Contacts of the helix formed by residues 45 - 52 (chain A) in PDB entry 3S51
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 45 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 6.1 7.0 - - + -
41A ARG 3.8 10.7 + - - -
42A ALA* 4.2 2.4 + - - -
44A GLY* 1.3 74.2 - - - +
46A LEU* 1.3 65.8 + - - +
47A LEU 3.1 3.8 + - - -
48A ARG* 3.3 36.1 + - + +
49A ALA* 3.5 11.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ASP* 5.0 10.1 - - + +
5A ILE* 4.7 19.0 - - + +
32A LEU* 3.7 31.6 - - + -
35A ASN* 4.3 17.9 - - + +
42A ALA 3.6 13.1 + - - +
43A VAL* 3.0 31.2 + - + +
45A THR* 1.3 78.2 - - - +
47A LEU* 1.3 60.9 + - + +
49A ALA* 4.0 2.9 + - - +
50A VAL* 3.0 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 5.0 15.9 - - + -
43A VAL* 3.8 11.6 + - + +
45A THR 3.1 0.4 - - - -
46A LEU* 1.3 77.6 - - + +
48A ARG* 1.3 60.1 + - - +
49A ALA 3.1 2.2 - - - -
50A VAL* 2.8 6.5 + - + +
51A LEU* 2.5 49.4 + - + +
68A ILE* 3.8 28.9 - - + -
72A CYS* 4.0 22.4 - - - -
89A ILE* 4.7 13.0 - - + +
92A LEU* 4.0 33.0 - - + -
93A LEU* 4.4 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLY 4.6 1.6 - - - +
45A THR* 3.3 30.4 + - + +
47A LEU* 1.3 78.4 - - - +
49A ALA* 1.3 58.9 + - - +
51A LEU* 4.3 5.9 - - - +
52A LYS* 3.4 30.9 + - - +
92A LEU* 3.6 37.0 - - + +
96A GLU* 5.6 4.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 4.1 23.8 - - + +
6A LEU* 6.0 0.7 - - + -
9A ALA* 3.8 29.6 - - + -
17A LEU* 3.5 16.7 - - + +
45A THR* 3.5 12.2 + - + +
46A LEU* 4.4 2.2 - - - +
47A LEU 3.1 0.8 - - - -
48A ARG* 1.3 75.6 - - - +
50A VAL* 1.3 61.8 + - - +
52A LYS* 3.3 4.2 + - - +
53A GLY 2.9 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 4.3 18.8 - - + -
17A LEU* 5.6 0.2 - - - -
21A LEU* 4.1 23.9 - - + +
46A LEU* 3.0 35.4 + - + +
47A LEU* 2.8 10.3 + - + +
49A ALA* 1.3 73.8 - - - +
51A LEU* 1.3 53.5 + - - +
53A GLY* 3.2 7.9 + - - +
54A SER* 2.5 30.1 + - - +
64A ARG* 5.2 2.2 - - - +
68A ILE* 3.7 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 2.5 47.9 + - + +
48A ARG* 4.3 5.6 - - - +
50A VAL* 1.3 70.8 - - - +
52A LYS* 1.3 58.9 + - - +
53A GLY 3.1 4.9 - - - -
54A SER* 3.4 12.1 + - - +
55A PRO* 4.3 0.7 - - - +
65A ARG* 3.4 42.5 + - + +
68A ILE* 4.4 17.5 - - + -
69A TYR* 3.9 27.1 - - + +
92A LEU* 5.0 10.5 - - + +
93A LEU* 5.2 3.6 - - + -
96A GLU* 3.8 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A THR* 4.5 7.1 + - - -
17A LEU* 3.4 18.4 - - + +
18A GLN* 5.3 0.5 + - - -
48A ARG* 3.4 18.6 + - - +
49A ALA* 3.3 6.3 + - - +
51A LEU* 1.3 76.8 - - - +
53A GLY* 1.3 56.3 + - - +
54A SER 3.3 3.4 - - - -
55A PRO* 4.5 7.9 - - - +
65A ARG* 5.5 0.9 - - - +
96A GLU* 4.9 15.7 - - - +
----------------------------------------------------------
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