Contacts of the helix formed by residues 301 - 311 (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 GLY 301 (chain B).
----------------------------------------------------------
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
Residues in contact with GLU 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ARG* 3.2 55.3 + - - +
233B ASP* 6.1 0.7 - - - +
235B ARG* 5.9 2.4 + - - +
300B VAL 3.4 8.2 + - - +
301B GLY* 1.4 67.9 - - - -
303B GLU* 1.4 62.2 + - + +
305B ARG* 4.3 11.7 - - - +
306B ASN* 2.9 48.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LYS* 3.7 27.1 + - - +
62B LYS* 5.9 2.3 + - - -
65B THR* 6.2 0.3 - - - +
66B ASP* 5.3 4.7 - - - +
229B LYS* 3.5 29.1 - - - -
233B ASP* 4.9 7.2 - - - +
236B LEU* 6.0 1.9 - - - +
301B GLY 3.4 0.4 - - - -
302B GLU* 1.4 75.9 - - + +
304B PHE* 1.3 68.0 + - + +
306B ASN* 4.0 4.4 - - - +
307B TYR* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B VAL* 4.4 21.1 - - + -
54B ILE* 4.5 34.3 - - + +
55B LEU* 4.2 24.5 - - + -
59B LYS* 4.5 6.7 - - + +
69B LEU* 4.2 20.2 - - + -
236B LEU* 4.9 5.6 - - + -
297B TYR* 3.4 54.5 - + + +
298B ALA* 4.7 3.5 - - - +
301B GLY* 3.5 8.4 + - - +
302B GLU 3.4 0.2 - - - -
303B GLU* 1.3 85.5 - - + +
305B ARG* 1.4 59.7 + - - +
307B TYR* 3.4 8.5 + - - +
308B LEU* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B TYR 4.1 0.2 + - - -
298B ALA 3.7 24.7 - - - +
299B PHE* 4.5 12.3 - - - +
300B VAL 6.1 0.2 - - - -
301B GLY 2.8 24.2 + - - +
302B GLU* 3.9 11.5 + - - +
304B PHE* 1.4 72.9 - - - +
306B ASN* 1.4 75.1 + - - +
308B LEU* 3.2 8.1 + - - +
309B LEU* 2.9 49.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B GLU* 2.9 36.7 + - - +
303B GLU* 4.2 5.0 - - - +
305B ARG* 1.4 85.9 + - - +
307B TYR* 1.4 58.9 + - - +
309B LEU* 3.8 11.8 - - - +
310B VAL* 2.9 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ILE* 3.8 37.4 - - + +
58B TYR* 3.4 55.6 - + + +
59B LYS* 3.8 9.6 - - - +
303B GLU 3.0 20.5 + - - +
304B PHE* 3.4 8.3 - - - +
305B ARG 3.3 0.2 - - - -
306B ASN* 1.4 75.6 - - - +
308B LEU* 1.4 60.5 + - + +
310B VAL* 3.6 4.4 + - - +
311B PHE* 3.0 44.9 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ALA* 5.9 4.5 - - + +
304B PHE 3.0 13.1 + - - +
305B ARG* 3.2 9.6 + - - +
307B TYR* 1.4 78.9 - - + +
309B LEU* 1.4 52.8 + - + +
311B PHE* 2.8 34.9 - - + +
312B PHE* 3.2 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B ARG* 2.9 50.7 + - + +
306B ASN* 3.4 12.5 + - - +
308B LEU* 1.4 77.7 - - + +
310B VAL* 1.4 57.2 + - - +
311B PHE 3.0 9.2 - - - +
312B PHE* 5.0 4.3 - - + +
313B GLN 4.4 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ASN 2.9 17.9 + - - +
307B TYR* 4.1 4.7 - - - +
309B LEU* 1.4 70.6 - - - +
311B PHE* 1.4 64.0 + - - +
313B GLN* 3.7 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B TYR* 3.0 37.7 + + + +
308B LEU* 2.8 19.9 + - + +
309B LEU 3.0 8.1 - - - +
310B VAL* 1.4 78.3 - - - +
312B PHE* 1.3 109.3 + + - +
313B GLN 3.2 1.1 - - - +
----------------------------------------------------------
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