Contacts of the helix formed by residues 2945 - 2958 (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 SER2945 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2939C LEU* 3.4 32.7 - - - +
2942C ILE* 3.2 20.8 + - - +
2944C THR* 1.3 77.8 - - - +
2946C GLU* 1.3 64.1 + - - +
2947C ILE 2.9 1.6 + - - -
2948C GLY* 3.3 3.5 + - - -
2949C THR* 2.5 37.1 + - - -
2991C LYS* 3.0 32.3 - - - +
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Residues in contact with GLU2946 (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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2936C TYR* 3.2 32.2 + - - +
2939C LEU 3.6 2.3 + - - +
2942C ILE 3.8 0.2 + - - -
2943C PHE* 3.1 30.1 - - - +
2944C THR 2.9 2.7 + - - +
2945C SER* 1.3 77.1 - - - +
2947C ILE* 1.3 96.5 + - + +
2950C LYS* 2.8 53.3 + - - +
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Residues in contact with ILE2947 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2943C PHE 5.6 0.2 - - - +
2944C THR 3.7 4.2 + - - +
2945C SER 2.9 2.0 + - - -
2946C GLU* 1.3 106.3 - - + +
2948C GLY* 1.3 58.9 + - - +
2950C LYS* 4.8 3.2 - - - +
2951C GLN* 2.9 34.5 + - - +
2983C ASP* 4.8 20.6 - - + +
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Residues in contact with GLY2948 (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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2944C THR 5.1 0.6 + - - -
2945C SER 3.3 2.8 + - - -
2947C ILE* 1.3 80.6 - - - +
2949C THR* 1.3 65.5 + - - +
2951C GLN* 3.0 7.9 - - - +
2952C ILE* 3.0 16.3 + - - +
2972C TYR* 2.7 46.5 + - - -
2991C LYS* 6.1 0.2 - - - -
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Residues in contact with THR2949 (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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2935C GLU 3.1 28.3 - - - +
2936C TYR* 3.3 22.2 - - + -
2939C LEU* 3.5 13.7 - - + -
2945C SER* 2.5 39.0 + - - -
2948C GLY* 1.3 73.9 - - - +
2950C LYS* 1.3 68.4 + - - +
2952C ILE* 3.0 12.0 + - - +
2953C THR* 2.9 25.4 + - - +
2991C LYS* 3.6 11.6 - - - +
2994C TRP* 3.8 9.2 - - + -
2995C GLU* 4.5 0.2 + - - -
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Residues in contact with LYS2950 (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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2936C TYR* 3.2 44.1 + - + -
2940C ARG* 5.2 7.8 - - - +
2946C GLU* 2.8 44.8 + - + +
2947C ILE* 4.8 2.7 - - - +
2949C THR* 1.3 71.4 - - - +
2951C GLN* 1.3 58.5 + - + +
2953C THR* 2.1 36.1 + - - -
2954C GLN* 4.3 3.8 + - - +
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Residues in contact with GLN2951 (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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2947C ILE* 2.9 38.2 + - - +
2948C GLY* 3.0 4.3 - - - +
2950C LYS* 1.3 82.7 - - + +
2952C ILE* 1.3 61.7 + - + +
2953C THR 2.9 4.0 + - - -
2954C GLN* 3.0 28.6 + - - +
2968C ALA* 4.4 5.2 - - + +
2972C TYR* 2.2 35.8 + - - +
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Residues in contact with ILE2952 (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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2935C GLU* 4.8 0.2 - - - +
2948C GLY 3.4 0.4 - - - +
2949C THR* 3.0 22.9 - - + +
2951C GLN* 1.3 69.6 - - + +
2953C THR* 1.3 67.2 + - - +
2954C GLN 3.1 0.4 - - - -
2955C SER* 3.0 21.7 + - - -
2956C ALA* 3.9 1.6 + - - +
2965C TYR* 3.4 27.8 - - + -
2968C ALA* 3.5 15.3 - - + -
2969C ALA* 3.3 38.8 - - + +
2972C TYR* 3.0 35.2 - - + +
2994C TRP* 4.1 10.5 - - + -
2995C GLU* 3.8 12.1 - - - +
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Residues in contact with THR2953 (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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2935C GLU* 2.9 42.4 - - + +
2936C TYR* 3.4 32.1 - - + +
2949C THR 2.9 20.9 + - - +
2950C LYS* 2.1 31.4 + - - +
2952C ILE* 1.3 75.4 - - - +
2954C GLN* 1.3 69.8 + - - +
2955C SER 2.9 1.2 + - - -
2956C ALA 3.0 2.4 + - - -
2957C LEU* 2.8 28.0 + - - +
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Residues in contact with GLN2954 (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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2950C LYS 4.3 2.8 + - - +
2951C GLN* 3.0 19.5 + - - +
2953C THR* 1.3 87.7 + - - +
2955C SER* 1.3 52.0 + - - +
2957C LEU* 3.4 16.2 - - + -
2958C LEU* 2.2 56.4 + - + +
4101C GLU* 3.6 29.1 + - - +
4105C LYS* 5.4 4.2 - - - +
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Residues in contact with SER2955 (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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2952C ILE* 3.0 14.1 + - - -
2953C THR 2.9 0.4 + - - -
2954C GLN* 1.3 76.9 - - - +
2956C ALA* 1.3 52.0 + - - +
2958C LEU* 2.9 10.5 - - - +
2959C ALA 2.4 15.2 + - - -
2960C GLU* 2.3 48.3 + - - +
2964C ASP* 3.3 8.5 + - - +
2965C TYR* 2.8 38.1 + - - -
2968C ALA* 4.4 2.8 - - - +
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Residues in contact with ALA2956 (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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2928C LYS* 3.3 14.0 + - - -
2931C ARG* 3.1 38.9 + - + +
2932C SER* 5.8 0.7 - - - -
2935C GLU* 3.1 22.4 - - + +
2952C ILE 3.9 2.1 + - - +
2953C THR 3.0 1.8 + - - -
2955C SER* 1.3 77.8 - - - +
2957C LEU* 1.3 57.7 + - - +
2959C ALA* 2.8 18.5 + - - +
2960C GLU 3.7 11.3 + - - +
3002C TYR* 6.1 3.8 - - + -
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Residues in contact with LEU2957 (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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2928C LYS* 4.4 4.8 + - - +
2932C SER* 4.2 8.1 - - - -
2935C GLU* 3.0 19.7 - - - +
2953C THR* 2.8 25.3 + - - +
2954C GLN* 3.0 35.0 - - + +
2956C ALA* 1.3 74.6 - - - +
2958C LEU* 1.3 52.1 + - + +
2959C ALA* 2.8 9.1 + - - +
3981C TYR* 5.4 5.8 - - + -
3982C SER* 3.3 34.8 - - - +
3985C VAL* 6.1 6.7 - - + -
3986C HIS* 5.3 11.6 + - - +
3989C ARG* 2.3 27.9 + - - +
4101C GLU* 5.3 5.6 - - - +
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Residues in contact with LEU2958 (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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2954C GLN* 2.2 47.0 + - + +
2955C SER* 2.9 10.3 - - - +
2957C LEU* 1.3 67.1 - - + -
2959C ALA* 1.3 67.7 + - - +
2960C GLU* 4.5 5.0 - - + +
2964C ASP* 5.3 12.8 - - + +
3251C ASN* 4.4 9.5 + - - +
3252C PHE* 6.3 2.5 - - + -
3289C ARG* 4.8 27.6 - - + +
3291C GLN* 5.8 0.9 - - - +
3989C ARG* 3.2 36.8 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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