Contacts of the helix formed by residues 2232 - 2246 (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 ARG2232 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2227C LYS* 3.1 38.9 - - + +
2231C PHE* 1.3 90.1 - - + +
2233C HIS* 1.3 94.0 + - + +
2234C ASN 2.6 16.1 + - - -
2235C LEU 3.1 7.1 + - - -
2236C GLU* 2.6 17.3 - - - +
2275C GLN* 5.2 8.5 - - - +
48E T 5.4 14.4 + - - -
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Residues in contact with HIS2233 (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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2231C PHE* 4.3 6.3 - + + -
2232C ARG* 1.3 112.0 + - + +
2234C ASN* 1.3 65.2 + - - +
2236C GLU* 2.9 34.3 + - + +
2237C ILE* 2.9 27.0 + - - +
49E T 6.6 0.2 - - - -
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Residues in contact with ASN2234 (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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2183C HIS* 4.5 6.3 - - - +
2226C PRO* 5.1 1.3 + - + -
2227C LYS* 4.8 5.2 - - - +
2230C VAL* 4.8 3.8 - - - +
2231C PHE* 2.3 79.3 + - - +
2232C ARG 2.6 3.6 + - - -
2233C HIS* 1.3 69.9 - - - +
2235C LEU* 1.3 66.2 + - - +
2237C ILE* 2.9 38.5 - - + +
2238C ILE* 3.1 7.8 - - - +
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Residues in contact with LEU2235 (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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2223C VAL* 3.4 48.0 - - + +
2224C PHE* 4.4 2.0 - - + +
2227C LYS* 4.1 21.4 - - + +
2232C ARG 3.1 4.1 + - - +
2234C ASN* 1.3 78.6 - - - +
2236C GLU* 1.3 65.6 + - - +
2238C ILE* 2.0 51.0 + - + +
2239C LYS* 2.8 30.2 + - + +
2242C VAL* 5.2 1.8 - - + -
2272C VAL* 4.0 27.4 - - + -
2275C GLN* 5.2 2.2 - - - +
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Residues in contact with GLU2236 (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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2227C LYS* 3.0 29.3 - - - -
2232C ARG 2.6 17.6 - - - +
2233C HIS* 2.9 43.6 + - + +
2235C LEU* 1.3 74.7 + - - +
2237C ILE* 1.3 61.6 + - - +
2239C LYS* 2.7 43.0 + - + +
2240C THR* 2.8 19.0 + - - +
2275C GLN* 4.5 6.5 + - - +
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Residues in contact with ILE2237 (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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2183C HIS* 3.2 33.4 - - + +
2233C HIS 2.9 8.3 + - - +
2234C ASN* 2.9 35.2 - - - +
2235C LEU 2.7 3.0 + - - -
2236C GLU* 1.3 73.5 - - - +
2238C ILE* 1.3 50.7 + - - +
2240C THR* 1.9 34.6 + - + +
2241C LEU* 3.3 8.4 - - + +
18K ALA* 5.2 19.5 - - + +
19K ALA* 6.0 4.0 - - - +
22K ALA* 5.0 0.5 - - - +
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Residues in contact with ILE2238 (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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2182C ILE* 5.7 7.2 - - + -
2183C HIS* 3.3 25.8 - - + +
2186C VAL* 5.5 5.4 - - + -
2219C LEU* 5.8 7.0 - - + -
2223C VAL* 3.5 33.4 - - + -
2234C ASN 3.1 16.2 - - - +
2235C LEU* 2.0 39.6 + - + +
2237C ILE* 1.3 65.6 - - - +
2239C LYS* 1.3 55.0 + - - +
2240C THR 2.8 2.0 - - - -
2241C LEU* 2.2 52.8 + - + +
2242C VAL* 2.8 24.5 + - + -
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Residues in contact with LYS2239 (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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2235C LEU* 2.8 19.4 + - + +
2236C GLU* 2.7 41.1 + - + +
2238C ILE* 1.3 71.9 - - - +
2240C THR* 1.3 66.2 + - - +
2242C VAL* 2.9 15.5 - - + +
2243C GLU* 2.9 29.2 + - - +
2275C GLN* 3.2 48.2 + - - +
2276C LEU* 4.4 8.1 - - + +
2279C ILE* 3.7 34.7 - - + +
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Residues in contact with THR2240 (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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2236C GLU 2.8 14.8 + - - +
2237C ILE* 1.9 36.5 + - - +
2239C LYS* 1.3 72.7 - - - +
2241C LEU* 1.3 73.1 + - - +
2243C GLU* 2.4 49.9 + - - +
2244C CYS* 2.8 16.1 + - - -
22K ALA* 3.7 28.7 - - + +
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Residues in contact with LEU2241 (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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2183C HIS* 5.5 2.0 - - - +
2186C VAL* 4.4 25.1 - - + -
2187C VAL* 5.2 14.6 - - - +
2190C VAL* 5.0 16.0 - - + +
2191C ALA* 5.6 4.7 - - + +
2237C ILE* 3.5 8.1 - - + +
2238C ILE* 2.2 50.5 + - + +
2240C THR* 1.3 87.9 + - - +
2242C VAL* 1.3 49.1 + - - +
2244C CYS* 2.7 31.6 + - - +
2245C TRP* 2.7 36.8 + - + +
22K ALA* 5.3 5.4 - - + -
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Residues in contact with VAL2242 (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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2220C MET* 5.6 13.7 - - + -
2223C VAL* 5.8 1.6 - - + -
2235C LEU* 5.2 2.2 - - + -
2238C ILE* 2.8 28.2 + - + +
2239C LYS* 2.9 18.8 - - - +
2241C LEU* 1.3 72.2 - - - +
2243C GLU* 1.3 53.8 - - + +
2245C TRP* 2.7 24.0 - - + +
2246C LYS* 2.0 37.1 + - + +
2276C LEU* 3.6 30.7 - - + -
2279C ILE* 5.3 2.5 - - + -
2280C VAL* 4.4 10.8 - - + -
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Residues in contact with GLU2243 (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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2239C LYS* 2.9 28.8 + - - +
2240C THR* 2.4 36.7 + - - +
2242C VAL* 1.3 69.5 - - - +
2244C CYS* 1.3 59.1 + - - +
2245C TRP 2.8 1.4 + - - -
2246C LYS* 2.2 31.3 + - - +
2279C ILE* 3.6 28.2 - - + +
2283C ASN* 4.1 10.6 - - - +
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Residues in contact with CYS2244 (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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2190C VAL* 4.9 11.4 - - + -
2193C ILE* 6.1 1.2 - - - +
2194C LEU* 5.4 18.6 - - + -
2240C THR* 2.8 32.3 + - - -
2241C LEU* 2.7 24.9 + - - +
2243C GLU* 1.3 76.2 - - - +
2245C TRP* 1.3 64.7 + - - +
2246C LYS 3.5 0.3 + - - -
2247C ASP* 5.4 1.4 - - - +
22K ALA* 5.8 4.9 - - - -
25K ALA* 5.9 3.8 - - - -
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Residues in contact with TRP2245 (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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2164C TRP* 3.1 35.2 - + - -
2186C VAL* 5.4 0.4 - - + -
2190C VAL* 3.4 37.2 - - + -
2193C ILE* 5.8 4.0 - - + +
2203C THR* 5.5 4.9 - - - +
2212C ALA* 4.4 4.5 - - + -
2215C LEU* 3.6 23.8 - - + -
2216C LEU* 3.4 32.2 - - + +
2219C LEU* 3.9 15.0 - - + +
2241C LEU* 2.7 35.1 + - + +
2242C VAL* 2.7 23.5 + - + +
2243C GLU 2.8 2.2 + - - -
2244C CYS* 1.3 82.1 - - - +
2246C LYS* 1.3 78.2 + - + +
2247C ASP* 3.4 5.5 + - - +
2249C LEU* 3.2 28.0 - - + +
2253C TYR* 5.4 0.2 - - - +
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Residues in contact with LYS2246 (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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2242C VAL* 2.0 42.1 + - + +
2243C GLU* 2.2 28.5 + - - +
2244C CYS 3.5 1.2 + - - -
2245C TRP* 1.3 80.7 - - + +
2247C ASP* 1.3 70.7 + - - +
2248C CYS 5.1 3.8 - - - +
2249C LEU* 3.4 9.4 - - + -
2253C TYR* 3.6 32.3 - - + +
2280C VAL* 5.4 8.1 - - + -
2283C ASN* 3.3 44.2 - - + +
2284C ASP* 4.9 7.8 - - - +
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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