Contacts of the helix formed by residues 29 - 39 (chain A) in PDB entry 1DMO
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 29 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE 4.1 1.0 + - - -
28A THR* 1.3 71.3 - - - +
30A LYS* 1.3 64.6 + - - +
32A LEU* 3.1 25.1 - - - +
33A GLY 4.4 0.7 + - - -
48A LEU* 5.2 0.9 - - - +
52A ILE* 3.7 42.7 - - + +
55A VAL* 4.8 4.9 - - + -
56A ASP* 5.6 4.5 - - + -
61A GLY 3.4 22.9 + - - +
63A ILE* 3.8 23.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 6.1 2.9 - - + -
28A THR* 2.5 38.0 + - + +
29A THR* 1.3 82.0 + - - +
31A GLU* 1.3 77.5 + - + +
32A LEU 3.1 0.7 + - - -
33A GLY* 4.3 4.3 + - - -
34A THR* 4.3 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 3.6 27.4 - - + +
20A ASP 5.1 2.1 + - - -
21A LYS* 4.5 20.8 + - - +
27A ILE* 4.5 8.7 - - + +
28A THR* 2.6 33.3 + - - +
30A LYS* 1.3 81.0 - - + +
32A LEU* 1.3 68.0 + - - +
33A GLY 3.4 0.4 - - - -
34A THR* 3.0 14.4 + - - +
35A VAL* 2.9 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 3.7 21.5 - - + +
28A THR 3.1 4.4 + - - -
29A THR* 3.1 18.2 - - - +
30A LYS 3.1 0.8 - - - -
31A GLU* 1.3 74.5 - - - +
33A GLY* 1.3 56.5 + - - +
35A VAL* 2.6 27.2 + - - +
36A MET* 3.0 15.9 + - + +
48A LEU* 3.9 20.4 - - + +
52A ILE* 3.7 26.0 - - + -
63A ILE* 3.6 20.9 - - + -
68A PHE* 3.9 21.3 - - + -
71A MET* 3.6 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A THR 4.4 0.2 + - - -
30A LYS 4.3 4.0 + - - -
31A GLU 3.4 0.4 - - - -
32A LEU* 1.3 79.6 - - - +
34A THR* 1.3 62.6 + - - +
36A MET* 3.2 3.6 + - - +
37A ARG* 3.0 23.4 + - - +
43A PRO* 5.1 2.5 - - - +
48A LEU* 3.0 35.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 3.2 32.1 - - + -
30A LYS 4.3 4.6 + - - -
31A GLU* 3.0 21.3 + - - +
32A LEU 2.9 0.2 + - - -
33A GLY* 1.3 75.6 - - - +
35A VAL* 1.3 62.0 + - - +
37A ARG* 3.4 8.1 + - + +
38A SER* 2.8 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA* 3.9 22.4 - - + +
16A PHE* 4.2 6.1 - - + +
19A PHE* 3.5 35.7 - - + -
27A ILE* 3.5 21.8 - - + -
31A GLU 3.0 15.0 - - - +
32A LEU 2.6 12.2 + - - +
34A THR* 1.3 71.7 - - - +
36A MET* 1.3 67.0 + - - +
38A SER* 2.9 10.9 + - - -
39A LEU* 2.9 33.2 + - + +
68A PHE* 4.0 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.0 19.2 + - + +
33A GLY 3.6 3.8 - - - +
35A VAL* 1.3 76.9 - - - +
37A ARG* 1.3 62.5 + - - +
39A LEU* 3.4 21.6 + - - +
41A GLN* 3.6 15.6 + - - +
43A PRO* 3.4 26.5 - - + -
48A LEU* 3.3 28.9 - - + -
51A MET* 4.6 10.1 - - - -
68A PHE* 3.1 33.2 - - + +
71A MET* 4.7 7.2 - - + +
72A MET* 3.2 41.1 - - + +
75A LYS* 6.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLY 3.0 16.1 + - - +
34A THR* 3.6 8.1 - - - +
35A VAL 3.1 0.2 - - - -
36A MET* 1.3 77.8 - - - +
38A SER* 1.3 62.1 + - - +
40A GLY* 3.5 9.9 + - - -
41A GLN 3.6 19.4 + - - +
42A ASN* 4.5 22.1 - - - +
43A PRO* 4.5 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA* 4.7 8.1 - - - -
18A LEU* 5.2 8.3 - - - -
19A PHE* 3.0 28.0 - - - -
34A THR* 2.8 14.4 + - - +
35A VAL* 2.9 8.6 + - - -
37A ARG* 1.3 77.0 - - - +
39A LEU* 1.3 67.7 + - - +
40A GLY* 3.1 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU* 5.1 14.7 - - + +
12A PHE* 3.1 59.3 - - + +
15A ALA* 3.2 28.3 - - + -
35A VAL* 2.9 41.3 + - + +
36A MET* 3.5 10.1 - - - +
37A ARG 3.3 0.2 - - - -
38A SER* 1.3 78.0 - - - +
40A GLY* 1.3 57.8 + - - +
41A GLN* 4.6 2.5 - - + +
68A PHE* 3.8 12.3 - - + -
72A MET* 3.7 17.3 - - + -
----------------------------------------------------------
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