Contacts of the helix formed by residues 12 - 27 (chain A) in PDB entry 3ADB
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 GLY 12 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLY 3.2 1.2 + - - -
11A VAL* 1.3 80.1 - - - +
13A LYS* 1.3 60.3 + - - +
14A SER 3.5 1.8 - - - -
15A THR* 3.6 11.8 + - - +
16A PHE* 2.9 31.2 + - - +
102A LEU* 3.9 4.4 - - - +
112A ARG* 4.4 3.8 - - - -
150A THR* 4.8 3.3 - - - +
2001A PO4 3.0 14.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 3.9 12.1 - - + +
7A GLY 3.0 32.0 + - - +
8A LEU 3.7 7.3 + - - -
9A PRO* 4.3 2.0 - - - +
11A VAL* 3.6 12.3 - - + -
12A GLY* 1.3 73.8 - - - +
14A SER* 1.3 55.9 + - - +
16A PHE* 3.1 2.1 + - - +
17A SER* 2.7 39.0 + - - -
74A ASP* 3.1 15.0 - - - +
75A ASP* 3.2 43.1 - - - +
76A THR* 3.3 12.8 + - - +
102A LEU* 3.7 16.4 - - + -
2001A PO4 2.9 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLY 3.5 0.2 - - - -
13A LYS* 1.3 76.2 - - - +
15A THR* 1.3 62.9 + - - +
17A SER* 3.4 2.3 - - - -
18A LYS* 3.1 48.5 + - - +
74A ASP* 3.3 24.3 + - - -
2001A PO4 2.7 19.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLY* 3.6 13.1 + - - +
13A LYS 3.2 0.4 - - - -
14A SER* 1.3 77.4 - - - +
16A PHE* 1.3 69.0 + - - +
18A LYS* 3.3 9.1 + - - +
19A ASN* 3.0 41.1 + - - +
156A PHE* 5.6 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 3.7 34.3 - - + -
12A GLY 2.9 20.5 + - - +
13A LYS 3.5 2.9 - - - +
15A THR* 1.3 78.1 - - - +
17A SER* 1.3 60.3 + - - +
19A ASN 3.2 1.0 + - - -
20A LEU* 2.8 51.9 + - + +
100A ILE* 4.0 13.5 - - + -
102A LEU* 3.8 20.0 - - + -
148A ILE* 3.4 34.3 - - + -
150A THR* 5.8 0.7 - - + -
154A ILE* 4.2 13.0 - - + -
156A PHE* 3.6 28.1 - + - -
159A ILE* 3.6 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 3.1 17.7 - - - +
13A LYS 2.7 27.3 + - - -
14A SER* 3.4 7.6 - - - -
16A PHE* 1.3 77.4 - - - +
18A LYS* 1.3 55.1 + - - +
20A LEU* 3.2 3.1 + - - +
21A ALA* 2.8 36.6 + - - +
33A VAL* 3.7 25.8 - - - -
72A ILE* 3.8 14.5 - - - +
74A ASP* 3.6 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A SER* 3.1 35.8 + - - +
15A THR* 3.7 6.7 - - - +
17A SER* 1.3 81.5 - - - +
19A ASN* 1.3 64.6 + - - +
21A ALA* 3.6 6.0 + - - +
22A LYS* 3.1 38.9 + - - +
33A VAL* 5.1 10.5 - - + -
74A ASP* 5.7 1.3 - - - -
44B PRO* 5.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A THR* 3.0 35.2 + - - +
18A LYS* 1.3 75.8 - - - +
20A LEU* 1.3 64.5 + - - +
22A LYS* 3.6 17.8 + - - +
23A ILE* 3.2 27.2 + - - +
156A PHE* 3.4 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 3.9 8.3 - - + -
16A PHE* 2.8 39.4 + - + +
17A SER* 3.7 3.8 - - - +
19A ASN* 1.3 74.4 - - - +
21A ALA* 1.3 66.6 + - - +
23A ILE* 3.3 4.5 + - + +
24A LEU* 3.0 36.0 + - + +
72A ILE* 3.8 20.6 - - + -
100A ILE* 4.5 3.6 - - + -
156A PHE* 4.0 15.0 - - + +
159A ILE* 4.0 22.0 - - + -
160A ALA* 4.3 14.1 - - + +
163A LEU* 3.8 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A SER 2.8 17.9 + - - +
18A LYS* 3.8 5.4 - - - +
20A LEU* 1.3 77.1 - - - +
22A LYS* 1.3 63.2 + - - +
24A LEU* 3.0 4.7 + - - +
25A SER* 2.9 21.5 + - - -
31A VAL* 3.7 21.6 - - + +
33A VAL* 4.0 20.4 - - + -
72A ILE* 4.3 6.3 - - + -
44B PRO* 3.8 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LYS* 3.1 28.0 + - - +
19A ASN* 3.8 16.9 + - - +
20A LEU 3.3 0.2 - - - -
21A ALA* 1.3 77.0 - - - +
23A ILE* 1.3 64.7 + - + +
25A SER* 3.4 5.4 + - - -
26A LYS* 3.2 39.1 + - - +
44B PRO* 4.2 27.6 - - + +
45B VAL* 5.7 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASN 3.2 16.8 + - - +
20A LEU* 3.3 7.1 + - + +
21A ALA 3.2 0.4 - - - -
22A LYS* 1.3 75.0 - - + +
24A LEU* 1.3 67.4 + - - +
26A LYS* 2.9 30.7 + - + +
27A ASN* 2.8 33.2 + - - +
156A PHE* 3.7 27.1 - - + +
157A ASN* 4.2 26.0 - - - +
160A ALA* 3.7 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 4.5 3.6 - - + -
20A LEU* 3.0 34.3 + - + +
21A ALA 3.0 8.1 + - - +
23A ILE* 1.3 77.2 - - - +
25A SER* 1.3 56.8 + - - +
27A ASN* 2.8 19.6 + - - +
29A ILE* 3.0 43.5 + - + +
31A VAL* 3.9 26.2 - - + -
70A TRP* 3.9 29.8 - - + -
72A ILE* 4.4 5.6 - - + -
160A ALA* 4.0 25.8 - - + -
163A LEU* 5.3 0.9 - - + -
164A ILE* 4.4 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA 2.9 9.8 + - - -
22A LYS 3.5 10.8 - - - -
24A LEU* 1.3 76.4 - - - +
26A LYS* 1.3 58.8 - - - +
28A ASN* 2.9 23.6 + - - +
29A ILE 3.5 15.4 + - - -
31A VAL 5.4 0.2 + - - -
44B PRO* 3.1 25.1 - - - +
45B VAL* 3.5 30.0 - - - +
47B LYS* 5.7 4.1 + - - +
50B TYR* 5.1 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LYS* 3.2 27.7 + - - +
23A ILE* 2.9 24.0 + - + +
25A SER* 1.3 77.8 - - - +
27A ASN* 1.3 60.5 + - - +
28A ASN* 3.0 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 2.8 41.8 + - - +
24A LEU* 2.8 12.0 + - - +
26A LYS* 1.3 78.7 - - - +
28A ASN* 1.3 71.5 + - - +
29A ILE* 3.2 9.1 + - + +
157A ASN* 5.7 0.4 + - - -
160A ALA* 4.3 9.1 - - - +
164A ILE* 3.8 27.9 - - + +
----------------------------------------------------------
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