Contacts of the helix formed by residues 2269 - 2282 (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 ASP2269 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2228C ARG* 2.9 51.8 + - - +
2263C LYS* 2.5 36.9 + - + -
2267C SER* 3.1 6.0 - - - -
2268C LYS* 1.3 78.6 - - - +
2270C ASN* 1.3 61.1 + - - +
2271C SER 3.3 0.2 + - - -
2272C VAL* 3.9 7.9 + - - +
2273C GLY 3.8 4.9 + - - -
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Residues in contact with ASN2270 (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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2260C PHE* 3.3 10.1 - - + -
2263C LYS* 3.1 36.1 - - + +
2267C SER* 2.6 26.6 + - - +
2268C LYS* 2.7 10.9 - - - +
2269C ASP* 1.3 71.5 - - - +
2271C SER* 1.3 83.7 + - - -
2273C GLY* 2.5 27.5 + - - -
2274C ILE* 2.7 21.9 + - + +
2306C ASN* 4.2 12.0 + - - +
2309C PHE* 5.1 3.8 - - - +
2310C VAL* 6.1 3.0 - - - +
2314C GLU* 5.1 12.1 - - - +
2315C VAL* 5.5 5.1 - - - +
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Residues in contact with SER2271 (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* 5.4 6.3 - - - -
2268C LYS* 2.7 32.1 + - - +
2270C ASN* 1.3 87.1 + - - +
2272C VAL* 1.3 67.9 + - - +
2274C ILE* 2.8 25.0 - - - +
2275C GLN* 3.0 22.9 - - - +
2314C GLU* 4.2 15.5 - - - +
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Residues in contact with VAL2272 (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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2224C PHE* 3.3 64.4 - - + +
2225C HIS* 5.3 0.4 - - - -
2227C LYS* 5.0 12.3 - - + +
2228C ARG* 5.4 7.2 - - + +
2235C LEU* 4.0 19.2 - - + +
2268C LYS 4.4 0.9 + - - +
2269C ASP* 3.9 8.2 + - - +
2270C ASN 3.2 0.4 - - - -
2271C SER* 1.3 76.4 - - - +
2273C GLY* 1.3 71.6 + - - +
2275C GLN* 2.8 22.5 + - - +
2276C LEU* 2.9 13.7 + - + +
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Residues in contact with GLY2273 (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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2224C PHE* 6.1 1.8 - - - -
2260C PHE* 3.2 24.0 - - - -
2263C LYS* 4.2 1.5 - - - +
2269C ASP 3.8 2.8 + - - -
2270C ASN 2.5 12.9 + - - -
2272C VAL* 1.3 79.8 - - - +
2274C ILE* 1.3 50.8 + - - -
2276C LEU* 3.1 7.2 + - - +
2277C LEU* 2.7 42.5 + - - +
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Residues in contact with ILE2274 (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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2260C PHE* 3.3 30.1 - - + -
2270C ASN* 2.7 22.2 + - + +
2271C SER* 2.8 35.7 - - - +
2273C GLY* 1.3 69.1 - - - +
2275C GLN* 1.3 83.6 + - + +
2277C LEU* 2.6 23.5 + - + -
2278C GLY* 2.9 11.1 + - - -
2306C ASN* 4.9 4.7 - - - +
2314C GLU* 4.0 32.5 - - + +
2315C VAL* 5.6 5.8 - - + -
2318C ALA* 4.0 22.9 - - + +
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Residues in contact with GLN2275 (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* 4.2 27.5 + - - +
2232C ARG* 5.2 8.1 - - - +
2235C LEU* 5.2 2.8 - - - +
2236C GLU* 4.5 3.7 + - - +
2239C LYS* 3.2 26.8 + - - +
2271C SER* 3.0 28.3 - - - +
2272C VAL* 2.8 12.3 + - - +
2274C ILE* 1.3 88.9 - - + +
2276C LEU* 1.3 69.5 + - - +
2278C GLY* 3.5 1.6 + - - -
2279C ILE* 2.9 24.1 + - - +
2318C ALA* 5.7 1.3 - - - -
2321C GLU* 4.6 1.3 - - - +
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Residues in contact with LEU2276 (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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2220C MET* 5.1 5.6 - - + -
2224C PHE* 4.9 16.2 - - + -
2239C LYS* 4.4 9.9 - - + +
2242C VAL* 3.6 25.4 - - + -
2256C ILE* 3.6 30.7 - - + -
2272C VAL* 2.9 13.9 + - + +
2273C GLY* 3.1 10.8 - - - +
2275C GLN* 1.3 75.4 - - - +
2277C LEU* 1.3 55.2 + - + +
2279C ILE* 2.1 40.7 + - + -
2280C VAL* 2.7 40.9 + - + +
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Residues in contact with LEU2277 (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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2256C ILE* 3.6 29.2 - - + +
2257C PHE* 4.0 22.9 - - + -
2260C PHE* 3.2 49.4 - - + -
2273C GLY* 2.7 26.4 + - - +
2274C ILE* 2.6 15.9 + - + +
2276C LEU* 1.3 73.0 - - - +
2278C GLY* 1.3 57.1 + - - +
2280C VAL* 4.3 4.3 - - + -
2281C MET* 2.8 41.3 + - + +
2303C LEU* 4.2 12.6 - - + -
2322C VAL* 5.7 5.6 - - + -
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Residues in contact with GLY2278 (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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2274C ILE 2.9 10.6 + - - -
2275C GLN 3.9 1.6 - - - -
2276C LEU 2.7 2.6 + - - -
2277C LEU* 1.3 74.8 - - - +
2279C ILE* 1.3 50.1 + - - -
2281C MET* 3.4 4.1 - - - +
2282C ALA* 2.4 37.9 + - - +
2318C ALA* 5.3 3.7 - - - +
2321C GLU* 3.1 32.6 - - - +
2322C VAL* 5.1 10.7 - - - +
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Residues in contact with ILE2279 (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* 3.7 29.8 - - + +
2242C VAL* 5.3 1.1 - - + -
2243C GLU* 3.6 37.0 - - + +
2275C GLN 2.9 15.4 + - - +
2276C LEU* 2.1 29.6 + - + +
2278C GLY* 1.3 67.5 - - - -
2280C VAL* 1.3 61.7 + - - +
2282C ALA* 3.0 16.8 - - + +
2283C ASN* 2.8 13.8 + - - +
2321C GLU* 3.6 18.4 - - - +
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Residues in contact with VAL2280 (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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2242C VAL* 4.4 10.1 - - + -
2246C LYS* 5.4 8.3 - - + -
2253C TYR* 4.9 18.4 - - + -
2256C ILE* 4.1 21.3 - - + -
2257C PHE* 6.5 0.7 - - + -
2276C LEU* 2.7 46.9 + - + +
2277C LEU* 3.7 9.6 - - + +
2279C ILE* 1.3 69.2 - - - +
2281C MET* 1.3 65.1 + - + +
2283C ASN* 2.3 49.5 + - - +
2286C PRO* 6.3 0.9 - - + -
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Residues in contact with MET2281 (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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2257C PHE* 4.0 21.8 - - + -
2277C LEU* 2.8 30.9 + - + +
2278C GLY* 3.7 4.0 - - - +
2280C VAL* 1.3 82.3 - - + +
2282C ALA* 1.3 48.3 + - - +
2283C ASN 2.5 22.8 + - - +
2286C PRO* 3.4 37.2 - - + +
2290C PRO* 3.6 28.9 - - + -
2292C CYS* 5.2 3.4 - - + -
2321C GLU* 6.4 0.2 - - + -
2322C VAL* 5.8 14.4 - - + -
2326C ILE* 6.1 4.5 - - + -
2329C TYR* 2.0 38.2 + - + +
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Residues in contact with ALA2282 (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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2278C GLY 2.4 23.4 + - - +
2279C ILE* 3.0 20.0 - - + +
2280C VAL 2.8 0.4 + - - -
2281C MET* 1.3 69.7 - - - +
2283C ASN* 1.3 58.1 + - - +
2284C ASP* 3.2 10.6 + - - +
2321C GLU* 3.1 20.6 - - + +
2325C LEU* 5.3 7.0 - - + -
2329C TYR* 3.4 6.0 + - - -
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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