Contacts of the helix formed by residues 31 - 47 (chain A) in PDB entry 2ADS
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 GLN 31 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLU* 4.3 6.9 + - + +
30A ILE* 1.3 82.5 - - - +
32A LYS* 1.3 66.1 + - - +
33A GLU 3.4 2.5 - - - -
34A LYS* 2.9 45.1 + - + +
35A LEU* 2.8 28.6 + - - +
77A ILE* 5.3 7.0 - - - +
79A GLU* 5.6 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ILE* 4.1 6.8 - - + -
31A GLN* 1.3 69.9 - - - +
33A GLU* 1.3 68.8 + - + +
35A LEU* 3.1 30.1 + - + +
36A ASN* 3.7 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLN 3.4 1.0 - - - -
32A LYS* 1.3 79.2 - - + +
34A LYS* 1.3 63.6 + - + +
36A ASN* 2.7 33.5 + - - +
37A LYS* 3.2 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLN* 2.9 45.2 + - + +
33A GLU* 1.3 84.7 - - + +
35A LEU* 1.3 57.9 + - - +
36A ASN 3.3 0.9 - - - -
37A LYS* 2.9 22.3 + - + +
38A VAL* 2.8 37.7 + - + +
73A SER* 5.3 13.5 - - - +
75A GLY* 5.9 6.3 - - - +
77A ILE* 3.7 29.2 - - + +
79A GLU* 5.7 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PRO* 6.0 2.7 - - + -
29A GLU 5.8 0.4 - - - +
30A ILE* 3.8 27.6 - - + -
31A GLN 2.8 23.7 + - - +
32A LYS* 3.1 22.4 + - + +
34A LYS* 1.3 77.1 - - - +
36A ASN* 1.3 57.7 + - - +
38A VAL* 4.6 4.3 - - + +
39A ARG* 3.0 29.5 + - - +
52A ARG* 4.0 35.8 - - - +
54A GLU 5.5 4.3 - - - +
55A ASP* 5.9 3.6 - - - +
57A PHE* 3.8 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LYS 3.7 5.3 + - - -
33A GLU* 2.7 25.9 + - - +
35A LEU* 1.3 78.2 - - - +
37A LYS* 1.3 89.7 + - - +
39A ARG* 3.3 16.3 + - - +
40A TRP* 3.2 20.8 + - - +
52A ARG* 5.4 4.6 - - - +
16G C 5.1 11.2 + - - +
17G C 4.8 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU* 3.2 35.3 + - - +
34A LYS* 2.9 21.0 + - + +
36A ASN* 1.3 87.4 - - - +
38A VAL* 1.3 66.0 + - + +
40A TRP* 3.6 7.5 - - - +
41A ARG* 3.4 31.8 + - - +
73A SER* 5.6 8.5 - - - -
74A ASN 6.2 0.9 - - - +
1M G 2.9 48.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PRO* 6.0 1.6 - - + -
34A LYS* 2.8 24.5 + - + +
35A LEU* 3.8 6.1 - - + +
37A LYS* 1.3 73.7 - - + +
39A ARG* 1.3 52.8 + - - +
41A ARG* 2.7 15.1 + - - +
42A VAL* 2.6 48.2 + - + +
57A PHE* 3.9 17.0 - - + -
71A THR* 4.3 6.3 - - - +
73A SER* 5.5 4.0 - - - -
79A GLU* 4.1 31.6 - - + +
81A LYS* 3.9 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU 3.0 18.9 + - - +
36A ASN* 3.3 14.1 + - - +
38A VAL* 1.3 74.7 - - - +
40A TRP* 1.3 94.7 + - - +
42A VAL* 3.0 15.0 + - - +
43A PHE* 3.0 32.4 + - - +
50A THR* 3.1 24.3 + - + +
51A PHE* 4.5 1.8 - - - +
52A ARG* 4.2 19.5 - - + +
57A PHE* 3.7 17.2 - - + -
17G C 2.7 35.4 + - - -
18G C 2.5 42.4 + - - -
19G C 5.7 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ASN 3.2 12.1 + - - +
37A LYS* 3.6 7.9 - - - +
39A ARG* 1.3 99.8 - - - +
41A ARG* 1.3 63.2 + - + +
43A PHE* 3.1 18.0 + - + +
44A LEU* 3.1 42.2 + - + +
18G C 4.2 19.7 - + - -
19G C 4.0 49.8 - + - -
20G C 4.5 13.7 - + - -
21G C 5.9 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LYS* 3.4 19.5 + - - +
38A VAL* 2.7 15.8 + - - +
40A TRP* 1.3 74.7 - - + +
42A VAL* 1.3 63.8 + - - +
43A PHE 3.1 1.8 - - - -
44A LEU* 4.0 21.7 - - + +
45A GLN* 3.1 29.7 + - + +
71A THR* 3.7 27.1 - - + +
72A LEU 2.9 33.6 + - - +
73A SER* 3.6 10.9 - - - +
74A ASN* 3.0 39.8 - - - +
79A GLU* 5.2 0.9 - - - -
1M G 4.6 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 4.8 2.2 - - + -
38A VAL* 2.6 30.5 + - + +
39A ARG* 3.0 15.0 + - - +
41A ARG* 1.3 72.3 - - - +
43A PHE* 1.3 66.4 + - - +
46A THR* 2.9 25.0 + - - +
50A THR* 3.3 28.3 + - + -
57A PHE* 3.7 20.0 - - + -
59A CYS* 3.6 16.6 - - - -
69A TYR* 5.2 0.9 - - - -
71A THR* 5.1 0.2 - - - -
81A LYS* 3.5 37.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ARG* 3.0 24.5 + - - +
40A TRP* 3.1 8.0 + - + +
41A ARG 3.1 0.8 - - - -
42A VAL* 1.3 79.8 - - - +
44A LEU* 1.3 81.5 + - + +
46A THR 2.8 0.5 + - - -
47A GLY* 2.6 52.1 + - - -
48A LEU 3.2 22.4 - - - -
49A PRO* 3.2 31.0 - - + -
50A THR* 4.2 4.2 + - - +
18G C 4.6 8.1 - - - +
19G C 3.0 36.1 - - - +
20G C 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP* 3.5 39.5 - - + +
41A ARG* 3.6 25.1 - - + +
43A PHE* 1.3 92.6 - - + +
45A GLN* 1.3 67.5 - - + +
46A THR 3.0 0.7 + - - -
47A GLY* 3.2 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ARG* 3.1 15.7 + - + +
44A LEU* 1.3 80.2 - - + +
46A THR* 1.3 61.1 + - - +
69A TYR* 4.2 20.5 + - + -
70A LEU 2.7 35.8 + - - +
71A THR* 3.5 21.0 - - + +
72A LEU 4.7 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL 2.9 18.5 + - - -
43A PHE 2.8 1.2 + - - -
44A LEU 3.6 0.7 - - - -
45A GLN* 1.3 80.5 - - - +
47A GLY* 1.3 58.3 + - - +
48A LEU* 3.4 27.0 - - + +
59A CYS* 4.4 13.4 - - - -
63A VAL* 3.6 25.8 - - + +
69A TYR* 2.6 44.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE* 2.6 45.9 + - - -
44A LEU 3.2 6.7 + - - -
46A THR* 1.3 72.6 - - - +
48A LEU* 1.3 63.1 + - - +
49A PRO* 4.0 1.7 - - - +
----------------------------------------------------------
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