Contacts of the helix formed by residues 2133 - 2147 (chain C) in PDB entry 1Y1S
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 ASP2133 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2131C VAL 4.1 0.2 + - - -
2132C ALA* 1.3 70.8 - - - +
2134C PHE* 1.3 63.4 + - - +
2135C ALA* 2.8 39.8 + - - +
2136C CYS* 3.2 5.4 + - - +
2137C THR* 2.8 30.6 + - - -
2211C LEU 5.2 0.6 - - - +
2212C ARG* 3.2 33.3 - - + +
2213C ALA 2.9 31.0 + - - +
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Residues in contact with PHE2134 (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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2132C ALA 3.5 4.4 + - - -
2133C ASP* 1.3 73.3 + - - +
2135C ALA* 1.3 57.3 + - - +
2137C THR* 3.7 4.8 - - - -
2138C THR* 2.7 60.9 + - + -
3111D THR* 4.2 9.9 - - + +
3134D PHE* 4.0 12.1 - + - -
3137D THR* 4.0 24.2 - - + -
3138D THR* 3.9 28.7 - - + -
3141D VAL* 3.8 35.7 - - + -
3153D VAL* 4.2 26.2 - - + -
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Residues in contact with ALA2135 (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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2133C ASP* 2.8 19.9 + - - +
2134C PHE* 1.3 78.2 - - - +
2136C CYS* 1.3 55.1 + - - +
2138C THR* 3.6 5.1 - - - -
2139C ALA* 2.8 31.2 + - - +
2212C ARG* 3.7 24.5 - - - +
2252C LEU* 3.8 8.5 - - + +
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Residues in contact with CYS2136 (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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2088C THR* 3.7 29.8 - - - -
2090C LEU* 3.8 12.3 - - + +
2133C ASP* 3.2 6.1 + - - +
2135C ALA* 1.3 77.5 - - - +
2137C THR* 1.3 58.6 + - - +
2139C ALA* 3.3 3.1 + - - +
2140C LEU* 2.9 35.3 + - - +
2212C ARG* 3.8 22.7 - - - -
2213C ALA 3.5 27.8 - - - +
2214C GLY* 3.8 6.3 - - - -
2252C LEU* 4.1 15.3 - - - +
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Residues in contact with THR2137 (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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2109C VAL* 3.9 19.5 - - + -
2110C THR 4.1 3.1 + - - +
2111C THR* 4.2 17.7 - - + -
2132C ALA* 3.4 22.5 - - - +
2133C ASP 2.8 27.1 + - - -
2134C PHE* 3.7 6.5 - - - -
2136C CYS* 1.3 72.2 - - - +
2138C THR* 1.3 63.9 + - - +
2140C LEU* 3.2 9.7 + - - +
2141C VAL* 3.0 30.7 + - + +
2153C VAL* 4.7 0.2 - - + -
2214C GLY* 4.9 1.0 - - - -
3134D PHE* 3.7 25.4 - - + -
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Residues in contact with THR2138 (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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2134C PHE* 2.7 56.4 + - + -
2135C ALA* 3.6 7.0 - - - +
2137C THR* 1.3 73.0 - - - +
2139C ALA* 1.3 63.4 + - - +
2141C VAL* 3.3 2.1 + - - +
2142C GLU* 2.8 50.9 + - + +
3134D PHE* 3.7 17.0 - - + -
3138D THR* 4.9 1.7 + - + -
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Residues in contact with ALA2139 (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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2135C ALA 2.8 17.7 + - - +
2136C CYS 3.5 4.7 - - - +
2137C THR 3.3 0.2 - - - -
2138C THR* 1.3 77.4 - - - +
2140C LEU* 1.3 57.4 + - - +
2142C GLU* 3.3 4.9 + - - +
2143C ALA* 2.9 31.2 + - - +
2248C ALA* 4.0 11.7 - - + +
2251C ARG* 3.8 18.2 - - + +
2252C LEU* 3.9 30.3 - - + -
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Residues in contact with LEU2140 (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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2090C LEU* 5.1 6.5 - - + -
2091C ARG 5.6 0.2 - - - +
2109C VAL* 3.8 19.1 - - + -
2136C CYS 2.9 18.7 + - - +
2137C THR* 3.2 7.6 + - - +
2139C ALA* 1.3 76.8 - - - +
2141C VAL* 1.3 57.7 + - - +
2143C ALA* 3.3 2.1 + - - +
2144C ALA* 2.9 30.2 + - - +
2214C GLY* 3.9 7.0 - - - -
2215C MET* 3.3 45.1 - - - +
2216C VAL* 3.6 29.2 - - + +
2244C ILE* 4.1 5.2 - - + +
2245C VAL* 4.4 11.0 - - + -
2248C ALA* 3.8 22.2 - - + -
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Residues in contact with VAL2141 (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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2109C VAL* 4.0 14.4 - - + -
2137C THR* 3.0 19.4 + - + +
2138C THR 3.8 3.4 - - - +
2140C LEU* 1.3 75.4 - - - +
2142C GLU* 1.3 59.9 + - + +
2144C ALA* 3.3 6.6 + - - +
2145C LYS* 2.8 31.2 + - + +
2151C THR* 4.9 6.9 + - + -
2153C VAL* 3.8 31.2 - - + -
3134D PHE* 3.9 28.3 - - + -
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Residues in contact with GLU2142 (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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2138C THR* 2.8 42.3 + - + +
2139C ALA* 3.6 3.1 - - - +
2141C VAL* 1.3 75.0 - - + +
2143C ALA* 1.3 55.7 + - - +
2144C ALA 3.1 1.3 - - - -
2145C LYS* 3.3 14.7 + - - +
2146C SER* 2.8 35.9 + - - -
2251C ARG* 3.5 29.8 + - - +
3134D PHE* 6.4 0.2 - - + -
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Residues in contact with ALA2143 (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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2139C ALA 2.9 18.3 + - - +
2140C LEU 3.7 3.6 - - - +
2142C GLU* 1.3 76.3 - - - +
2144C ALA* 1.3 58.1 - - - +
2146C SER* 2.9 21.1 + - - -
2147C ILE* 3.2 19.8 - - - +
2244C ILE* 3.3 28.0 - - + +
2247C GLU* 3.7 9.2 - - + -
2248C ALA* 3.6 17.0 - - + +
2251C ARG* 3.8 6.9 - - - +
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Residues in contact with ALA2144 (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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2107C VAL* 4.3 2.5 - - + -
2109C VAL* 5.0 2.2 - - + -
2140C LEU 2.9 17.4 + - - +
2141C VAL* 3.4 8.1 - - - +
2143C ALA* 1.3 76.4 - - - +
2145C LYS* 1.3 64.8 + - - +
2147C ILE* 3.2 10.2 + - - -
2149C ALA* 3.2 21.5 + - - +
2151C THR* 3.2 29.4 - - + +
2244C ILE* 4.0 26.0 - - + +
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Residues in contact with LYS2145 (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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2141C VAL* 2.8 21.5 + - + +
2142C GLU* 3.7 14.8 + - - +
2144C ALA* 1.3 76.3 - - - +
2146C SER* 1.3 70.4 + - - +
2148C GLY* 3.0 15.9 + - - -
2149C ALA 4.8 6.1 - - - +
2151C THR* 4.6 1.3 + - - -
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Residues in contact with SER2146 (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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2142C GLU 2.8 18.6 + - - -
2143C ALA* 2.9 19.9 + - - -
2145C LYS* 1.3 84.3 - - - +
2147C ILE* 1.3 62.8 + - - +
2148C GLY 3.1 3.2 + - - -
2247C GLU* 4.3 8.4 - - - +
2251C ARG* 4.3 10.8 - - - -
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Residues in contact with ILE2147 (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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2143C ALA 3.2 18.4 - - - +
2144C ALA 3.2 5.1 + - - +
2145C LYS 3.2 0.8 - - - -
2146C SER* 1.3 82.8 - - - +
2148C GLY* 1.3 64.4 + - - +
2149C ALA* 3.0 8.6 + - + +
2240C HIS* 5.1 13.8 - - + +
2243C LYS* 3.5 56.8 - - + +
2244C ILE* 3.8 27.6 - - + -
2247C GLU* 4.5 7.9 - - + -
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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