Contacts of the helix formed by residues 47 - 58 (chain A) in PDB entry 1DUL
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 LYS 47 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLU 3.1 25.5 + - - -
45A ILE* 3.0 14.5 + - - +
46A ILE* 1.3 75.9 - - - +
48A GLY* 1.3 68.6 + - - +
49A SER 3.5 2.5 - - - +
50A ARG* 3.3 6.9 + - - +
51A LYS* 2.9 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LYS* 1.3 76.6 - - - +
49A SER* 1.3 61.8 + - - +
51A LYS* 3.3 11.2 + - - +
52A ARG* 3.0 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LYS* 3.5 1.6 - - - +
48A GLY* 1.3 74.5 - - - +
50A ARG* 1.3 62.9 + - - +
52A ARG* 3.3 28.3 + - - +
53A ARG* 3.1 22.3 + - - +
140B A 2.7 32.9 + - - -
141B C 3.3 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A THR* 4.4 2.8 + - - -
38A LYS* 5.7 3.6 - - - +
39A GLU* 2.8 54.6 + - - +
45A ILE* 3.3 45.6 + - - +
46A ILE* 4.0 13.5 - - + +
47A LYS* 3.3 8.5 + - - +
49A SER* 1.3 73.8 - - - +
51A LYS* 1.3 61.2 + - - +
53A ARG* 3.2 2.7 + - - +
54A ILE* 2.9 36.7 + - + +
140B A 3.3 70.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 3.7 31.8 - - + +
47A LYS* 2.9 25.4 + - - +
48A GLY* 3.5 8.9 - - - +
50A ARG* 1.3 76.9 - - - +
52A ARG* 1.3 58.2 + - - +
54A ILE* 3.4 1.4 + - - +
55A ALA* 2.8 32.3 + - - +
62A VAL* 4.2 19.2 - - + +
65A VAL* 4.1 17.8 - - + +
66A ASN* 2.9 31.5 + - - +
69A LEU* 4.1 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLY* 3.0 17.8 + - - +
49A SER* 3.5 36.1 + - - +
51A LYS* 1.3 77.6 - - - +
53A ARG* 1.3 61.3 + - - +
55A ALA* 3.5 0.9 + - - +
56A ALA* 3.1 26.2 + - - +
62A VAL* 3.9 23.1 - - + -
141B C 5.3 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A SER 2.9 23.2 + - - -
35A MSE 3.8 1.0 - - - +
36A THR 4.0 1.0 - - - +
39A GLU* 2.8 42.2 + - - -
49A SER 3.1 13.4 + - - +
50A ARG* 3.6 10.6 - - - +
52A ARG* 1.3 78.2 - - - +
54A ILE* 1.3 66.6 + - - +
56A ALA* 3.9 2.6 - - - +
57A GLY* 2.9 27.7 + - - -
140B A 3.0 40.4 + - + -
141B C 3.2 36.1 - - - +
163B C 3.1 41.9 + - - +
164B A 3.9 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE* 3.6 42.2 - - + +
34A SER* 3.8 11.2 - - - +
35A MSE 3.8 23.3 - - + -
39A GLU* 3.8 12.3 - - - +
46A ILE* 3.9 28.9 - - + -
50A ARG 2.9 21.8 + - - +
51A LYS* 3.8 4.5 - - - +
53A ARG* 1.3 91.9 - - - +
55A ALA* 1.3 64.0 + - - +
57A GLY 3.4 0.7 + - - -
58A SER* 2.8 28.8 + - - -
65A VAL* 4.0 9.2 - - + -
163B C 4.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LYS 2.8 19.7 + - - +
52A ARG 3.8 2.9 - - - +
53A ARG 3.3 0.2 - - - -
54A ILE* 1.3 76.5 - - - +
56A ALA* 1.3 62.9 + - - +
58A SER* 3.1 4.5 + - - -
59A GLY 3.0 3.8 + - - -
60A MSE 2.9 41.1 + - - +
61A GLN 3.7 20.2 - - - -
62A VAL* 3.7 10.5 - - + +
65A VAL* 3.7 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ARG 3.1 14.6 + - - +
53A ARG* 4.2 2.7 - - - +
55A ALA* 1.3 77.6 - - - +
57A GLY* 1.3 63.3 + - - +
59A GLY* 3.2 12.2 + - - +
60A MSE 4.5 3.1 - - - -
150B G 3.8 6.4 + - - -
161B A 5.8 0.7 - - - -
162B G 4.8 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A SER* 3.1 6.8 + - - -
53A ARG 2.9 13.7 + - - -
54A ILE 3.8 1.1 - - - -
56A ALA* 1.3 79.7 - - - +
58A SER* 1.3 55.7 + - - +
59A GLY 3.5 0.4 - - - -
149B G 2.9 21.7 + - - -
150B G 3.4 2.0 + - - -
162B G 4.2 2.2 - - - -
163B C 3.2 30.5 - - - +
703B K 3.0 15.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA* 3.8 12.1 - - - -
31A ILE* 3.8 15.3 - - - +
34A SER* 3.6 8.5 - - - -
54A ILE 2.8 19.8 + - - -
55A ALA* 3.1 7.1 + - - -
57A GLY* 1.3 75.9 - - - +
59A GLY* 1.3 60.4 + - - +
60A MSE 3.4 18.9 + - - +
149B G 3.6 15.3 - - - +
150B G 2.7 34.5 + - - +
----------------------------------------------------------
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