Contacts of the helix formed by residues 43 - 48 (chain B) in PDB entry 1S9C
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 ASP 43 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLY 4.7 0.3 - - - +
36B ALA* 3.4 14.5 - - + -
37B SER* 3.0 46.4 + - - +
40B ASP* 2.7 21.6 + - - +
42B LYS* 1.3 71.1 - - - +
44B LEU* 1.3 62.4 + - - +
45B LYS 2.8 6.3 - - - -
46B PHE* 2.8 32.4 + - - +
47B ILE* 3.3 15.7 + - + +
225B ARG* 4.4 9.7 + - - +
229B GLN* 4.1 17.7 + - - -
234B ASN* 4.3 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ILE* 4.1 24.5 - - + +
200A ASP* 5.0 2.2 - - - +
201A PRO* 4.0 27.6 - - + -
38B ILE* 4.2 18.3 - - + +
40B ASP 3.9 1.2 + - - -
41B PRO* 3.1 20.6 + - + +
43B ASP* 1.3 76.9 - - - +
45B LYS* 1.3 57.5 + - - +
47B ILE* 3.8 5.4 - - - +
48B TYR* 2.9 60.2 + - + +
51B SER* 3.9 8.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PRO 4.6 0.2 + - - -
42B LYS 3.4 15.6 + - - +
44B LEU* 1.3 79.2 - - - +
46B PHE* 1.3 72.0 + - + +
51B SER* 4.1 11.6 + - - -
53B ASP* 3.4 43.8 + - + +
54B PHE* 3.2 10.3 - - - -
55B SER* 3.0 52.7 + - - +
233B ASP 4.7 1.2 + - - -
234B ASN* 2.4 41.4 + - + +
235B ASP* 4.0 7.3 + - - +
236B VAL* 4.2 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ALA 4.9 0.5 - - - +
28B ILE* 3.8 13.5 + - - +
31B ALA* 3.6 28.8 - - + +
36B ALA* 4.6 5.4 - - + -
42B LYS 4.5 4.3 - - - -
43B ASP* 2.8 29.1 + - - +
45B LYS* 1.3 91.2 - - + +
47B ILE* 1.3 63.0 + - + +
48B TYR 3.8 0.2 - - - -
54B PHE* 4.0 6.1 - - - -
55B SER* 3.7 19.1 - - - +
57B LEU* 3.5 30.5 - - + -
225B ARG* 5.3 4.7 - - + -
228B LEU* 3.7 19.7 - - + -
234B ASN* 3.8 36.1 - - + -
236B VAL* 3.9 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ASN* 4.0 2.9 - - - +
186A ALA* 3.7 27.3 - - + +
189A ARG* 4.0 7.4 + - - -
199A ILE* 4.2 5.6 - - + +
28B ILE* 3.2 35.0 - - + +
31B ALA* 5.1 0.7 - - + -
32B LEU* 4.1 11.0 - - + -
36B ALA* 3.9 14.8 - - + +
37B SER* 3.6 18.6 - - - +
38B ILE* 3.5 41.7 - - + +
43B ASP 3.3 16.7 + - - +
44B LEU* 4.3 2.0 - - - +
46B PHE* 1.3 84.0 - - - +
48B TYR* 1.3 58.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ARG* 3.8 3.8 - - - -
196A PRO* 3.5 28.3 - - + +
199A ILE* 3.6 35.9 - - + -
200A ASP* 3.5 32.2 + - + +
44B LEU* 2.9 30.9 + - + +
47B ILE* 1.3 77.2 - - - +
49B GLU* 1.3 80.2 + - - +
50B GLY* 3.3 35.3 - - - -
51B SER* 3.0 31.9 + - - -
54B PHE* 3.0 14.9 - - - -
----------------------------------------------------------
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