Contacts of the helix formed by residues 883 - 889 (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 TYR 883 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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881C LYS* 3.1 65.1 - - + -
882C SER* 1.3 72.5 - - - +
884C VAL* 1.3 82.0 + - + +
886C TRP* 2.9 5.5 + - - -
887C ASP* 2.2 34.2 + - - +
888C ARG* 4.7 3.0 - - - +
908C ASP* 6.4 0.2 - - - -
910C PHE* 4.6 19.3 - + + +
911C LEU* 3.1 38.2 + - + +
914C VAL* 5.2 1.0 - - - +
957C PRO* 5.4 6.2 - - + +
958C MET* 4.6 29.9 - - + +
961C LEU* 5.5 10.1 - - + -
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Residues in contact with VAL 884 (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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883C TYR* 1.3 91.4 - - + +
885C ALA* 1.3 66.9 + - + +
888C ARG* 2.8 39.5 + - + +
892C LEU* 3.5 34.8 - - + -
907C LEU* 3.2 31.4 - - - +
908C ASP* 5.0 3.6 - - + -
910C PHE* 3.6 15.3 - - + -
958C MET* 3.6 13.9 - - + -
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Residues in contact with ALA 885 (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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884C VAL* 1.3 83.4 - - + +
886C TRP* 1.3 80.8 + - - +
888C ARG* 2.5 28.5 + - + -
889C GLU 2.7 16.1 + - - -
890C LYS 3.0 32.1 - - - +
891C ARG 4.1 0.2 - - - -
892C LEU* 3.8 14.5 - - + +
958C MET* 3.6 4.4 - - - -
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Residues in contact with TRP 886 (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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883C TYR 2.9 5.7 + - - -
884C VAL* 4.0 0.4 - - - +
885C ALA* 1.3 98.0 - - - +
887C ASP* 1.3 54.6 + - - +
889C GLU* 3.1 36.2 + - + +
890C LYS* 3.3 35.4 - - + +
891C ARG 3.2 26.0 - - - -
892C LEU* 4.1 11.9 - - + -
950C GLU* 3.3 41.9 + - + +
951C GLY* 5.6 2.2 - - - -
953C GLN 4.9 1.1 - - - +
954C GLY* 3.3 44.6 - - - +
957C PRO* 5.5 6.3 - - + -
958C MET* 4.3 10.5 - - + -
3889C ARG* 2.7 27.5 + - - -
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Residues in contact with ASP 887 (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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882C SER* 2.9 24.6 - - - +
883C TYR* 2.2 30.5 + - - +
886C TRP* 1.3 68.9 - - - +
888C ARG* 1.3 60.4 + - - +
957C PRO* 6.1 0.8 - - - +
3815C LEU* 4.4 10.9 - - - +
3889C ARG* 2.2 92.0 + - - +
3890C MET* 4.1 3.0 + - - -
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Residues in contact with ARG 888 (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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881C LYS 5.1 0.4 + - - -
882C SER* 3.5 16.2 + - - +
883C TYR 4.7 1.3 - - - +
884C VAL* 2.8 33.8 + - + +
885C ALA* 2.5 22.6 + - + -
887C ASP* 1.3 78.8 - - - +
889C GLU* 1.3 61.1 + - - +
890C LYS 3.5 2.7 - - - -
3885C ARG* 4.9 9.9 + - - -
3888C VAL* 3.2 8.9 + - - +
3889C ARG* 3.2 31.2 + - + +
3891C SER 2.2 36.0 + - - -
3892C THR* 3.0 39.2 + - - +
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Residues in contact with GLU 889 (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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885C ALA 2.7 11.5 + - - -
886C TRP* 3.1 28.0 + - - +
888C ARG* 1.3 73.1 - - - +
890C LYS* 1.3 66.9 + - + +
3818C ASN* 4.0 14.6 - - - +
3819C THR* 6.4 0.9 - - - -
3822C GLN* 5.4 12.0 - - - +
3885C ARG* 5.6 3.8 + - - +
3889C ARG* 2.4 48.0 + - - +
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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