Contacts of the helix formed by residues 2297 - 2307 (chain B) in PDB entry 5WBY
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 ASP2297 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1402B LEU* 5.9 2.6 - - - +
1405B GLN* 5.4 3.4 - - - +
2253B TYR* 4.7 2.9 + - - -
2295B ALA* 3.3 22.7 - - - +
2296B GLY* 1.3 77.4 - - - +
2298B ASP* 1.3 62.4 + - - +
2299B LEU 3.4 2.5 - - - -
2300B ALA* 3.4 3.4 + - + -
2301B LYS* 2.9 59.3 + - + +
2382B MET* 5.3 0.9 - - - +
2385B ASN* 3.7 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP2298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2250B ILE* 4.3 9.6 - - + +
2253B TYR* 3.3 41.8 - - + -
2254B ARG* 2.7 39.4 + - - +
2259B ILE* 4.9 2.9 - - - +
2295B ALA* 3.2 20.6 - - - +
2296B GLY 3.7 1.4 - - - -
2297B ASP* 1.3 81.0 - - - +
2299B LEU* 1.3 58.0 + - - +
2301B LYS* 3.7 1.0 - - - +
2302B LEU* 2.8 35.3 + - + +
2382B MET* 3.7 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2246B LEU* 3.7 17.0 - - + -
2249B LEU* 4.5 4.5 - - + -
2250B ILE* 5.1 3.1 - - + +
2297B ASP 3.4 0.4 - - - -
2298B ASP* 1.3 75.8 - - - +
2300B ALA* 1.3 66.5 + - - +
2302B LEU* 3.7 19.3 - - + +
2303B LEU* 3.2 41.9 + - + +
2320B TYR* 3.9 4.3 - - + +
2346B LEU* 3.6 28.5 - - + -
2382B MET* 3.7 24.9 - - + +
2383B LEU* 3.7 29.8 - - + -
2386B ALA* 3.7 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2297B ASP* 3.4 7.7 + - + +
2299B LEU* 1.3 82.4 - - - +
2301B LYS* 1.3 62.6 + - + +
2303B LEU* 3.3 4.8 + - - +
2304B TRP* 3.2 18.9 + - - +
2313B TRP* 5.0 3.1 + - - -
2382B MET 4.6 1.0 + - - -
2385B ASN* 3.2 42.8 - - - +
2386B ALA* 3.8 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1398B HIS* 6.4 1.8 - - + -
1402B LEU* 5.3 19.5 - - - +
2253B TYR* 4.0 23.8 - - + +
2297B ASP* 2.9 39.9 + - + +
2298B ASP 3.9 2.2 - - - +
2300B ALA* 1.3 78.1 - - + +
2302B LEU* 1.3 61.5 + - - +
2304B TRP* 3.5 9.3 + - + +
2305B LEU* 3.2 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2249B LEU* 3.7 44.2 - - + +
2250B ILE* 4.4 4.7 - - + +
2253B TYR* 3.7 26.8 - - + -
2298B ASP 2.8 23.2 + - - +
2299B LEU* 3.6 24.5 - - + +
2301B LYS* 1.3 74.1 - - - +
2303B LEU* 1.3 72.2 + - + +
2305B LEU* 3.3 7.7 + - - +
2306B LYS* 3.0 53.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2249B LEU* 5.8 1.8 - - + -
2299B LEU* 3.2 45.8 + - + +
2300B ALA* 3.3 5.1 + - - +
2302B LEU* 1.3 82.2 - - + +
2304B TRP* 1.3 61.7 + - - +
2306B LYS* 4.0 24.7 + - + +
2307B SER* 3.8 13.3 + - - -
2313B TRP* 3.6 18.5 - - + +
2316B ARG* 5.5 9.1 + - + -
2317B ARG* 6.1 3.8 - - + -
2320B TYR* 5.2 13.0 - - + -
2346B LEU* 4.9 13.9 - - + -
2347B ASP 6.2 0.2 - - - +
2348B ARG* 6.1 2.9 - - - +
2351B GLY* 6.2 4.0 - - - -
2386B ALA* 4.4 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP2304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1395B LYS* 4.7 14.4 - - + -
1398B HIS* 3.3 61.4 + + + -
1399B TYR* 4.5 15.6 + + - -
2300B ALA 3.2 11.5 + - - +
2301B LYS* 3.5 14.6 - - + +
2302B LEU 3.2 0.6 - - - -
2303B LEU* 1.3 77.0 - - - +
2305B LEU* 1.3 80.0 + - + +
2307B SER* 2.7 25.3 + - - +
2309B SER 5.5 0.4 - - - -
2310B SER* 4.5 19.5 - - - -
2313B TRP* 3.6 46.4 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2253B TYR* 5.3 6.3 - - + -
2256B LYS* 4.1 16.2 - - - +
2257B LYS* 3.8 26.0 - - - +
2301B LYS* 3.2 26.0 + - + +
2302B LEU* 3.3 7.4 + - - +
2304B TRP* 1.3 94.9 - - + +
2306B LYS* 1.3 62.3 + - + +
2307B SER 3.4 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2244B ASP* 4.3 5.1 + - - -
2249B LEU* 3.7 24.3 - - + +
2302B LEU* 3.0 41.1 + - + +
2303B LEU* 4.2 21.1 - - - +
2304B TRP 3.4 0.2 - - - -
2305B LEU* 1.3 78.0 - - + +
2307B SER* 1.3 61.1 + - - +
2308B PRO* 3.7 4.3 - - - +
2316B ARG* 4.1 9.3 + - - +
2348B ARG* 3.8 35.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER2307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2303B LEU 3.8 7.9 + - - -
2304B TRP* 2.7 29.4 + - - +
2305B LEU 3.3 4.0 - - - +
2306B LYS* 1.3 78.4 - - - +
2308B PRO* 1.4 69.1 - - - +
2309B SER* 3.4 16.4 + - - -
2313B TRP* 3.6 29.4 - - - +
2316B ARG* 3.6 10.3 - - - +
----------------------------------------------------------
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