Contacts of the helix formed by residues 38 - 52 (chain A) in PDB entry 1D4O
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 ALA 38 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.0 16.4 + - + +
36A ALA* 3.2 0.6 - - + -
37A LYS* 1.3 72.4 - - - +
39A GLN* 1.3 64.3 + - - +
40A TYR 3.1 3.4 - - - -
41A PRO* 3.3 10.0 - - - +
42A ILE* 3.0 40.1 + - + +
167A ALA* 3.8 33.0 - - + +
168A LYS* 3.9 10.5 - - - +
171A CYS* 4.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.5 24.9 - - + +
34A CYS* 3.8 8.6 + - - +
37A LYS* 3.2 22.1 - - - +
38A ALA* 1.3 77.6 + - - +
40A TYR* 1.3 89.5 + - + +
42A ILE* 3.7 5.6 - - - +
43A ALA* 3.0 30.8 + - - +
74A LEU* 3.9 40.2 + - + +
75A LEU* 4.0 13.7 - - + +
78A ALA* 3.8 23.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LYS* 3.4 32.2 - - + +
38A ALA 3.1 0.8 - - - -
39A GLN* 1.3 99.9 + - + +
41A PRO* 1.3 72.5 - - + +
42A ILE 3.3 0.2 + - - -
43A ALA* 3.3 12.6 + - - +
44A ASP* 3.4 10.4 + - - +
74A LEU* 5.8 1.8 - - - +
77A GLU* 5.5 1.9 - - + +
78A ALA* 4.0 29.2 - - + -
168A LYS* 5.7 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LYS 3.9 5.6 - - - +
38A ALA* 3.3 23.6 - - - +
40A TYR* 1.3 94.6 - - + +
42A ILE* 1.3 60.5 + - - +
44A ASP* 3.1 3.8 + - - +
45A LEU* 2.9 23.1 + - - +
168A LYS* 4.3 8.7 - - + -
171A CYS* 3.9 24.5 - - + +
172A ASP* 3.3 28.5 - - - +
175A GLN* 3.5 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 4.4 7.0 - - + -
33A LEU* 3.4 34.8 - - + -
38A ALA* 3.0 26.4 + - + +
39A GLN 3.7 4.3 - - - +
41A PRO* 1.3 78.3 - - - +
43A ALA* 1.3 64.4 + - - +
45A LEU* 3.2 10.8 + - + +
46A VAL* 2.9 28.0 + - + +
58A PHE* 3.8 31.2 - - + -
75A LEU* 4.6 4.7 - - + -
104A ILE* 3.9 12.1 - - + -
171A CYS* 3.6 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLN 3.0 17.9 + - - +
40A TYR 3.3 5.3 + - - +
42A ILE* 1.3 77.0 - - - +
44A ASP* 1.3 60.8 + - - +
46A VAL* 3.5 3.9 + - - +
47A LYS* 3.2 24.0 + - - +
78A ALA 3.8 22.2 - - - +
79A GLY 4.7 1.8 - - - -
80A VAL* 3.7 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR 3.4 7.3 + - - +
41A PRO 3.1 4.5 + - - +
42A ILE 3.1 0.4 - - - -
43A ALA* 1.3 78.6 - - - +
45A LEU* 1.3 65.0 + - - +
47A LYS* 3.1 21.6 + - - +
48A MET* 2.9 39.2 + - - +
175A GLN* 2.7 37.9 - - - +
179A ARG* 5.2 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 5.1 4.7 - - + -
27A ILE* 5.5 3.8 - - + -
41A PRO 2.9 17.3 + - - +
42A ILE* 3.6 13.5 - - + +
44A ASP* 1.3 76.6 - - - +
46A VAL* 1.3 61.6 + - + +
48A MET* 3.3 8.9 + - - +
49A LEU* 2.9 52.1 + - + +
102A LEU* 4.8 17.3 - - + -
171A CYS* 5.6 7.0 - - + +
174A LEU* 4.0 27.1 - - + +
175A GLN* 4.2 10.5 - - + +
178A VAL* 3.5 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 3.6 31.9 - - + -
42A ILE* 2.9 20.5 + - + +
43A ALA* 4.0 5.6 - - - +
45A LEU* 1.3 78.6 - - + +
47A LYS* 1.3 65.1 + - - +
49A LEU* 3.8 2.9 - - + +
50A SER* 2.9 34.9 + - - +
56A VAL* 3.9 22.4 - - + -
58A PHE* 3.9 14.1 - - + -
80A VAL* 5.6 1.6 - - + -
81A PRO* 5.9 1.1 - - + -
84A ILE* 3.5 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ALA* 3.2 16.0 + - - +
44A ASP* 3.1 22.7 + - - +
46A VAL* 1.3 78.9 - - - +
48A MET* 1.3 65.4 + - + +
50A SER* 3.4 5.4 + - - -
51A GLU* 3.0 45.6 + - - +
79A GLY 5.8 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASP* 2.9 44.3 + - - +
45A LEU* 3.7 8.3 - - - +
47A LYS* 1.3 82.3 - - + +
49A LEU* 1.3 63.2 + - - +
51A GLU* 3.2 21.0 + - - +
52A GLN* 3.2 21.8 + - - +
175A GLN* 3.7 29.2 - - + +
178A VAL* 3.8 21.3 - - + +
179A ARG* 3.7 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 3.6 34.5 - - + -
25A ILE* 4.1 13.9 - - + -
27A ILE* 6.5 0.7 - - + -
45A LEU* 2.9 49.4 + - + +
46A VAL* 4.0 3.4 - - + +
48A MET* 1.3 73.3 - - - +
50A SER* 1.3 62.1 + - - +
52A GLN* 3.2 29.9 + - - +
54A LYS* 3.3 29.2 + - + +
56A VAL* 3.8 20.2 - - + -
102A LEU* 5.7 2.0 - - + -
178A VAL* 4.1 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A VAL* 2.9 29.4 + - - +
47A LYS* 3.7 5.8 - - - -
49A LEU* 1.3 76.5 - - - +
51A GLU* 1.3 58.4 + - - +
53A GLY* 2.9 21.3 + - - -
54A LYS 3.7 12.5 + - - +
56A VAL* 4.0 13.9 + - - +
84A ILE* 5.3 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LYS* 3.0 39.7 + - + +
48A MET* 3.2 14.2 + - - +
50A SER* 1.3 76.7 - - - +
52A GLN* 1.3 57.8 + - + +
53A GLY* 3.0 4.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ARG* 5.7 6.3 - - - +
48A MET* 3.2 14.5 + - - +
49A LEU* 3.5 16.1 - - - +
50A SER 3.1 0.6 - - - -
51A GLU* 1.3 76.4 - - + +
53A GLY* 1.3 59.4 + - - +
54A LYS* 3.3 29.4 + - - +
178A VAL* 3.7 27.6 - - - +
181A SER* 5.5 4.3 - - - -
----------------------------------------------------------
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