Contacts of the helix formed by residues 19 - 35 (chain B) in PDB entry 2HKU
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 THR 19 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ARG* 1.3 64.9 + - - +
21B ASP* 2.7 15.2 + - - +
22B ALA* 2.9 35.7 + - + +
23B LEU* 3.4 14.5 + - + +
47B ALA 5.6 1.6 - - - +
48B GLY 5.8 1.8 - - - +
49B ALA* 5.4 6.3 - - + -
53B GLN* 4.4 20.2 - - - +
57B TYR* 5.2 6.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B THR* 1.3 75.0 - - - +
21B ASP* 1.3 73.1 + - - +
23B LEU* 3.4 7.5 + - - +
24B PHE* 3.0 22.9 + - - +
57B TYR* 3.3 61.1 - - + -
58B TYR* 3.0 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B THR* 2.7 14.7 + - - -
20B ARG* 1.3 100.4 + - - +
22B ALA* 1.3 55.4 + - - +
24B PHE* 3.7 7.4 - - - +
25B THR* 2.4 42.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B THR* 2.9 28.5 + - + +
21B ASP* 1.3 78.7 - - - +
23B LEU* 1.3 62.9 + - + +
25B THR* 3.6 5.2 - - - -
26B ALA* 3.0 20.3 + - - +
47B ALA* 3.4 34.2 - - + +
49B ALA* 6.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B THR* 3.4 10.7 + - + +
20B ARG 3.4 8.0 + - - +
21B ASP 3.3 0.2 - - - -
22B ALA* 1.3 79.7 - - - +
24B PHE* 1.3 54.4 + - - +
26B ALA* 3.6 1.6 - - - +
27B ALA* 2.6 39.7 + - - +
43B ILE* 4.0 14.0 - - + +
44B CYS* 4.0 9.6 - - - -
47B ALA* 4.0 10.3 - - + -
49B ALA* 3.7 25.4 - - + -
53B GLN* 3.6 35.9 - - + +
54B VAL* 3.9 29.6 - - + -
57B TYR* 4.8 5.4 - - + -
58B TYR* 4.3 15.3 - - + -
64B LEU* 4.9 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ARG 3.0 17.4 + - - +
21B ASP* 3.7 9.0 - - - +
23B LEU* 1.3 73.9 - - - +
25B THR* 1.3 54.4 + - - +
27B ALA* 3.9 0.7 - - - +
28B THR* 2.6 56.6 + - + +
58B TYR* 3.5 21.2 + + - +
64B LEU* 4.3 11.2 - - + +
67B GLU* 3.7 26.9 - - + -
68B VAL* 3.7 33.4 - - + +
71B ALA* 3.8 20.6 - - + -
75B ARG* 4.7 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ASP* 2.4 28.0 + - - +
22B ALA* 3.6 6.0 - - - -
24B PHE* 1.3 75.3 - - - +
26B ALA* 1.3 65.6 + - - +
28B THR* 3.3 7.1 + - - +
29B GLU* 3.0 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ALA 3.0 19.4 + - - +
23B LEU 3.6 2.2 - - - +
25B THR* 1.3 72.3 - - - +
27B ALA* 1.3 64.2 + - - +
29B GLU* 3.2 10.6 + - - +
30B LEU* 3.0 29.5 + - + +
43B ILE* 3.7 24.2 - - + +
46B ALA* 3.7 23.3 - - + +
47B ALA* 3.8 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU 2.6 21.3 + - - +
24B PHE 3.9 3.4 - - - +
26B ALA* 1.3 74.2 - - - +
28B THR* 1.3 58.5 + - - +
30B LEU 4.6 0.2 - - - +
31B PHE* 2.8 48.8 + - + +
43B ILE* 3.8 32.5 - - + +
64B LEU* 4.1 10.1 - - + -
68B VAL* 3.9 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 2.6 64.5 + - + +
25B THR* 3.3 6.1 + - - +
26B ALA 3.3 0.4 - - - -
27B ALA* 1.3 77.0 - - - +
29B GLU* 1.3 62.3 + - - +
32B LEU* 3.0 38.1 + - - +
68B VAL* 3.7 22.4 - - + +
72B ALA* 5.7 0.2 - - - -
75B ARG* 3.3 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B THR* 3.0 32.5 + - + +
26B ALA* 3.2 7.8 + - - +
28B THR* 1.3 76.6 + - - +
30B LEU* 1.3 64.7 + - + +
32B LEU* 4.0 7.0 - - - +
33B GLU* 3.2 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA 3.0 20.3 + - - +
27B ALA 4.1 0.9 - - - +
29B GLU* 1.3 75.9 - - + +
31B PHE* 1.3 57.2 + - - +
33B GLU* 3.9 3.5 - - - +
34B HIS* 2.6 50.4 + - + +
38B VAL* 3.6 21.4 - - + +
42B GLN* 4.0 27.4 - - + +
43B ILE* 3.7 40.2 - - + +
46B ALA* 4.1 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ALA* 2.8 32.2 + - + +
30B LEU* 1.3 74.3 - - - +
32B LEU* 1.3 62.8 + - - +
35B GLY* 2.7 48.7 + - - +
36B GLU 3.9 14.6 - - - -
38B VAL* 4.0 10.5 - - + -
43B ILE* 3.4 30.7 - - + -
61B LYS* 4.0 18.2 - - + -
64B LEU* 4.4 3.8 - - + -
65B PHE* 3.7 41.7 - + + -
68B VAL* 3.9 14.4 - - + -
111B LEU* 3.7 27.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B THR* 3.0 41.3 + - - +
29B GLU* 4.0 6.1 - - - +
31B PHE* 1.3 76.7 - - - +
33B GLU* 1.3 62.3 + - + +
72B ALA* 4.5 2.2 - - + -
75B ARG* 4.3 11.9 - - - +
107B PRO* 3.5 44.4 - - + +
108B SER* 3.6 26.5 - - - +
111B LEU* 3.9 18.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 4.6 12.5 + - - +
29B GLU 3.2 16.4 + - - +
30B LEU* 3.9 3.9 - - - +
31B PHE 3.1 0.2 - - - -
32B LEU* 1.3 83.2 - - - +
34B HIS* 1.3 93.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 5.5 6.6 + - - -
30B LEU* 2.6 27.4 + - + -
33B GLU* 1.3 110.2 + - + +
35B GLY* 1.3 59.3 + - - +
37B GLY* 4.8 2.6 + - - -
38B VAL* 3.7 20.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PHE* 2.7 39.9 + - - -
32B LEU 4.9 0.2 + - - -
33B GLU 3.8 0.4 - - - -
34B HIS* 1.3 73.6 - - - +
36B GLU* 1.3 65.7 + - - -
37B GLY 3.0 5.7 + - - -
38B VAL* 3.3 7.8 - - - +
65B PHE* 4.2 0.7 - - - -
111B LEU* 4.5 8.3 - - - -
----------------------------------------------------------
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