Contacts of the helix formed by residues 27 - 39 (chain A) in PDB entry 4HRO
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 27 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASP 4.2 6.3 - - - +
26A ALA* 1.3 76.9 - - - +
28A VAL* 1.3 64.9 + - - +
29A GLY* 3.3 3.6 + - - -
30A ASP* 3.0 32.0 + - - +
31A ALA* 2.9 18.9 + - - +
68A LEU 3.2 13.1 + - - +
69A GLY* 3.7 21.1 - - - +
70A GLU 3.2 9.2 - - - +
71A ALA* 4.7 0.9 - - - +
72A THR* 3.7 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A TRP* 4.1 7.2 - - + -
27A THR* 1.3 72.6 - - - +
29A GLY* 1.3 58.3 + - - +
31A ALA* 3.1 4.7 + - - +
32A LEU* 2.8 27.0 + - - +
59A VAL* 3.7 30.7 - - + -
61A ARG* 4.4 11.0 - - + -
66A ALA* 4.3 11.7 - - + -
67A ALA 3.7 19.1 - - - +
68A LEU* 4.0 9.9 - - + -
70A GLU* 2.8 24.2 + - + +
71A ALA 3.7 14.1 - - - +
72A THR* 3.6 11.8 - - + +
78A LEU* 5.0 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR* 3.7 1.6 - - - -
28A VAL* 1.3 78.2 - - - +
30A ASP* 1.3 56.2 + - - +
32A LEU* 3.2 5.4 + - - +
33A ASP* 2.9 33.8 + - - +
47A PHE* 5.7 0.2 - - - -
68A LEU* 2.8 42.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 4.6 2.9 - - + +
25A ASP 4.4 1.4 - - - +
26A ALA* 3.4 17.9 - - + -
27A THR* 3.0 40.2 + - - +
29A GLY* 1.3 75.8 - - - +
31A ALA* 1.3 58.0 + - - +
33A ASP* 3.2 11.8 + - - +
34A ALA* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.2 15.3 - - - -
3A TRP* 3.0 17.7 + - - +
20A VAL* 4.5 1.4 - - + +
22A VAL* 4.1 16.1 - - + +
26A ALA* 4.9 0.4 - - - +
27A THR 2.9 12.2 + - - +
28A VAL 3.5 7.9 - - - +
30A ASP* 1.3 75.4 - - - +
32A LEU* 1.3 58.5 + - - +
34A ALA* 3.3 3.5 + - - +
35A LEU 3.0 18.2 + - - -
72A THR* 4.3 3.1 - - + -
78A LEU* 3.7 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A TRP* 3.5 18.5 - - + -
28A VAL 2.8 13.2 + - - +
29A GLY* 3.5 9.9 - - - +
30A ASP 3.2 0.2 - - - -
31A ALA* 1.3 74.7 - - - +
33A ASP* 1.3 60.1 + - - +
35A LEU* 3.2 15.7 + - + +
36A VAL* 3.0 34.7 + - + +
46A VAL* 3.9 15.7 - - + -
47A PHE* 3.7 28.3 - - + -
53A LEU* 4.0 14.1 - - + -
59A VAL* 4.9 5.2 - - + -
68A LEU* 4.1 20.4 - - + -
80A LEU* 3.9 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLY 2.9 16.3 + - - +
30A ASP* 3.6 14.5 - - - +
32A LEU* 1.3 75.2 - - - +
34A ALA* 1.3 56.5 + - - +
36A VAL* 3.4 5.4 + - - +
37A GLY* 2.8 26.2 + - - -
47A PHE* 3.6 26.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 4.1 14.7 - - + +
21A ASP 5.2 2.7 - - - +
22A VAL* 3.9 22.4 - - + -
30A ASP 2.9 13.1 + - - +
31A ALA 3.5 8.3 - - - +
32A LEU 3.2 0.2 - - - -
33A ASP* 1.3 74.3 - - - +
35A LEU* 1.3 65.4 + - - +
37A GLY* 3.3 2.5 + - - +
38A ALA* 3.0 22.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
3A TRP* 3.7 34.5 - - + +
5A LEU* 3.7 26.7 - - + -
18A VAL* 3.7 37.5 - - + -
20A VAL* 3.9 8.0 - - - +
31A ALA 3.0 7.3 + - - +
32A LEU* 3.3 14.8 - - + +
34A ALA* 1.3 74.9 - - - +
36A VAL* 1.3 64.2 + - + +
38A ALA* 3.1 6.8 + - - +
39A HIS* 3.1 19.4 + - + +
42A LEU* 3.8 19.7 - - + +
80A LEU* 3.9 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.0 21.5 + - + +
33A ASP* 3.9 6.1 - - - +
35A LEU* 1.3 77.5 - - + +
37A GLY* 1.3 62.9 + - - +
39A HIS 2.9 5.0 - - - -
40A PRO* 2.9 34.1 - - + +
42A LEU* 4.3 15.9 - - + -
43A GLU* 3.6 40.6 - - + +
46A VAL* 4.5 11.4 - - + -
47A PHE* 4.0 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASP 2.8 15.7 + - - -
34A ALA* 3.7 4.3 - - - -
35A LEU 3.3 0.2 - - - -
36A VAL* 1.3 78.4 - - - +
38A ALA* 1.3 59.2 + - - +
40A PRO* 3.5 16.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 4.3 11.7 - - + -
19A ARG 5.4 2.0 - - - +
20A VAL* 5.3 3.1 - - + -
34A ALA 3.0 13.4 + - - +
35A LEU* 3.1 11.0 + - - +
37A GLY* 1.3 76.3 - - - +
39A HIS* 1.3 83.5 + - + +
40A PRO* 3.7 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL 5.3 1.5 + - - +
13A ALA* 3.3 35.6 + - + -
15A SER* 5.7 2.9 - - - -
18A VAL* 3.9 32.8 - - + +
35A LEU* 3.1 6.8 + - + -
36A VAL 2.9 7.5 + - - +
38A ALA* 1.3 97.4 + - + +
40A PRO* 1.3 61.4 - - - +
41A ALA* 3.1 4.5 - - + +
42A LEU* 2.9 43.1 + - + +
----------------------------------------------------------
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