Contacts of the helix formed by residues 35 - 46 (chain Z) 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 Z).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Z ASP 3.5 0.8 + - - -
34Z GLU* 1.3 76.0 - - - +
36Z VAL* 1.3 65.3 + - - +
37Z GLY* 3.4 4.1 + - - -
38Z THR* 2.8 40.1 + - - -
39Z MET* 3.0 22.9 + - - +
55Z ARG* 6.2 0.4 - - - -
79Z PHE* 3.3 26.4 - - - -
107Z LYS* 4.4 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Z SER* 1.3 75.6 - - - +
37Z GLY* 1.3 58.3 + - - +
39Z MET* 4.2 0.6 - - - +
40Z GLY 3.5 3.5 + - - -
50Z ASN* 2.9 24.7 - - - +
55Z ARG* 3.8 31.6 + - - +
79Z PHE* 3.4 22.2 - - + -
81Z GLU* 5.0 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 37 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Z SER* 3.0 5.0 + - - -
36Z VAL* 1.3 78.8 - - - +
38Z THR* 1.3 60.2 + - - +
40Z GLY* 2.8 18.7 + - - -
41Z ASN* 3.0 16.2 - - - +
50Z ASN* 4.7 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 38 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34Z GLU* 3.8 19.1 - - + -
35Z SER* 2.8 34.8 + - - -
37Z GLY* 1.3 65.8 - - - +
39Z MET* 1.3 69.2 + - - +
40Z GLY 2.8 3.1 + - - -
41Z ASN* 2.8 29.0 + - - +
42Z ARG* 3.0 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 39 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34Z GLU* 4.0 18.9 - - + +
35Z SER 3.0 18.1 + - - +
36Z VAL 4.2 3.6 - - - +
38Z THR* 1.3 76.7 - - - +
40Z GLY* 1.3 57.1 + - - +
42Z ARG* 3.2 37.8 + - + +
43Z LEU* 2.8 67.6 + - + +
55Z ARG* 3.6 27.8 - - + +
58Z PHE* 5.3 8.1 - - + -
59Z ARG* 3.3 28.3 - - - +
306Z GLN* 5.0 3.8 - - - +
310Z LEU* 4.7 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 40 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36Z VAL 3.5 0.2 + - - -
37Z GLY 2.8 9.8 + - - -
38Z THR 2.8 2.8 + - - -
39Z MET* 1.3 79.6 - - - +
41Z ASN* 1.3 55.9 + - - -
43Z LEU 3.8 0.2 - - - -
44Z GLN* 2.8 38.0 + - - +
50Z ASN* 2.9 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 41 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Z GLY 3.0 12.1 - - - +
38Z THR* 2.8 30.4 + - - +
40Z GLY* 1.3 70.7 - - - -
42Z ARG* 1.3 73.5 + - - +
44Z GLN* 3.5 14.7 - - - +
45Z ARG* 2.5 48.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 42 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34Z GLU* 4.0 14.0 + - - +
38Z THR* 3.0 34.6 + - + +
39Z MET* 3.3 27.8 - - + +
41Z ASN* 1.3 102.8 - - - +
43Z LEU* 1.3 62.0 + - - +
45Z ARG* 3.0 64.1 - - - +
46Z ILE* 3.6 3.1 + - - +
303Z ARG* 4.1 33.8 - - - +
306Z GLN* 5.5 1.1 - - - -
310Z LEU* 3.6 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Z MET* 2.8 53.3 + - + +
40Z GLY 4.0 2.7 - - - +
42Z ARG* 1.3 71.8 - - - +
44Z GLN* 1.3 64.3 + - - +
46Z ILE* 2.5 35.0 + - + +
48Z VAL* 3.3 13.6 - - + +
49Z GLU 4.2 14.8 - - - +
50Z ASN* 4.1 20.4 - - - +
54Z ASN* 4.5 11.9 - - - +
55Z ARG* 4.2 10.3 - - + -
58Z PHE* 4.9 5.4 - - + -
310Z LEU* 4.1 8.7 - - + -
313Z TRP* 3.7 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 44 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40Z GLY* 2.8 25.4 + - - +
41Z ASN* 2.9 17.1 + - - +
43Z LEU* 1.3 73.6 - - - +
45Z ARG* 1.3 56.5 + - - +
47Z LYS* 2.7 30.3 + - - -
48Z VAL 3.3 16.7 + - - +
49Z GLU* 5.6 0.4 - - - +
50Z ASN* 4.6 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 45 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41Z ASN* 2.5 33.0 + - + +
42Z ARG* 3.0 61.6 - - - +
44Z GLN* 1.3 73.1 - - + +
46Z ILE* 1.3 54.3 + - + +
47Z LYS* 2.8 18.5 + - - +
303Z ARG* 5.7 4.9 - - - +
310Z LEU* 5.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 46 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42Z ARG 4.3 1.8 - - - +
43Z LEU* 2.5 50.3 - - + +
45Z ARG* 1.3 75.9 - - + +
47Z LYS* 1.3 75.4 + - - +
48Z VAL* 3.4 19.2 - - + +
310Z LEU* 3.5 43.7 - - + +
311Z ALA* 3.7 18.6 - - + +
313Z TRP* 4.0 19.3 - - + -
314Z GLY* 4.1 9.6 - - - -
----------------------------------------------------------
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