Contacts of the helix formed by residues 42 - 50 (chain D) in PDB entry 3ECS
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 42 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D GLY 3.1 31.4 + - - -
43D GLN* 1.3 63.5 + - - +
44D GLY* 3.8 6.1 - - - +
45D LEU* 3.2 46.8 - - + +
46D ARG* 3.3 17.2 + - - +
88D LYS* 3.1 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ILE* 1.3 71.4 - - - +
44D GLY* 1.3 68.3 + - - +
46D ARG* 3.3 7.9 + - - +
47D ALA* 3.1 19.9 + - - +
78D LEU* 4.9 12.6 - - - +
87D SER* 3.8 27.2 - - - -
88D LYS* 4.1 25.5 - - + +
93D MSE 5.9 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ILE* 3.6 8.4 - - - +
43D GLN* 1.3 77.5 - - - +
45D LEU* 1.3 66.2 + - - +
47D ALA* 3.0 21.2 + - - +
48D ASN* 3.2 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D GLY* 3.9 25.1 - - - -
42D ILE* 3.2 48.7 - - + +
44D GLY* 1.3 74.5 - - - +
46D ARG* 1.3 66.2 + - - +
47D ALA 2.7 1.2 + - - -
48D ASN* 3.0 3.0 + - - +
49D LEU* 2.7 46.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D LEU* 3.7 31.9 - - + -
37D ASP* 2.7 48.5 + - - +
38D LYS* 4.3 0.8 - - - +
39D GLY 3.1 25.2 + - - -
42D ILE 3.3 7.2 + - - +
43D GLN* 3.4 11.2 - - - +
45D LEU* 1.3 77.9 - - - +
47D ALA* 1.3 57.4 + - - +
49D LEU* 3.6 1.2 - - - +
50D THR* 2.8 35.8 + - + +
88D LYS* 2.9 32.5 - - - +
91D LYS* 2.5 45.6 - - - +
93D MSE 4.9 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D GLN 3.1 11.1 + - - +
44D GLY* 3.0 14.1 + - - +
45D LEU 2.7 4.6 + - - -
46D ARG* 1.3 70.9 - - - +
48D ASN* 1.3 63.1 + - - +
49D LEU 3.0 4.2 + - - -
50D THR* 3.2 11.2 - - - +
51D SER* 3.1 20.6 + - - -
73D LEU* 5.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D GLY 3.2 5.1 + - - +
45D LEU* 3.0 7.3 + - - +
47D ALA* 1.3 76.2 - - - +
49D LEU* 1.3 58.1 + - + +
51D SER* 3.5 11.1 + - - -
52D ALA* 2.6 42.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D PHE* 4.1 7.4 - - + -
37D ASP* 3.5 32.3 - - - +
39D GLY* 4.7 9.0 - - - -
45D LEU* 2.7 57.6 + - + +
46D ARG* 3.6 2.2 - - - +
48D ASN* 1.3 78.5 - - + +
50D THR* 1.3 58.3 + - - +
51D SER 2.8 8.2 + - - -
52D ALA* 3.4 5.2 + - + -
53D ILE* 2.9 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D LEU* 4.0 14.4 + - - +
33D PHE* 4.1 11.6 - - - -
34D LEU* 4.7 17.0 - - + +
46D ARG* 2.8 21.3 + - + +
47D ALA* 3.2 13.2 - - - +
49D LEU* 1.3 74.9 - - - +
51D SER* 1.3 53.9 + - - +
53D ILE* 3.3 26.1 - - - +
54D GLU* 3.7 17.2 - - - +
72D PHE* 5.2 2.8 - - - -
73D LEU* 3.7 26.9 - - + +
76D ILE* 6.0 3.1 - - + -
----------------------------------------------------------
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