Contacts of the helix formed by residues 2210 - 2230 (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 VAL2210 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2208C ASP 3.1 2.7 - - - -
2209C GLU* 1.3 79.5 - - + +
2211C LEU* 1.3 79.1 + - + +
2212C ALA 3.7 0.2 - - - -
2213C ASN* 3.3 20.6 + - + +
2214C ARG* 3.2 51.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2211 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2161C ALA* 4.5 30.3 - - + +
2164C TRP* 4.5 19.1 - - + -
2165C LEU* 5.5 8.1 - - + +
2168C LEU* 4.1 3.6 - - + +
2207C LYS* 3.0 31.4 - - + +
2208C ASP* 2.3 31.6 + - - +
2209C GLU* 5.6 0.7 - - + +
2210C VAL* 1.3 83.4 - - + +
2212C ALA* 1.3 65.0 + - - +
2214C ARG* 3.1 27.3 + - - +
2215C LEU* 3.0 20.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2212 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2164C TRP* 3.4 18.6 - - + -
2208C ASP* 2.4 45.3 + - - +
2211C LEU* 1.3 69.2 - - - +
2213C ASN* 1.3 57.6 + - - +
2215C LEU* 3.4 16.6 - - + -
2216C LEU* 2.8 41.2 + - + +
2245C TRP* 4.4 7.9 - - + -
2249C LEU* 5.8 4.0 - - + -
2250C SER* 4.2 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2213 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2209C GLU 5.2 1.6 - - - +
2210C VAL* 3.3 15.2 + - + +
2211C LEU 3.0 1.0 + - - -
2212C ALA* 1.3 80.2 - - - +
2214C ARG* 1.3 67.9 + - + +
2216C LEU* 3.2 4.0 + - - +
2217C ASN* 3.0 29.1 + - - +
2250C SER* 3.4 30.7 + - - +
2251C ILE 4.2 0.4 + - - -
2252C PRO* 3.2 32.2 - - - +
2255C LEU* 6.3 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2214 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2165C LEU* 5.0 4.0 - - - +
2168C LEU* 3.2 37.4 - - + +
2210C VAL* 3.2 44.8 + - + +
2211C LEU* 3.1 36.0 + - - +
2213C ASN* 1.3 79.4 - - + +
2215C LEU* 1.3 67.9 + - - +
2217C ASN* 2.9 24.6 + - - +
2218C PHE* 3.0 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2215 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2164C TRP* 3.4 61.0 - - + +
2167C PRO* 3.5 28.9 - - + -
2168C LEU* 3.5 13.2 - - + +
2186C VAL* 6.3 0.4 - - + -
2189C ILE* 5.5 0.9 - - + -
2190C VAL* 5.4 0.9 - - + -
2211C LEU 3.0 13.5 + - - +
2212C ALA* 3.1 11.9 - - - +
2214C ARG* 1.3 80.9 - - - +
2216C LEU* 1.3 62.5 + - - +
2218C PHE* 3.1 3.4 + - - +
2219C LEU* 2.8 38.7 + - + +
2245C TRP* 3.6 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2212C ALA* 2.8 35.6 + - + +
2213C ASN* 3.4 2.9 - - - +
2215C LEU* 1.3 70.9 - - - +
2217C ASN* 1.3 67.1 + - - +
2219C LEU* 2.8 7.8 + - + -
2220C MET* 2.7 48.4 + - + +
2245C TRP* 3.4 50.5 - - + +
2249C LEU* 5.3 3.8 - - + -
2250C SER* 4.6 6.3 - - - +
2252C PRO* 3.6 27.1 - - + -
2253C TYR* 4.1 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2217 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2213C ASN* 3.0 24.8 + - - +
2214C ARG* 2.9 21.4 + - - +
2216C LEU* 1.3 77.2 - - - +
2218C PHE* 1.3 65.0 + - - +
2220C MET* 3.4 9.4 - - - +
2221C LYS* 2.8 23.0 + - - +
2252C PRO* 2.8 31.8 - - - +
2255C LEU* 5.6 2.6 - - - +
2259C LYS* 4.6 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE2218 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2167C PRO* 4.3 16.4 - - + -
2168C LEU* 4.7 11.7 - - + +
2171C LEU* 4.4 17.5 - - + -
2172C ALA* 4.3 30.7 - - + -
2175C GLU* 5.2 7.9 - - - -
2182C ILE* 5.2 5.4 - - + -
2214C ARG 3.0 7.0 + - - +
2215C LEU* 3.5 7.0 - - - +
2217C ASN* 1.3 77.8 - - - +
2219C LEU* 1.3 103.2 + - + +
2221C LYS* 2.7 20.7 + - + +
2222C HIS* 2.8 40.7 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2219 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2167C PRO* 4.3 9.2 - - + -
2171C LEU* 5.6 1.6 - - + -
2182C ILE* 5.6 6.8 - - + +
2186C VAL* 5.0 20.0 - - + -
2215C LEU* 2.8 53.1 + - + +
2216C LEU* 2.8 16.3 + - + +
2218C PHE* 1.3 99.8 - - + +
2220C MET* 1.3 66.8 + - + +
2222C HIS* 3.4 3.5 + - - +
2223C VAL* 2.9 25.9 + - - +
2238C ILE* 5.8 6.5 - - + -
2245C TRP* 3.9 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET2220 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2216C LEU* 2.7 52.7 + - + +
2217C ASN* 3.3 12.6 - - - +
2219C LEU* 1.3 72.2 - - + +
2221C LYS* 1.3 66.0 + - - +
2223C VAL* 2.8 20.9 + - - -
2224C PHE* 2.9 39.0 + - + -
2238C ILE* 6.0 0.2 - - - +
2242C VAL* 5.6 15.0 - - + -
2252C PRO* 3.8 10.8 - - + -
2253C TYR* 5.5 1.3 - - - -
2256C ILE* 3.6 27.6 - - + -
2259C LYS* 3.5 22.2 - - - +
2276C LEU* 5.1 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2221 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2217C ASN 2.8 17.0 + - - +
2218C PHE* 2.7 23.8 + - + +
2220C MET* 1.3 72.4 - - - +
2222C HIS* 1.3 67.7 + - - +
2224C PHE* 2.9 28.9 - - + +
2225C HIS* 4.0 19.9 + - - +
2259C LYS* 5.6 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS2222 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2175C GLU 5.5 0.7 - - - -
2176C ASN* 4.1 19.6 + - + -
2182C ILE* 3.2 51.3 - - + +
2218C PHE* 2.8 37.1 + + + +
2219C LEU 3.5 7.2 + - - +
2221C LYS* 1.3 78.8 - - - +
2223C VAL* 1.3 74.5 + - + +
2224C PHE 2.6 14.4 + - - -
2225C HIS* 3.0 15.8 + - - +
2226C PRO* 3.0 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2223 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2182C ILE* 6.0 2.7 - - + -
2219C LEU 2.9 15.4 + - - +
2220C MET* 2.8 26.5 + - - +
2222C HIS* 1.3 83.4 - - + +
2224C PHE* 1.3 72.5 + - + +
2226C PRO* 3.2 9.4 - - + +
2227C LYS 4.4 1.2 + - - -
2235C LEU* 3.4 45.0 - - + +
2238C ILE* 3.5 40.6 - - + -
2242C VAL* 5.8 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE2224 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2220C MET* 2.9 44.4 - - + -
2221C LYS* 2.9 34.5 - - + +
2222C HIS 2.6 4.0 + - - -
2223C VAL* 1.3 80.5 - - + +
2225C HIS* 1.3 77.3 + - + +
2227C LYS* 4.0 5.5 - - - +
2235C LEU* 4.4 1.4 - - + +
2259C LYS* 3.7 30.7 - - + -
2272C VAL* 3.3 50.8 - - + +
2273C GLY* 6.2 1.6 - - - -
2276C LEU* 4.9 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS2225 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2221C LYS* 4.0 30.5 + - - -
2222C HIS* 3.0 9.4 + - - -
2224C PHE* 1.3 84.0 - - + +
2226C PRO* 1.3 56.5 - - + -
2227C LYS 2.5 1.2 + - - -
2228C ARG* 2.0 88.3 + - + -
2229C ALA* 3.6 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO2226 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2176C ASN* 5.2 8.3 - - - +
2182C ILE* 5.9 0.4 - - + -
2222C HIS* 3.0 60.6 - - + +
2223C VAL* 3.2 14.4 - - + +
2225C HIS* 1.3 76.8 - - + +
2227C LYS* 1.3 50.4 + - - +
2229C ALA* 3.1 16.3 - - + +
2230C VAL* 2.4 41.1 + - + +
2231C PHE 4.6 0.2 - - - -
2234C ASN* 5.5 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2227 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2223C VAL 4.4 1.0 + - - -
2224C PHE 4.0 8.7 - - - +
2225C HIS 2.5 3.9 + - - +
2226C PRO* 1.3 73.9 - - - +
2228C ARG* 1.3 64.4 + - - +
2230C VAL 3.0 13.0 + - - +
2231C PHE* 3.0 24.6 + - - +
2232C ARG* 3.1 56.1 - - + +
2234C ASN* 4.8 3.0 - - - +
2235C LEU* 4.1 22.3 - - + +
2236C GLU* 3.0 28.3 - - - +
2271C SER* 5.4 7.1 - - - -
2272C VAL* 5.0 9.1 - - + +
2275C GLN* 4.2 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2228 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2224C PHE 4.1 2.4 + - - +
2225C HIS* 2.0 68.3 + - + +
2227C LYS* 1.3 72.5 - - - +
2229C ALA* 1.3 62.3 + - - +
2230C VAL 5.0 0.3 - - - +
2269C ASP* 2.9 45.4 + - - +
2272C VAL* 5.4 6.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2229 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2225C HIS* 2.9 8.6 + - + +
2226C PRO* 3.1 20.2 - - + +
2228C ARG* 1.3 82.3 - - - +
2230C VAL* 1.3 71.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2230 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2226C PRO* 2.4 28.9 + - + +
2227C LYS 3.3 4.4 - - - +
2228C ARG 5.0 0.3 - - - +
2229C ALA* 1.3 82.1 - - + +
2231C PHE* 1.3 85.2 + - + +
2234C ASN* 4.8 2.9 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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