Contacts of the helix formed by residues 2826 - 2847 (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 LEU2826 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2820C MET* 3.2 22.9 - - + +
2821C ASP* 5.0 4.7 - - - +
2823C PHE 3.4 3.1 - - - +
2824C LYS* 3.2 17.0 + - - +
2825C THR* 1.3 82.1 - - - +
2827C SER* 1.3 63.7 + - - +
2828C GLU 3.1 2.7 - - - +
2829C LYS* 2.6 31.5 + - + +
2830C ASN* 2.7 18.2 + - - +
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Residues in contact with SER2827 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2826C LEU* 1.3 75.8 - - - +
2828C GLU* 1.3 59.3 + - - +
2830C ASN* 2.8 32.9 + - - +
2831C ASN* 2.7 21.5 - - - +
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Residues in contact with GLU2828 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2825C THR* 4.7 18.1 - - + +
2826C LEU 3.1 1.4 - - - +
2827C SER* 1.3 78.7 - - - +
2829C LYS* 1.3 58.0 + - + +
2831C ASN* 2.1 49.3 + - - +
2832C ILE* 2.8 35.9 + - + +
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Residues in contact with LYS2829 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2537C ASP* 5.9 0.8 + - - -
2540C LEU* 5.8 2.2 - - - +
2820C MET* 3.4 37.7 - - + +
2823C PHE* 2.9 37.2 - - - -
2825C THR* 2.9 46.2 + - - +
2826C LEU* 2.6 21.8 + - + +
2828C GLU* 1.3 73.1 - - + +
2830C ASN* 1.3 61.9 + - - +
2832C ILE* 2.8 25.3 + - + +
2833C THR* 2.8 27.7 + - + +
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Residues in contact with ASN2830 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2826C LEU 2.7 15.4 + - - +
2827C SER* 2.9 29.8 + - - +
2829C LYS* 1.3 71.6 - - - +
2831C ASN* 1.3 62.8 + - - +
2833C THR* 2.0 34.7 + - - +
2834C GLN* 2.7 14.9 - - - +
2865C HIS* 4.6 14.1 - - - -
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Residues in contact with ASN2831 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2827C SER* 2.7 14.4 + - - +
2828C GLU* 2.1 55.9 + - - +
2830C ASN* 1.3 77.6 - - - +
2832C ILE* 1.3 62.1 + - - +
2834C GLN* 3.0 27.9 + - - +
2835C LYS* 3.4 9.4 + - - +
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Residues in contact with ILE2832 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2540C LEU* 4.4 20.9 - - + -
2820C MET* 3.6 24.2 - - + -
2828C GLU* 2.8 26.4 + - + +
2829C LYS* 2.8 44.2 + - + +
2831C ASN* 1.3 72.3 - - - +
2833C THR* 1.3 68.1 + - - +
2834C GLN 3.0 0.5 + - - -
2835C LYS* 3.0 12.2 + - + +
2836C LEU* 2.9 38.0 + - + +
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Residues in contact with THR2833 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2816C ILE* 5.5 2.5 - - + -
2820C MET* 5.5 4.5 - - - -
2829C LYS* 2.8 18.9 + - + +
2830C ASN* 2.0 35.2 + - - +
2832C ILE* 1.3 70.5 - - - +
2834C GLN* 1.3 71.1 + - - +
2836C LEU* 2.4 45.4 + - + -
2837C LEU* 2.7 26.0 + - - +
2865C HIS* 3.3 34.3 - - + +
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Residues in contact with GLN2834 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2830C ASN* 2.7 17.9 - - - +
2831C ASN* 3.0 17.9 + - - +
2832C ILE 3.0 0.4 + - - -
2833C THR* 1.3 105.8 + - - +
2835C LYS* 1.3 69.8 + - - +
2837C LEU* 3.4 13.5 - - - +
2838C GLN* 2.8 42.5 + - - +
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Residues in contact with LYS2835 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2831C ASN 4.1 6.1 + - - +
2832C ILE* 3.0 11.4 + - + +
2834C GLN* 1.3 82.3 - - - +
2836C LEU* 1.3 72.6 + - + +
2838C GLN* 2.8 23.0 + - - +
2839C ASP* 2.7 39.4 + - - +
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Residues in contact with LEU2836 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2540C LEU* 5.1 16.2 - - + +
2543C ASN* 5.0 10.5 - - + +
2816C ILE* 4.3 19.1 - - + -
2820C MET* 4.8 0.7 - - + -
2832C ILE* 2.9 37.0 + - + +
2833C THR* 2.4 36.7 + - + +
2835C LYS* 1.3 75.7 - - + +
2837C LEU* 1.3 65.9 + - + +
2839C ASP* 3.2 3.4 + - - +
2840C PHE* 2.8 57.4 + - + -
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Residues in contact with LEU2837 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2833C THR* 2.7 40.4 + - - +
2834C GLN* 3.4 14.8 - - - +
2836C LEU* 1.3 73.8 - - + +
2838C GLN* 1.3 56.4 + - - +
2840C PHE* 2.6 35.8 + - + +
2841C ASN* 2.7 22.5 + - - +
2865C HIS* 5.3 4.0 - - + -
2867C ALA* 5.0 1.6 - - + +
2868C LEU* 3.6 56.1 - - + +
2871C LEU* 4.1 13.7 - - + -
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Residues in contact with GLN2838 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2834C GLN* 2.8 39.6 - - - +
2835C LYS* 2.8 41.4 + - - +
2837C LEU* 1.3 74.7 - - - +
2839C ASP* 1.3 59.1 + - - +
2841C ASN* 2.4 36.4 + - - +
2842C ARG* 2.9 15.5 + - - +
2871C LEU* 4.4 13.0 - - + -
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Residues in contact with ASP2839 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2543C ASN* 6.1 1.3 - - + +
2544C SER* 5.3 10.5 + - - -
2547C SER* 4.0 2.2 + - - -
2835C LYS* 2.7 43.9 + - - +
2836C LEU* 3.3 8.8 + - - +
2838C GLN* 1.3 77.5 - - - +
2840C PHE* 1.3 67.7 + - + +
2842C ARG* 3.2 39.9 + - - +
2843C PHE* 2.8 25.5 + - - +
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Residues in contact with PHE2840 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2543C ASN* 4.0 33.7 - - + -
2836C LEU* 2.8 63.5 + - + -
2837C LEU* 2.6 21.5 + - + +
2839C ASP* 1.3 83.2 - - + +
2841C ASN* 1.3 59.4 + - - +
2843C PHE* 3.0 21.3 - + + +
2844C LEU* 2.8 29.7 + - - +
2860C ASP* 5.0 22.3 - - + +
2863C CYS* 6.1 6.1 - - - -
2868C LEU 6.1 0.7 - - - -
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Residues in contact with ASN2841 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2837C LEU* 2.7 31.3 + - - +
2838C GLN* 2.4 21.3 + - - +
2840C PHE* 1.3 74.0 - - - +
2842C ARG* 1.3 63.3 + - - +
2844C LEU* 2.9 19.0 - - - +
2845C ASN* 2.8 19.9 + - - +
2868C LEU 4.7 5.5 + - - -
2869C LEU 4.0 3.8 + - - -
2871C LEU* 3.0 44.2 - - + +
2872C ASP* 3.7 12.1 - - - +
2876C VAL* 4.6 2.6 - - + +
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Residues in contact with ARG2842 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2544C SER* 4.6 6.1 + - - +
2547C SER* 2.3 38.8 + - - +
2838C GLN* 2.9 7.2 + - - +
2839C ASP* 3.2 44.0 + - - +
2841C ASN* 1.3 74.6 - - - +
2843C PHE* 1.3 54.2 + - - +
2845C ASN* 2.2 38.2 + - + +
2846C THR* 2.8 31.8 + - + +
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Residues in contact with PHE2843 (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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2546C TYR* 4.3 18.6 - - + -
2547C SER* 3.9 23.1 - - - +
2549C LYS* 5.7 0.9 - - + -
2554C PHE* 4.2 30.1 - + - -
2555C LEU* 6.1 0.4 - - + -
2839C ASP 2.8 18.1 + - - +
2840C PHE* 3.0 28.5 - + + +
2841C ASN 3.1 0.2 - - - -
2842C ARG* 1.3 74.3 - - - +
2844C LEU* 1.3 57.2 + - + +
2846C THR* 2.7 16.9 + - - -
2847C THR* 2.4 45.4 + - + -
2853C PRO* 4.5 11.7 - - + -
2856C SER* 4.1 26.7 - - - -
2860C ASP* 5.7 3.4 - - - -
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Residues in contact with LEU2844 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2840C PHE 2.8 14.8 + - - +
2841C ASN* 2.9 26.2 - - - +
2843C PHE* 1.3 76.1 - - + +
2845C ASN* 1.3 53.8 + - - +
2846C THR 2.6 16.9 + - - -
2847C THR* 2.9 21.7 - - - +
2848C PHE* 3.0 10.3 - - - -
2857C CYS* 3.8 18.8 - - - -
2860C ASP* 5.3 4.9 - - - +
2872C ASP* 3.2 38.6 - - + +
2876C VAL* 3.1 32.3 - - + +
2877C SER 3.7 13.0 - - - +
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Residues in contact with ASN2845 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2841C ASN 2.8 13.2 + - - +
2842C ARG* 2.2 30.9 + - + +
2844C LEU* 1.3 68.0 - - - +
2846C THR* 1.3 59.5 + - + +
2848C PHE* 2.9 22.1 - - - -
2876C VAL* 5.5 5.4 - - + -
3032C SER* 4.5 4.3 - - - +
3033C GLU* 2.1 47.4 + - - +
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Residues in contact with THR2846 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2547C SER* 4.2 7.8 + - - +
2548C PRO* 6.3 0.7 - - + -
2550C ILE* 3.3 37.1 - - + +
2842C ARG* 2.8 35.5 + - + +
2843C PHE* 2.7 25.5 + - - -
2844C LEU 2.6 7.3 + - - -
2845C ASN* 1.3 79.8 - - + +
2847C THR* 1.3 63.7 + - - +
2848C PHE* 2.9 18.4 + - - -
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Residues in contact with THR2847 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2547C SER 4.7 0.7 - - - +
2549C LYS* 5.6 0.7 - - + -
2550C ILE* 3.6 26.7 - - - +
2551C GLU 4.5 3.4 - - - +
2554C PHE* 6.2 0.7 - - + -
2843C PHE* 2.4 49.7 + - + +
2844C LEU* 2.9 12.0 + - - +
2846C THR* 1.3 81.6 + - - +
2848C PHE* 1.3 69.8 + - - +
2850C PHE* 3.4 20.9 - - + -
2853C PRO* 4.5 15.8 - - + +
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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