Contacts of the helix formed by residues 12 - 28 (chain A) in PDB entry 3LB2
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 ASP 12 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A THR 3.6 3.8 + - - +
9A ILE 3.1 5.7 + - - -
11A GLY* 1.3 79.6 - - - +
13A LEU* 1.3 64.1 + - - +
14A ARG* 3.3 2.5 + - - +
15A THR* 2.8 36.0 + - - +
16A TYR* 3.1 36.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 3.0 37.9 + - + +
10A ARG 3.4 13.8 - - - +
11A GLY 3.7 0.2 - - - -
12A ASP* 1.3 76.1 - - - +
14A ARG* 1.3 59.9 + - - +
16A TYR* 3.4 0.6 + - - -
17A ALA* 2.8 32.7 + - - +
57A GLU* 3.8 40.8 - - + +
60A PHE* 3.9 25.6 - - + +
61A ASN* 3.9 22.2 - - + +
64A MET* 4.3 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASP* 3.3 2.5 + - - +
13A LEU* 1.3 76.8 - - - +
15A THR* 1.3 63.1 + - - +
17A ALA* 3.8 4.4 - - - +
18A GLN* 3.0 48.7 + - + +
50A ALA 4.9 0.8 + - - -
53A GLY* 3.4 28.7 + - - +
54A ASP* 3.0 31.9 + - - +
56A THR* 5.1 0.2 - - + -
57A GLU* 3.0 38.3 + - + +
----------------------------------------------------------
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 ASP* 2.8 35.8 + - - +
14A ARG* 1.3 79.0 - - - +
16A TYR* 1.3 61.5 + - + +
18A GLN* 3.4 6.5 + - - +
19A ASP* 2.9 51.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A THR* 3.5 38.2 - - + +
9A ILE* 3.7 32.5 - - + -
12A ASP* 3.1 37.5 + - + +
13A LEU 4.0 1.8 - - - +
15A THR* 1.3 79.9 - - + +
17A ALA* 1.3 57.9 + - - +
19A ASP* 3.8 2.4 - - - -
20A ILE* 2.9 43.4 + - + +
107A TYR* 3.6 30.3 - + - -
115A PHE* 3.9 22.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU 2.8 23.5 + - - +
14A ARG 3.8 3.6 - - - +
16A TYR* 1.3 73.5 - - - +
18A GLN* 1.3 57.8 + - - +
21A PHE* 2.9 32.2 + - - +
56A THR* 3.3 34.4 + - + +
57A GLU* 4.2 6.1 - - - -
60A PHE* 3.6 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 3.0 36.1 + - - +
15A THR* 3.9 5.8 - - - +
17A ALA* 1.3 76.0 - - - +
19A ASP* 1.3 61.0 + - - +
21A PHE* 3.4 2.2 + - - +
22A LEU* 2.9 36.3 + - - +
47A LYS* 3.9 29.9 + - - +
52A PHE* 3.7 26.2 - - + -
53A GLY* 3.4 27.5 - - - -
56A THR* 3.4 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A THR* 2.9 37.5 + - - +
16A TYR* 4.0 1.7 - - - +
18A GLN* 1.3 79.3 - - - +
20A ILE* 1.3 57.1 + - - +
22A LEU* 3.9 7.0 - - - +
23A ALA* 2.9 28.4 + - - +
47A LYS* 4.0 18.2 + - - -
107A TYR* 3.8 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 5.1 13.5 - - + -
16A TYR* 2.9 31.9 + - + +
19A ASP* 1.3 73.0 - - - +
21A PHE* 1.3 61.4 + - - +
23A ALA* 3.1 7.5 + - - +
24A PHE* 2.9 27.2 + - - +
60A PHE* 3.6 34.3 - - + -
100A LEU* 4.7 5.6 - - + -
103A ALA* 5.1 0.6 - - - +
104A LEU* 3.9 40.4 - - + +
107A TYR* 3.6 35.0 - - + -
108A MET* 5.3 3.1 - - + -
115A PHE* 6.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA 2.9 19.5 + - - +
18A GLN 3.9 2.5 - - - +
20A ILE* 1.3 77.2 - - - +
22A LEU* 1.3 56.9 + - + +
24A PHE* 3.2 25.8 + + - +
25A LEU* 3.0 41.7 + - + +
35A PHE* 3.8 20.6 - + - -
38A TYR* 3.2 42.6 - + - -
52A PHE* 3.6 23.3 - + - -
56A THR* 3.7 9.9 - - - +
60A PHE* 4.3 7.5 - - + -
100A LEU* 5.3 0.7 - - - -
191A BML 3.5 41.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLN 2.9 22.8 + - - +
19A ASP* 4.0 6.5 - - - +
21A PHE* 1.3 74.6 - - - +
23A ALA* 1.3 57.8 + - - +
25A LEU* 3.3 12.5 + - + +
26A ASN* 2.8 46.5 + - - +
32A ARG* 5.0 4.3 - - - +
43A ASP* 3.7 37.7 - - + +
46A LEU* 3.9 22.9 - - + -
47A LYS* 4.1 26.9 - - - +
52A PHE* 4.2 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASP 2.9 16.1 + - - +
20A ILE* 3.1 12.1 + - - +
22A LEU* 1.3 74.5 - - - +
24A PHE* 1.3 57.6 + - - +
26A ASN* 3.3 9.3 + - - +
27A LYS* 2.9 31.2 + - - +
103A ALA* 4.2 9.5 - - + +
106A GLU* 5.3 4.8 - - - +
107A TYR* 4.4 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE 2.9 13.0 + - - +
21A PHE* 3.2 31.6 + + - +
23A ALA* 1.3 74.0 - - - +
25A LEU* 1.3 70.4 + - + +
27A LYS 3.3 1.0 + - - -
28A TYR* 2.9 34.2 + + - +
31A GLU* 3.4 43.1 - - + -
35A PHE* 4.5 2.2 - + - -
96A ASN 4.1 1.8 - - - -
99A LYS* 4.0 12.8 - - + -
100A LEU* 3.5 51.4 - - + -
103A ALA* 3.5 12.5 - - + +
139A HEM 3.5 27.1 - - + -
191A BML 5.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 3.0 48.3 + - + +
22A LEU* 3.9 13.7 - - + +
24A PHE* 1.3 97.3 - - + +
26A ASN* 1.3 59.5 + - - +
28A TYR 4.1 2.5 - - - -
29A PRO* 3.0 32.6 - - - +
31A GLU* 4.0 3.4 - - + +
32A ARG* 3.8 69.6 + - + +
35A PHE* 4.3 1.3 - - + -
38A TYR* 4.8 6.3 - - + -
46A LEU* 5.4 0.9 - - + -
1B GLY* 5.3 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 2.8 35.7 + - - +
23A ALA* 3.8 7.7 - - - +
25A LEU* 1.3 80.1 - - - +
27A LYS* 1.3 61.6 + - - +
29A PRO* 3.7 9.4 - - - +
32A ARG* 4.6 4.7 + - - -
43A ASP* 5.2 10.3 + - - +
1B GLY 3.7 21.7 + - - +
4B GLN* 5.6 4.0 - - - +
114B SER* 2.9 40.2 + - - +
115B PHE 5.2 2.3 - - - +
116B ASP* 5.9 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA 2.9 17.6 + - - +
26A ASN* 1.3 77.1 - - - +
28A TYR* 1.3 102.7 + - + +
29A PRO* 3.4 7.1 - - - +
102A VAL* 3.8 15.0 - - - -
103A ALA* 4.3 12.3 - - + -
106A GLU* 3.2 39.2 + - - +
114B SER* 4.0 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 2.9 19.8 + + - +
25A LEU* 3.3 6.2 - - - +
27A LYS* 1.3 110.4 - - + +
29A PRO* 1.3 66.3 - - - +
30A ASP* 3.1 3.8 - - - -
31A GLU* 2.9 35.9 + - + +
99A LYS* 3.3 62.1 - - + +
102A VAL* 3.3 27.7 - - - +
103A ALA* 4.4 1.8 - - + -
----------------------------------------------------------
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