Contacts of the helix formed by residues 3040 - 3053 (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 TYR3040 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3018C SER* 3.1 28.0 - - - +
3019C ILE* 3.4 40.8 - - + +
3027C LEU* 2.2 29.5 + - - +
3028C ASN* 3.6 17.7 - - + -
3035C PHE* 5.7 0.4 - + - -
3036C TYR* 3.0 29.8 - + + -
3037C GLN* 2.9 55.0 + - + +
3039C THR* 1.3 75.7 - - - +
3041C LEU* 1.3 62.2 + - + +
3042C PRO* 3.2 0.7 - - - -
3043C TYR* 2.6 50.6 + - + +
3044C MET 4.2 0.7 + - - -
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Residues in contact with LEU3041 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3028C ASN* 4.8 20.0 - - + -
3031C TRP* 5.6 1.1 - - + -
3037C GLN 3.0 3.8 + - - -
3038C GLU* 2.5 53.6 + - + +
3040C TYR* 1.3 85.4 - - + +
3042C PRO* 1.3 64.5 - - + +
3043C TYR 3.0 0.2 + - - -
3044C MET* 4.2 3.1 + - - +
3045C ILE* 2.9 32.6 + - + +
3064C PHE* 4.9 4.9 - - + -
3067C LYS* 4.9 9.0 - - - +
3082C TYR* 4.3 20.9 - - + +
3083C SER* 5.6 1.8 - - - +
3085C GLU* 5.7 0.2 - - - +
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Residues in contact with PRO3042 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3004C HIS* 3.2 28.7 - - + +
3038C GLU 3.2 8.7 - - - +
3039C THR* 3.0 25.6 - - - +
3040C TYR 3.3 0.2 - - - -
3041C LEU* 1.3 83.7 - - + +
3043C TYR* 1.3 51.2 + - - +
3045C ILE* 2.8 13.1 - - + +
3046C ARG* 2.1 41.2 + - + +
3082C TYR 5.8 0.4 - - - +
3085C GLU* 3.5 13.0 - - - +
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Residues in contact with TYR3043 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2997C ALA* 4.2 3.8 + - - -
3000C ASP* 3.0 31.9 - - + -
3001C CYS* 3.2 24.3 - - - -
3004C HIS* 3.0 43.1 - + + +
3011C LEU* 3.3 1.4 - - - +
3015C SER* 3.1 22.4 - - - +
3018C SER* 4.1 4.7 - - - -
3036C TYR* 2.5 32.1 + - - -
3039C THR* 3.1 21.9 + - - +
3040C TYR* 2.6 35.1 + - + +
3042C PRO* 1.3 68.8 - - - +
3044C MET* 1.3 50.6 - - + +
3046C ARG* 2.6 5.7 - - - +
3047C SER* 2.1 38.4 + - - -
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Residues in contact with MET3044 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3012C GLU* 4.3 11.4 - - + +
3015C SER* 4.0 17.3 - - - -
3016C THR* 4.0 20.9 - - - +
3019C ILE* 6.6 0.2 - - + -
3021C SER* 3.1 29.2 - - - +
3024C PRO* 6.3 2.7 - - + -
3040C TYR 4.2 0.6 + - - -
3041C LEU 4.2 2.6 + - - +
3043C TYR* 1.3 75.6 - - - +
3045C ILE* 1.3 63.2 + - + +
3046C ARG 3.0 1.3 - - - -
3047C SER* 3.2 27.3 - - - -
3048C LYS* 2.8 26.0 + - - -
3051C LEU* 5.1 6.5 - - - -
3059C GLN* 4.8 14.4 - - + -
3060C SER* 3.8 17.2 + - - +
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Residues in contact with ILE3045 (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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3041C LEU* 2.9 41.9 + - + +
3042C PRO* 2.8 19.3 - - + +
3044C MET* 1.3 76.6 - - + +
3046C ARG* 1.3 53.4 + - - +
3048C LYS* 2.2 46.5 + - + +
3060C SER* 3.7 19.5 - - - +
3064C PHE* 3.7 37.7 - - + -
3067C LYS* 5.2 3.8 - - - +
3083C SER* 4.0 0.4 - - - +
3085C GLU* 2.9 37.9 - - + +
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Residues in contact with ARG3046 (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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3004C HIS* 2.3 51.0 + - + +
3005C LEU* 2.1 38.7 + - - +
3007C GLU* 2.7 46.1 + - - +
3011C LEU* 3.4 9.8 - - + +
3042C PRO* 2.1 28.6 + - + +
3043C TYR 2.6 10.5 - - - +
3045C ILE* 1.3 66.3 - - - +
3047C SER* 1.3 63.6 + - - -
3048C LYS* 2.8 4.1 + - - +
3049C LEU* 2.9 39.7 + - - +
3085C GLU* 4.5 2.2 + - - -
3180C ASP* 5.8 2.8 - - - +
3181C ASP* 4.6 14.1 + - - -
3184C THR* 6.1 2.4 - - - +
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Residues in contact with SER3047 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3011C LEU* 3.1 20.3 + - - +
3012C GLU* 4.4 1.1 - - - -
3015C SER* 3.0 21.3 + - - -
3043C TYR 2.1 30.9 + - - -
3044C MET* 2.8 33.0 + - - -
3046C ARG* 1.3 66.4 - - - +
3048C LYS* 1.3 62.3 + - - +
3049C LEU 2.8 1.9 + - - -
3050C LYS* 3.2 23.6 - - - +
3051C LEU* 3.1 19.6 - - - +
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Residues in contact with LYS3048 (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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3044C MET 2.8 11.2 + - - +
3045C ILE* 2.2 42.0 + - + +
3046C ARG* 2.8 1.0 + - - +
3047C SER* 1.3 77.0 - - - +
3049C LEU* 1.3 71.1 - - + +
3051C LEU* 2.8 15.8 + - - +
3052C LEU* 2.1 66.1 + - + +
3060C SER* 4.9 13.5 - - - -
3085C GLU* 3.6 17.1 - - - +
3088C LEU* 3.3 38.6 - - - +
3089C LEU* 3.9 13.0 - - + +
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Residues in contact with LEU3049 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3007C GLU* 3.0 18.8 - - + +
3046C ARG* 2.9 45.1 + - - +
3047C SER 2.8 3.4 + - - -
3048C LYS* 1.3 103.0 - - + +
3050C LYS* 1.3 64.0 + - - +
3051C LEU 2.9 0.9 - - - -
3052C LEU* 2.9 24.0 + - + +
3053C LEU* 2.9 18.3 + - - +
3088C LEU* 3.7 22.2 - - + -
3184C THR* 5.5 9.9 - - + -
3188C PHE* 3.9 15.1 - - + -
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Residues in contact with LYS3050 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3007C GLU* 2.3 33.5 + - + +
3008C TRP* 2.9 39.4 + - - +
3009C LYS* 3.5 16.4 - - + +
3011C LEU* 3.7 3.6 - - - +
3012C GLU* 3.0 58.6 - - - +
3047C SER* 3.2 22.1 + - - +
3049C LEU* 1.3 67.6 - - - +
3051C LEU* 1.3 70.7 + - + +
3053C LEU* 3.0 38.2 - - + +
3054C GLN* 5.9 0.2 - - - +
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Residues in contact with LEU3051 (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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3009C LYS* 3.7 7.2 - - - +
3012C GLU* 3.6 16.4 - - - +
3044C MET* 5.1 5.2 - - - -
3047C SER* 3.1 32.3 - - - +
3048C LYS* 2.8 15.3 + - - +
3050C LYS* 1.3 98.1 - - + +
3052C LEU* 1.3 58.8 + - + -
3053C LEU 2.8 10.8 + - - -
3054C GLN* 3.3 12.8 + - - +
3055C GLY 3.8 8.9 + - - +
3058C ASP* 4.8 21.1 - - + +
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Residues in contact with LEU3052 (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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3048C LYS* 2.1 81.9 + - + +
3049C LEU* 2.9 12.8 + - + +
3051C LEU* 1.3 69.0 - - + +
3053C LEU* 1.3 64.9 + - - +
3054C GLN 3.3 0.9 + - - -
3055C GLY* 3.6 13.1 + - - +
3088C LEU 4.4 3.6 - - - +
3089C LEU* 3.6 25.4 - - + +
3091C LEU* 6.2 0.2 - - + -
3092C LEU* 3.4 37.2 - - + +
3188C PHE* 3.2 26.5 - - + -
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Residues in contact with LEU3053 (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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3049C LEU 2.9 16.4 + - - +
3050C LYS* 3.0 35.2 - - + +
3051C LEU 2.8 2.0 + - - -
3052C LEU* 1.3 78.9 - - - +
3054C GLN* 1.3 61.7 + - + +
3183C ILE 5.2 0.2 - - - +
3184C THR* 4.5 11.4 - - + +
3187C CYS* 4.4 32.8 - - + +
3188C PHE* 3.5 19.6 - - + -
3191C SER* 5.5 4.5 - - - -
3257C LYS* 6.2 1.8 - - - +
3261C GLU* 6.1 3.1 - - - +
3264C LYS* 6.2 1.6 - - - +
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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