Contacts of the helix formed by residues 292 - 301 (chain B) in PDB entry 4MBS
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 ILE 292 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B VAL* 3.6 31.0 - - + -
247B PHE* 3.7 30.1 - - + -
288B THR* 3.7 21.5 - - + +
289B HIS* 3.3 18.2 + - + +
291B CYS* 1.4 84.0 - - - +
293B ASN* 1.4 62.0 + - - +
295B ILE* 2.9 36.7 + - + +
296B ILE* 3.2 17.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASN* 5.5 0.4 - - - +
72B LEU* 3.4 34.1 - - - +
76B ASP* 3.6 20.4 + - - +
119B ILE* 4.8 1.0 - - - +
240B ILE* 4.1 11.1 - - - +
243B VAL* 5.7 0.5 - - - +
289B HIS* 3.9 29.3 + - - -
290B CYS 5.3 0.2 - - - -
292B ILE* 1.4 74.4 - - - +
294B PRO* 1.4 68.1 - - + +
296B ILE* 3.0 44.7 + - + +
297B TYR* 3.1 22.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLY* 3.5 43.1 - - - +
48B ASN* 3.6 25.1 - - - +
51B VAL* 3.9 8.3 - - + -
76B ASP* 5.2 0.2 - - - +
290B CYS 4.7 0.9 - - - +
291B CYS* 3.3 20.6 - - - +
293B ASN* 1.4 91.7 - - + +
295B ILE* 1.4 60.1 + - + +
297B TYR* 3.7 15.0 + - + +
298B ALA* 3.4 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 4.7 21.3 - - + -
291B CYS* 3.7 24.0 - - - +
292B ILE* 2.9 26.0 + - + +
294B PRO* 1.4 74.4 - - + +
296B ILE* 1.4 63.9 + - + +
298B ALA* 3.4 10.1 + - + +
299B PHE* 3.2 48.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B LEU* 4.2 5.8 - - + -
239B THR* 4.8 6.3 - - + -
240B ILE* 3.2 42.6 - - + +
243B VAL* 4.7 16.2 - - + -
292B ILE* 3.2 27.8 + - + +
293B ASN* 3.0 36.5 + - - +
295B ILE* 1.4 73.4 - - + +
297B TYR* 1.4 65.2 + - + +
299B PHE* 3.1 2.6 + - - -
300B VAL* 2.7 49.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASN* 6.1 0.9 - - - -
51B VAL* 3.6 42.6 - - + -
69B LEU* 3.4 28.9 + - + +
72B LEU* 3.6 22.0 - - - +
73B ALA* 5.6 2.2 + - + -
236B LEU* 3.7 19.3 - - + -
240B ILE* 3.6 23.8 - - + -
293B ASN* 3.1 30.9 + - + +
294B PRO* 3.9 6.5 - - + +
295B ILE 3.4 0.2 - - - -
296B ILE* 1.4 79.5 - - + +
298B ALA* 1.3 60.5 + - - +
301B GLY* 3.1 33.1 + - - +
304B PHE* 3.4 34.3 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B PRO 3.4 11.0 + - - +
295B ILE* 3.4 13.6 + - + +
296B ILE 3.2 0.2 - - - -
297B TYR* 1.3 79.8 - - - +
299B PHE* 1.4 69.1 - - + +
304B PHE* 4.9 5.2 - - - -
305B ARG* 3.7 26.3 - - - +
308B LEU* 5.9 4.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ARG* 5.1 5.2 + - - -
295B ILE* 3.2 44.1 + - + +
296B ILE* 3.1 4.0 + - - +
298B ALA* 1.4 88.7 - - + +
300B VAL* 1.3 66.5 + - + +
301B GLY 5.1 0.9 - - - -
305B ARG* 4.5 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ARG* 4.0 40.5 + - + +
236B LEU* 4.0 23.9 + - + +
239B THR* 3.7 37.5 - - + +
296B ILE* 2.7 27.6 + - + +
299B PHE* 1.3 78.8 - - + +
301B GLY* 1.3 62.5 + - - +
302B GLU* 3.4 8.5 + - - +
305B ARG* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B LEU* 3.9 26.4 - - - +
296B ILE 3.6 1.8 + - - -
297B TYR* 3.1 16.4 + - - +
300B VAL* 1.3 76.8 - - - +
302B GLU* 1.4 54.5 + - - -
303B GLU 3.4 2.2 - - - -
304B PHE* 3.5 6.0 + - - -
305B ARG* 2.8 38.9 + - - +
----------------------------------------------------------
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