Contacts of the helix formed by residues 35 - 46 (chain B) in PDB entry 1XDM
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 SER 35 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ASP 3.2 3.6 + - - -
34B GLU* 1.3 73.0 - - - +
36B VAL* 1.3 69.8 + - - +
37B GLY* 4.1 3.3 + - - -
38B THR* 2.6 39.2 + - - -
39B MET* 3.0 2.2 + - - -
79B PHE* 4.0 23.6 - - - -
107B LYS* 4.4 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLU 3.7 2.2 + - - -
35B SER* 1.3 71.6 - - - +
37B GLY* 1.3 70.3 + - - +
38B THR 2.9 0.5 + - - -
39B MET* 2.9 16.9 + - - +
40B GLY 3.0 9.7 + - - -
50B ASN* 3.9 8.1 - - - +
55B ARG* 3.8 38.8 - - - +
79B PHE* 3.8 22.6 - - + -
81B GLU* 4.4 3.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B SER* 3.1 4.8 + - - -
36B VAL* 1.3 82.5 - - - +
38B THR* 1.3 53.3 - - - +
40B GLY* 3.4 2.3 + - - -
41B ASN* 2.5 34.0 + - - -
50B ASN* 5.0 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLU* 3.9 14.6 - - + -
35B SER* 2.6 36.1 + - - -
37B GLY* 1.3 66.5 - - - +
39B MET* 1.3 58.2 + - - +
40B GLY 3.0 1.3 - - - -
41B ASN* 2.7 36.6 + - - +
42B ARG* 3.0 40.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLU* 3.9 22.8 - - + +
35B SER 3.0 5.3 + - - +
36B VAL 2.9 11.9 + - - +
38B THR* 1.3 76.0 - - - +
40B GLY* 1.3 57.5 + - - +
42B ARG* 3.2 24.5 - - + +
43B LEU* 3.0 45.5 + - + +
55B ARG* 3.5 27.1 - - + -
58B PHE* 4.6 10.8 - - + -
59B ARG* 3.1 40.6 - - - +
306B GLN* 4.9 2.5 - - - +
310B LEU* 4.1 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL 3.0 8.9 + - - -
37B GLY 3.8 3.4 - - - -
38B THR 3.0 1.6 - - - -
39B MET* 1.3 74.6 - - - +
41B ASN* 1.3 54.0 + - - +
42B ARG 3.1 1.8 - - - -
43B LEU* 3.8 3.3 - - - +
44B GLN* 2.6 38.8 + - - +
48B VAL 4.9 0.9 - - - +
50B ASN* 3.2 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLY 2.5 32.0 + - - -
38B THR* 2.7 18.7 + - - +
40B GLY* 1.3 72.3 - - - +
42B ARG* 1.3 66.7 + - - +
44B GLN* 3.3 21.1 - - - +
45B ARG* 3.2 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLU* 4.4 15.5 + - - +
38B THR* 3.0 36.0 + - + +
39B MET* 3.2 29.6 - - + +
41B ASN* 1.3 77.5 - - - +
43B LEU* 1.3 61.8 + - - +
45B ARG* 2.8 58.0 + - - +
46B ILE* 3.5 7.1 + - - +
303B ARG* 3.6 40.8 - - - +
306B GLN* 6.5 0.9 - - - -
310B LEU* 4.0 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B MET* 3.0 26.2 + - + +
40B GLY* 3.8 3.6 - - - +
42B ARG* 1.3 79.3 - - - +
44B GLN* 1.3 58.3 + - - +
46B ILE* 2.8 47.7 + - + +
48B VAL* 2.8 30.3 + - + +
49B GLU 3.9 15.0 - - - +
50B ASN* 4.2 16.6 - - - +
54B ASN* 4.2 15.7 - - + -
55B ARG* 4.3 13.7 - - + +
58B PHE* 5.1 3.4 - - + -
310B LEU* 3.8 9.6 - - + -
313B TRP* 3.7 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B GLY 2.6 23.5 + - - +
41B ASN* 3.3 23.7 - - - +
42B ARG 3.0 0.2 - - - -
43B LEU* 1.3 74.0 - - - +
45B ARG* 1.3 56.5 + - - +
47B LYS* 3.0 20.2 + - - +
48B VAL 3.9 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ASN* 3.2 25.2 + - - +
42B ARG* 2.8 44.3 + - - +
44B GLN* 1.3 76.3 - - - +
46B ILE* 1.3 60.4 + - + +
47B LYS* 3.1 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ARG 3.5 4.9 + - - +
43B LEU* 2.8 41.2 + - + +
45B ARG* 1.3 78.8 - - + +
47B LYS* 1.3 76.5 + - - +
48B VAL* 3.2 23.6 + - + +
310B LEU* 3.4 55.0 - - + +
311B ALA* 3.9 16.2 - - + +
313B TRP* 3.8 7.6 - - + -
314B GLY* 4.2 12.8 - - - +
315B GLY 4.3 1.3 - - - +
----------------------------------------------------------
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