - + +
3981C TYR* 2.5 19.7 + - - +
3983C ILE* 1.3 72.8 - - - +
3985C VAL* 1.3 64.0 + - - +
3987C ALA* 2.8 23.7 - - - +
3988C LEU* 3.0 12.5 + - + +
4104C VAL* 3.5 20.4 - - + -
4108C MET* 4.2 19.7 - - + +
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Residues in contact with VAL3985 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2957C LEU* 6.1 7.0 - - + -
3981C TYR* 3.0 25.1 + - + +
3982C SER* 2.7 31.8 + - - +
3984C MET* 1.3 75.5 - - - +
3986C HIS* 1.3 56.0 + - + +
3988C LEU* 2.1 38.0 + - + +
3989C ARG* 2.8 39.0 + - + +
4101C GLU* 4.3 17.0 - - + +
4104C VAL* 4.2 16.4 - - + +
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Residues in contact with HIS3986 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2928C LYS* 4.9 3.8 + - + -
2929C LEU* 6.0 0.2 - - - -
2932C SER* 5.5 5.3 - - - -
2957C LEU* 5.3 11.9 + - - +
3778C ASP* 5.8 2.0 - - - +
3780C ALA* 5.8 1.3 - - + -
3781C CYS* 5.1 7.8 - - - -
3784C ARG* 2.7 58.3 + - - +
3786C LEU* 5.5 5.8 - - + -
3982C SER* 2.5 39.1 + - - -
3983C ILE* 2.7 28.4 + - + +
3985C VAL* 1.3 77.0 - - + +
3987C ALA* 1.3 62.3 + - - +
3989C ARG* 4.3 13.5 - - + +
3990C ALA* 2.9 25.3 + - - +
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Residues in contact with ALA3987 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3775C LEU* 6.4 2.0 - - - -
3786C LEU* 6.2 0.4 - - - +
3910C LEU* 6.0 3.1 - - + -
3913C ILE* 3.5 36.6 - - + -
3983C ILE 3.0 6.2 + - - +
3984C MET* 2.8 16.7 + - - +
3986C HIS* 1.3 76.5 - - - +
3988C LEU* 1.3 55.9 + - - +
3990C ALA* 3.0 6.6 - - - +
3991C PHE* 2.8 42.9 + - + -
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Residues in contact with LEU3988 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3913C ILE* 5.1 2.7 - - + -
3984C MET* 3.0 22.7 + - + +
3985C VAL* 2.1 28.6 + - + +
3987C ALA* 1.3 67.0 - - + +
3989C ARG* 1.3 53.9 + - + +
3990C ALA 3.0 1.1 - - - -
3991C PHE* 2.4 52.0 + - + +
3992C ARG* 2.6 20.9 + - - +
4100C GLU* 3.5 27.6 - - + +
4101C GLU* 4.6 0.4 - - - +
4103C GLN* 3.3 29.2 - - + +
4104C VAL* 3.7 13.9 - - + -
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Residues in contact with ARG3989 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2957C LEU* 2.3 41.8 + - - +
2958C LEU* 3.2 35.6 + - - +
3250C ASN 5.9 1.8 + - - -
3251C ASN* 5.9 1.4 - - - +
3288C SER* 6.0 4.9 - - - -
3289C ARG* 6.3 0.6 - - - +
3985C VAL* 2.8 39.0 + - + +
3986C HIS* 4.3 13.6 - - + +
3988C LEU* 1.3 71.3 - - + +
3990C ALA* 1.3 65.5 + - - +
3992C ARG* 3.6 10.5 + - - +
3993C SER* 3.2 12.0 + - - -
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Residues in contact with ALA3990 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3774C ILE* 4.1 25.1 - - + +
3775C LEU* 5.8 3.1 - - + -
3778C ASP* 5.5 6.7 - - + -
3781C CYS* 4.7 13.9 - - - -
3986C HIS 2.9 20.9 + - - +
3987C ALA* 3.0 9.0 - - - +
3989C ARG* 1.3 73.5 - - - +
3991C PHE* 1.3 58.0 + - + +
3993C SER* 2.6 42.8 + - - -
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Residues in contact with PHE3991 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3771C MET* 3.4 31.0 - - + -
3774C ILE* 5.9 1.6 - - + -
3913C ILE* 3.2 33.9 - - + -
3916C TRP* 6.1 2.2 - + - -
3917C ILE* 4.5 9.6 - - + -
3987C ALA* 2.8 42.4 + - + -
3988C LEU* 2.4 48.3 + - + +
3990C ALA* 1.3 74.1 - - + +
3992C ARG* 1.3 59.6 + - - +
3993C SER* 3.1 1.9 + - - -
3994C ASP 4.3 11.8 + - - +
3995C PRO* 5.4 1.4 - - - +
3997C LEU* 5.9 0.7 - - - +
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Residues in contact with ARG3992 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3287C ARG 4.6 3.8 + - - +
3288C SER* 3.1 23.8 + - - +
3289C ARG* 3.4 4.2 + - - +
3290C SER* 2.9 49.8 - - - +
3334C TYR* 5.2 17.4 + - - +
3335C ARG* 4.7 5.1 - - - +
3337C ILE* 6.2 1.4 - - - +
3988C LEU 2.6 16.9 + - - +
3989C ARG* 4.1 7.4 - - - +
3990C ALA 2.8 0.2 + - - -
3991C PHE* 1.3 72.6 - - - +
3993C SER* 1.3 67.5 + - - +
3994C ASP* 4.6 1.8 - - - -
3995C PRO* 5.1 1.6 - - - +
4098C LEU* 4.9 9.4 - - - +
4100C GLU* 2.7 43.3 + - - +
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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) + - + + + + + -
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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