Contacts of the strand formed by residues 299 - 304 (chain B) in PDB entry 1MPX
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 THR 299 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LEU* 3.6 33.6 - - + +
194B ALA* 3.3 4.2 - - - +
196B PRO* 3.7 22.7 - - + -
297B VAL 2.8 17.9 + - - -
298B PRO* 1.3 72.0 + - - +
300B MSE 1.3 63.4 + - - +
301B TRP* 3.7 25.6 - - + +
321B MSE 5.5 5.0 - - - -
330B LEU 2.9 9.9 + - - -
331B ASN* 3.5 5.5 - - - +
332B TYR* 2.8 27.5 + - - +
371B PHE* 4.4 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ALA 2.9 7.9 + - - -
195B VAL* 3.5 22.1 - - + +
196B PRO* 3.2 18.0 - - - +
299B THR* 1.3 71.9 - - - +
301B TRP* 1.3 61.5 + - - +
302B LEU* 3.5 2.9 + - + -
332B TYR* 3.7 18.2 - - + -
334B VAL* 3.7 21.8 - - + -
363B PHE* 3.7 30.7 - - + -
367B VAL* 3.7 15.0 - - + -
368B LEU* 4.9 4.0 - - - -
371B PHE* 3.8 32.5 - - + -
385B THR* 3.5 32.5 - - + -
386B PRO 5.3 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B VAL* 3.5 33.0 - - + -
184B LEU* 4.5 2.0 - - + -
196B PRO* 3.7 18.2 - - + -
199B PRO* 4.1 12.6 - - + -
290B MSE 3.9 17.9 - - + -
299B THR* 3.7 20.6 - - + +
300B MSE 1.3 70.6 - - - +
302B LEU* 1.3 58.7 + - - +
314B ALA* 3.6 22.9 - - + +
317B SER* 3.5 36.3 - - - -
318B TYR* 3.6 19.7 - - + +
321B MSE 3.8 22.3 - - - -
331B ASN* 3.0 27.6 + - - -
332B TYR 2.9 17.7 + - - +
333B LEU* 3.4 4.9 - - + +
334B VAL* 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B VAL* 4.7 2.2 - - + -
196B PRO 3.1 12.1 + - - +
197B GLU* 3.5 28.4 - - + +
198B SER* 2.6 32.0 + - - +
300B MSE 4.4 4.5 - - - +
301B TRP* 1.3 75.4 - - - +
303B GLN* 1.3 67.8 + - - +
314B ALA* 3.3 9.0 - - - +
334B VAL* 3.3 29.8 - - + +
338B TRP* 3.9 10.5 - - + -
343B VAL* 3.9 22.2 - - + -
363B PHE* 3.3 41.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B SER* 3.5 19.7 - - - +
302B LEU* 1.3 80.7 - - - +
304B GLY* 1.3 75.3 + - - +
307B ASP* 3.9 2.9 - - - +
310B ASP 4.1 4.4 + - - +
311B MSE 2.9 42.7 + - - +
314B ALA* 3.3 14.0 + - + +
315B ILE* 3.0 27.1 + - - +
334B VAL 3.1 5.3 + - - +
335B MSE 3.2 53.6 - - + +
336B GLY 3.3 4.3 + - - -
338B TRP* 3.8 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B SER* 4.0 0.8 + - - -
303B GLN* 1.3 98.5 + - - +
305B LEU* 1.3 65.0 + - - -
306B TRP 3.1 2.2 - - - -
307B ASP* 3.3 20.4 + - - +
335B MSE 5.1 0.7 - - - -
336B GLY 3.6 6.7 - - - -
338B TRP* 3.4 26.2 - - - +
339B ARG 4.8 1.3 + - - -
----------------------------------------------------------
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