Contacts of the helix formed by residues 12 - 24 (chain H) in PDB entry 2H1O
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 12 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER* 3.9 26.0 - - - +
29A ILE* 5.4 1.0 - - - +
40E ALA* 4.8 0.4 - - - +
10H SER* 2.6 12.5 + - - +
11H GLU* 1.3 76.0 - - - +
13H THR* 1.3 55.4 + - - +
14H HIS 2.9 3.4 - - - +
15H ASN* 2.9 24.3 + - - +
16H ALA* 2.7 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 13 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E LEU* 3.6 16.4 - - + -
37E ASP* 2.5 65.7 + - - +
40E ALA* 3.6 14.6 - - + +
9H LEU* 4.0 9.4 - - + -
10H SER* 2.7 18.3 + - - -
12H ALA* 1.3 76.6 - - - +
14H HIS* 1.3 62.9 + - - +
16H ALA* 3.1 2.9 + - - +
17H ILE* 3.0 24.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 14 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E ALA* 4.4 17.9 - - + -
3E SER 5.2 3.7 + - - -
4E VAL* 4.9 23.1 - - + +
9H LEU* 3.5 21.5 - - + +
10H SER 3.0 8.7 + - - +
11H GLU* 4.1 9.0 - - - -
12H ALA 4.0 4.3 - - - +
13H THR* 1.3 79.1 - - - +
15H ASN* 1.3 61.7 + - - +
17H ILE* 3.8 5.9 - - - +
18H LYS* 2.9 52.3 + - + +
28H THR* 5.0 10.6 - - + +
27U A 4.1 20.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 15 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TRP* 5.9 1.0 - - - +
27A SER* 3.1 32.3 + - - +
28A LEU* 4.8 9.5 - - + +
29A ILE* 4.7 6.3 - - + +
11H GLU* 4.0 5.7 + - - +
12H ALA* 2.9 24.1 + - - +
14H HIS* 1.3 80.7 + - - +
16H ALA* 1.3 65.9 + - - +
17H ILE 3.2 0.2 + - - -
18H LYS* 3.2 7.8 + - - +
19H PHE* 2.9 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 16 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 3.2 28.8 - - + +
40E ALA* 3.3 42.4 - - + +
43E GLN* 4.4 2.5 - - + -
12H ALA 2.7 13.2 + - - +
13H THR 3.1 2.0 + - - +
15H ASN* 1.3 72.8 - - - +
17H ILE* 1.3 63.9 + - - +
19H PHE* 3.2 5.2 - - - +
20H ARG* 3.1 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 17 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E LEU* 3.9 22.9 - - + +
39E ILE* 3.1 42.4 - - + -
9H LEU* 6.4 0.2 - - + -
13H THR* 3.0 22.5 + - + +
14H HIS* 3.8 5.2 - - - +
16H ALA* 1.3 73.4 - - + +
18H LYS* 1.3 69.2 + - - +
19H PHE 2.8 2.7 + - - -
20H ARG* 2.9 8.8 + - - +
21H ALA* 2.8 19.9 + - - +
28H THR* 3.9 13.5 - - + -
31H GLU* 4.3 14.3 - - + +
32H ILE* 3.5 26.9 - - + -
35H ILE* 4.1 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 18 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H HIS* 2.9 38.0 + - + +
15H ASN* 3.4 9.2 - - - +
17H ILE* 1.3 73.7 - - - +
19H PHE* 1.3 58.8 + - - +
21H ALA* 3.0 20.5 - - - +
22H ARG* 2.9 47.3 + - - +
28H THR* 2.9 24.6 - - - +
26U G 3.2 34.8 + - - -
27U A 4.7 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 19 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 4.1 18.2 - - + -
31A GLU* 3.6 43.3 - - + -
32A ASP* 3.7 27.1 - - + +
43E GLN* 3.0 30.5 - - - -
15H ASN 2.9 13.0 + - - +
16H ALA* 3.2 11.4 - - - +
17H ILE 2.8 0.2 + - - -
18H LYS* 1.3 72.4 - - - +
20H ARG* 1.3 66.6 + - - +
21H ALA 2.9 5.6 + - - -
22H ARG* 3.1 5.2 + - + +
23H ALA* 3.0 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 20 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E ILE* 4.6 29.7 - - - +
43E GLN* 2.9 47.2 - - - +
16H ALA 3.3 13.2 - - - +
17H ILE* 2.9 11.1 + - + +
19H PHE* 1.3 76.4 - - - +
21H ALA* 1.3 63.1 + - - +
23H ALA* 4.0 6.2 - - - +
24H ALA* 3.4 20.3 + - - +
26H ARG* 5.1 0.6 + - - +
31H GLU* 3.7 25.7 + - - +
34H LEU* 6.3 0.6 - - - +
35H ILE* 4.7 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 21 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H ILE 2.8 8.7 + - - +
18H LYS 3.0 12.1 - - - +
19H PHE 2.9 0.8 - - - -
20H ARG* 1.3 75.9 - - - +
22H ARG* 1.3 67.4 + - - +
24H ALA 3.0 9.5 + - - -
26H ARG* 3.0 35.2 + - - +
28H THR* 3.7 20.6 - - - +
31H GLU* 3.2 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 22 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H LYS* 2.9 44.6 + - + +
19H PHE* 4.0 4.3 - - + +
21H ALA* 1.3 80.4 - - - +
23H ALA* 1.3 56.4 + - - +
25H GLY* 2.6 26.5 + - - +
26H ARG 4.2 6.5 + - - +
27H SER* 4.0 5.2 - - - +
28H THR* 3.1 23.2 + - - +
26U G 3.0 30.4 + - - -
51V A 5.8 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H PHE* 3.0 33.7 + - + +
20H ARG* 4.0 9.2 - - - +
21H ALA 3.2 0.2 - - - -
22H ARG* 1.3 77.7 - - - +
24H ALA* 1.3 59.3 + - + +
25H GLY 3.6 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H ARG 3.4 10.0 + - - +
21H ALA 3.0 2.4 + - - +
22H ARG 3.0 0.6 - - - -
23H ALA* 1.3 78.0 - - - +
25H GLY* 1.3 62.2 + - - +
26H ARG* 3.2 47.1 + - - +
----------------------------------------------------------
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