Contacts of the helix formed by residues 237 - 247 (chain J) in PDB entry 6QY3
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 ASN 237 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235J HIS 4.0 0.2 + - - -
236J ASN* 1.3 78.3 - - - +
238J PHE* 1.3 61.0 + - - +
239J VAL* 3.1 8.4 + - + +
240J LYS* 3.2 9.6 + - + +
241J ILE* 2.9 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 238 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172J ASP* 4.4 23.8 - - + +
176J ALA* 6.2 2.2 - - + +
236J ASN 4.8 0.2 - - - -
237J ASN* 1.3 74.0 - - - +
239J VAL* 1.3 57.6 + - - +
241J ILE* 3.7 8.3 - - - +
242J LYS* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 239 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237J ASN* 3.1 6.7 - - + +
238J PHE* 1.3 76.7 - - - +
240J LYS* 1.3 59.3 + - - +
242J LYS* 3.1 8.9 + - - +
243J LYS* 2.9 26.9 + - - +
110K TYR* 6.0 0.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 240 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233J ASN* 5.5 0.7 - - - -
236J ASN* 4.1 18.6 - - + -
237J ASN* 3.2 12.6 + - + +
239J VAL* 1.3 78.1 - - - +
241J ILE* 1.3 57.5 + - - +
243J LYS* 3.3 7.8 + - - +
244J GLU* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 241 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176J ALA* 4.9 18.9 - - + +
230J VAL* 6.3 2.2 - - - -
233J ASN* 4.4 28.7 - - + +
236J ASN* 4.9 1.5 - - - +
237J ASN 2.9 17.2 + - - +
238J PHE* 3.7 9.4 - - - +
239J VAL 3.2 0.2 - - - -
240J LYS* 1.3 76.9 - - - +
242J LYS* 1.3 58.4 + - - +
244J GLU* 3.5 2.5 + - - +
245J LEU* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 242 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176J ALA* 6.5 0.2 - - - -
238J PHE 2.9 18.3 + - - +
239J VAL* 3.4 7.9 - - - +
241J ILE* 1.3 75.4 - - - +
243J LYS* 1.3 59.7 + - - +
245J LEU* 3.3 8.3 + - - +
246J PHE* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 243 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239J VAL 2.9 13.5 + - - +
240J LYS* 3.7 10.8 - - - +
242J LYS* 1.3 75.0 - - - +
244J GLU* 1.3 60.0 + - - +
246J PHE* 3.0 10.5 + - - +
247J SER* 2.9 25.7 + - - -
110K TYR* 5.0 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 244 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229J ILE* 4.9 18.1 - - + +
233J ASN* 4.8 12.1 - - + -
240J LYS 2.9 17.8 + - - +
241J ILE* 3.8 7.9 - - - +
243J LYS* 1.3 76.3 - - - +
245J LEU* 1.3 60.8 + - - +
247J SER* 3.2 22.3 + - - -
248J ILE* 3.7 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 245 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176J ALA 6.1 0.9 - - - +
180J GLY* 5.7 9.9 - - - +
229J ILE* 5.5 5.1 - - - +
241J ILE 2.9 18.0 + - - +
242J LYS* 3.4 10.1 - - - +
243J LYS 3.2 0.2 - - - -
244J GLU* 1.3 76.3 - - - +
246J PHE* 1.3 61.3 + - - +
248J ILE* 3.4 20.7 + - - +
249J PHE 4.6 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 246 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242J LYS 2.9 12.8 + - - +
243J LYS* 3.0 12.1 + - - +
245J LEU* 1.3 72.3 - - - +
247J SER* 1.3 60.3 + - - +
248J ILE 3.1 6.5 + - - -
249J PHE* 3.5 18.1 + - - +
250J SER 4.2 1.4 + - - -
103K LEU* 4.9 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 247 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243J LYS 2.9 11.4 + - - -
244J GLU* 3.2 16.9 + - - -
246J PHE* 1.3 75.1 - - - +
248J ILE* 1.3 59.4 + - - +
249J PHE 3.2 0.7 - - - -
250J SER* 3.3 11.9 + - - +
251J GLU* 3.0 27.6 + - - +
----------------------------------------------------------
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