Contacts of the helix formed by residues 35 - 46 (chain W) 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 W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33W ASP 3.2 6.0 + - - -
34W GLU* 1.3 75.3 - - - +
36W VAL* 1.3 70.3 + - - +
37W GLY* 4.3 2.1 + - - -
38W THR* 3.0 26.7 + - - -
39W MET* 2.8 20.0 + - - +
79W PHE* 4.3 24.2 - - - -
107W LYS* 4.9 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34W GLU 3.9 0.2 + - - -
35W SER* 1.3 72.5 - - - +
37W GLY* 1.3 58.5 + - - +
39W MET* 3.2 2.4 + - - +
40W GLY 2.8 13.7 + - - -
50W ASN* 2.7 28.7 - - - +
55W ARG* 3.6 44.2 - - - +
79W PHE* 4.3 19.3 - - + -
81W GLU* 4.9 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 37 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35W SER* 3.3 3.0 + - - -
36W VAL* 1.3 78.4 - - - +
38W THR* 1.3 55.1 + - - +
40W GLY* 2.7 21.8 + - - -
41W ASN* 3.0 10.6 + - - +
50W ASN* 4.7 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 38 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34W GLU* 4.0 15.3 - - + -
35W SER* 3.0 29.0 + - - -
37W GLY* 1.3 73.1 - - - +
39W MET* 1.3 63.1 + - - +
41W ASN* 3.1 23.3 + - + +
42W ARG* 3.3 37.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 39 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34W GLU* 3.7 33.2 - - + +
35W SER 2.8 20.9 + - - +
36W VAL 3.5 3.6 - - - +
38W THR* 1.3 73.4 - - - +
40W GLY* 1.3 64.3 + - - +
42W ARG* 3.1 17.7 + - - +
43W LEU* 3.0 41.2 + - + +
55W ARG* 3.8 32.5 - - - -
58W PHE* 4.0 27.4 - - + -
59W ARG* 3.8 26.9 - - + +
306W GLN* 4.5 1.8 - - - +
310W LEU* 4.7 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 40 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36W VAL 2.8 6.9 + - - -
37W GLY* 2.7 10.6 + - - -
39W MET* 1.3 77.3 - - - +
41W ASN* 1.3 59.5 + - - +
43W LEU* 3.4 2.4 + - - +
44W GLN* 3.1 32.8 + - - +
50W ASN* 3.0 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 41 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37W GLY 3.0 7.2 + - - +
38W THR* 3.1 15.3 - - - +
40W GLY* 1.3 77.5 - - - +
42W ARG* 1.3 70.1 + - - +
43W LEU 3.2 0.5 + - - -
44W GLN* 3.2 28.6 + - - +
45W ARG* 2.7 51.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 42 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34W GLU* 5.2 7.6 - - + +
38W THR* 3.3 43.7 + - + +
39W MET* 3.1 22.9 + - - +
41W ASN* 1.3 79.8 + - - +
43W LEU* 1.3 61.1 + - - +
45W ARG* 3.2 58.4 - - - +
46W ILE* 3.6 9.2 + - - +
303W ARG* 4.3 33.1 - - - +
310W LEU* 4.0 21.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39W MET* 3.0 36.9 + - + +
40W GLY* 3.6 5.2 - - - +
41W ASN 3.2 0.2 - - - -
42W ARG* 1.3 72.8 - - - +
44W GLN* 1.3 66.9 + - - +
45W ARG 3.0 1.6 - - - -
46W ILE* 3.0 24.6 + - + +
47W LYS 3.1 0.2 + - - -
48W VAL* 3.1 55.6 + - + +
49W GLU 4.2 1.6 - - - +
50W ASN* 3.5 43.5 - - - +
51W THR 4.8 0.2 - - - +
54W ASN* 5.3 5.4 - - + +
55W ARG* 4.5 6.7 - - + -
58W PHE* 6.1 1.3 - - + -
310W LEU* 4.9 8.1 - - + -
313W TRP* 4.8 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 44 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40W GLY 3.1 22.6 + - - +
41W ASN* 3.2 24.4 + - - +
43W LEU* 1.3 74.9 - - + +
45W ARG* 1.3 63.4 + - + +
47W LYS* 3.2 15.0 + - - +
48W VAL 3.9 5.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 45 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41W ASN* 2.7 50.6 + - - +
42W ARG* 3.2 44.4 - - - +
43W LEU 3.0 0.2 - - - -
44W GLN* 1.3 79.8 - - + +
46W ILE* 1.3 60.3 + - + +
47W LYS* 3.8 1.4 + - - +
310W LEU* 5.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 46 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42W ARG 3.9 7.2 - - - +
43W LEU* 3.3 17.3 - - + +
45W ARG* 1.3 80.8 - - + +
47W LYS* 1.3 70.3 + - - +
48W VAL* 3.6 23.1 - - + -
310W LEU* 3.3 47.8 - - + +
311W ALA* 3.7 24.5 - - + -
313W TRP* 4.2 7.6 - - + -
314W GLY* 3.7 28.0 - - - +
----------------------------------------------------------
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