Contacts of the helix formed by residues 2790 - 2801 (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 LEU2790 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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935C HIS* 5.7 7.0 - - + -
936C SER* 3.8 12.1 - - - +
939C MET* 6.0 4.5 - - + -
2572C TYR* 3.1 34.0 + - + +
2787C HIS* 3.1 31.4 - - + +
2788C SER 3.3 1.2 + - - -
2789C SER* 1.3 79.9 + - - +
2791C ILE* 1.3 65.4 + - + +
2792C THR 2.9 1.6 + - - -
2793C PRO* 2.9 11.3 - - - +
2794C LEU* 2.9 29.6 - - + +
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Residues in contact with ILE2791 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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896C VAL* 4.3 5.2 - - + -
906C PHE* 4.8 6.1 - - + -
933C LEU* 3.4 20.0 - - + -
936C SER* 3.3 20.9 - - - +
937C MET* 6.3 0.9 - - - -
940C PHE* 3.3 45.5 - - + -
2788C SER* 3.1 27.8 - - - +
2789C SER 2.8 0.2 + - - -
2790C LEU* 1.3 72.5 - - - +
2792C THR* 1.3 52.3 + - - +
2794C LEU* 2.7 16.6 + - - +
2795C GLN* 2.5 59.2 + - + +
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Residues in contact with THR2792 (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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896C VAL* 4.2 2.4 - - - +
897C PRO* 4.2 6.2 - - - +
898C PHE* 3.4 35.1 - - + -
2563C LEU* 5.1 5.8 - - + +
2567C SER* 3.5 10.3 - - - +
2571C ASP* 2.3 35.5 + - - +
2789C SER 2.9 7.1 + - - -
2790C LEU 2.9 1.0 + - - -
2791C ILE* 1.3 74.5 - - - +
2793C PRO* 1.3 70.1 - - + +
2795C GLN* 2.6 33.2 + - - +
2796C ALA* 3.2 7.2 + - + +
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Residues in contact with PRO2793 (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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2572C TYR* 3.2 28.7 - - + +
2790C LEU 2.9 17.5 - - - +
2792C THR* 1.3 86.2 - - + +
2794C LEU* 1.3 77.4 + - + +
2796C ALA* 2.8 8.2 + - + +
2797C VAL* 2.7 39.9 + - + +
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Residues in contact with LEU2794 (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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932C GLU* 4.7 16.0 - - + +
933C LEU* 3.4 26.4 + - + +
935C HIS* 6.0 2.0 - - + -
936C SER* 3.3 26.0 - - - +
2572C TYR* 5.6 0.4 - - - +
2790C LEU* 2.9 38.8 - - + +
2791C ILE 2.7 12.5 + - - +
2793C PRO* 1.3 77.4 - - + +
2795C GLN* 1.3 65.1 + - - +
2797C VAL* 3.3 9.7 - - + +
2798C ALA* 2.9 23.4 + - - +
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Residues in contact with GLN2795 (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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896C VAL* 3.5 23.2 - - - +
898C PHE* 4.2 9.1 - - - -
905C ILE* 5.9 3.3 - - - +
906C PHE* 3.9 12.9 - - + -
933C LEU* 3.3 10.0 - - + +
2563C LEU* 5.9 2.9 - - + +
2791C ILE* 2.5 44.0 + - + +
2792C THR* 2.6 34.6 + - - +
2794C LEU* 1.3 75.6 - - - +
2796C ALA* 1.3 55.9 + - - +
2799C GLN* 2.4 64.6 + - - +
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Residues in contact with ALA2796 (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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2560C ASN* 3.7 4.0 + - + +
2563C LEU* 3.7 38.6 - - + -
2792C THR 3.2 7.2 + - - +
2793C PRO* 2.8 13.1 + - + +
2795C GLN* 1.3 77.9 - - + +
2797C VAL* 1.3 55.0 + - + +
2799C GLN* 2.7 7.4 + - - -
2800C ARG* 2.2 43.1 + - - -
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Residues in contact with VAL2797 (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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932C GLU* 4.7 9.0 - - - +
2793C PRO* 2.7 39.6 + - + +
2794C LEU* 3.3 17.7 - - + +
2796C ALA* 1.3 73.3 - - + +
2798C ALA* 1.3 76.3 + - - +
2800C ARG* 2.9 11.9 + - - +
2801C ASP* 3.2 18.6 - - - +
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Residues in contact with ALA2798 (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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913C ARG* 3.7 21.1 - - - +
929C ALA* 3.3 36.6 - - + +
932C GLU* 4.4 3.1 + - - +
2794C LEU 2.9 17.9 - - - +
2795C GLN* 2.9 4.8 + - - +
2797C VAL* 1.3 84.4 - - - +
2799C GLN* 1.3 63.4 + - + +
2800C ARG 2.9 3.5 + - - -
2801C ASP* 3.1 7.9 + - - +
2802C PRO* 2.9 17.7 - - - +
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Residues in contact with GLN2799 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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906C PHE* 6.2 1.8 - - - -
909C VAL* 4.7 18.4 - - - +
913C ARG* 5.9 2.2 - - - +
933C LEU* 4.3 7.5 - - - +
2556C SER* 5.3 3.5 - - - -
2559C THR* 5.7 0.2 + - - -
2560C ASN* 4.5 2.7 + - - +
2563C LEU* 5.0 6.1 - - + +
2795C GLN* 2.4 53.7 + - - +
2796C ALA* 2.9 6.8 + - - +
2798C ALA* 1.3 77.4 - - + +
2800C ARG* 1.3 61.9 + - - +
2802C PRO* 3.1 21.2 - - + +
2805C ALA* 4.8 8.9 - - + +
2807C GLN* 5.0 13.3 - - + +
2808C LEU* 5.2 11.4 - - + +
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Residues in contact with ARG2800 (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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2512C ASP* 4.7 8.9 + - - -
2519C LEU* 4.3 15.0 - - - +
2556C SER* 3.7 17.7 - - - -
2557C LEU* 4.2 20.9 - - - +
2560C ASN* 3.0 38.2 + - - +
2796C ALA 2.2 29.1 + - - +
2797C VAL* 3.4 11.2 - - - +
2798C ALA 2.9 0.8 + - - -
2799C GLN* 1.3 73.5 - - - +
2801C ASP* 1.3 74.4 + - - +
2802C PRO 4.3 1.6 - - - +
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Residues in contact with ASP2801 (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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925C GLN* 3.3 68.7 + - + +
926C THR* 5.1 2.0 - - + -
2797C VAL 3.2 18.9 - - - +
2798C ALA* 3.8 2.5 - - - +
2800C ARG* 1.3 95.6 + - - +
2802C PRO* 1.3 71.0 - - + +
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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
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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