Contacts of the strand formed by residues 244 - 247 (chain C) in PDB entry 3MX0
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 ARG 244 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C PHE* 3.7 5.1 - - - -
225C THR* 4.7 17.7 + - + +
226C VAL 3.5 4.9 - - - +
227C ALA* 4.0 21.5 - - + +
241C GLU* 4.2 12.5 + - - -
242C GLU* 3.2 24.0 + - + +
243C PRO* 1.3 79.9 - - - +
245C MET* 1.3 62.5 + - - +
246C HIS* 4.4 9.2 + - + -
255C VAL 4.0 1.0 - - - +
256C PRO* 4.1 0.3 - - - +
257C ILE* 2.9 76.9 + - - +
258C GLY 4.7 0.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 245 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C LEU* 3.6 27.4 - - + -
206C GLN* 4.4 14.1 - - + +
211C PHE* 3.4 41.4 - - + -
224C ALA 3.2 2.3 - - - +
225C THR* 3.7 2.3 - - - -
226C VAL* 2.8 35.4 + - - +
244C ARG* 1.3 73.2 - - - +
246C HIS* 1.3 75.5 + - - +
253C TRP* 3.7 36.8 - - + -
254C LEU 4.5 4.3 - - - -
255C VAL 4.4 0.4 - - - -
256C PRO* 3.9 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 246 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C LEU* 4.2 20.4 - - + -
224C ALA 3.2 14.6 - - - -
225C THR* 3.3 19.9 + - - -
244C ARG* 4.4 10.2 + - - -
245C MET* 1.3 87.7 - - - +
247C CYS* 1.3 58.4 + - - +
248C ALA 4.0 1.1 - - - -
252C GLU 3.7 0.9 - - - +
253C TRP* 3.1 15.1 - - - -
254C LEU* 2.9 31.6 + - + +
255C VAL* 2.9 52.2 + - + +
257C ILE* 3.7 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C CYS* 2.1 44.4 - - - -
214C THR* 3.7 14.8 - - - -
215C ILE 4.5 1.1 - - - -
216C ALA* 4.1 13.6 - - - -
217C GLY 5.0 2.6 + - - -
222C SER 4.5 0.5 - - - +
223C LEU* 3.9 1.1 - - - -
224C ALA* 3.0 46.4 + - + +
226C VAL* 4.2 2.0 - - + -
246C HIS* 1.3 72.7 - - - +
248C ALA* 1.3 64.7 + - - +
253C TRP* 3.6 15.3 - - + -
----------------------------------------------------------
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