Contacts of the helix formed by residues 47 - 55 (chain A) in PDB entry 1HTI
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 TYR 47 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLY 3.2 24.0 + - - -
17A ARG* 3.0 18.3 - - - +
18A LYS* 3.5 19.3 - - + -
21A LEU* 3.8 20.2 - - + -
43A PRO* 3.8 4.1 - - + +
44A PRO* 2.8 23.9 + - + +
46A ALA* 1.3 83.0 - - + +
48A ILE* 1.3 57.6 + - - -
49A ASP 3.1 3.4 - - - +
50A PHE* 3.9 24.9 - + + -
51A ALA* 3.0 27.2 + - - +
82B MET* 3.6 26.0 - - + +
85B ASP* 2.8 35.1 + - - +
86B CYS* 3.8 17.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PRO* 4.2 17.0 - - + +
45A THR* 3.5 34.4 + - - +
46A ALA 3.6 0.6 - - - -
47A TYR* 1.3 78.1 - - - +
49A ASP* 1.4 62.4 + - - +
51A ALA* 4.7 0.7 - - - -
52A ARG* 3.3 20.4 + - - +
61A VAL* 3.9 8.1 - - + +
62A ALA 4.4 9.2 - - - +
63A ALA* 3.8 25.8 - - + -
64A GLN 5.1 0.2 - - - +
78A ILE* 4.2 14.8 - - + -
83A ILE* 4.9 4.7 - - + +
86A CYS* 4.2 16.5 - - + +
88A ALA* 3.8 30.1 - - + -
46B ALA* 5.1 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ALA 5.0 2.6 + - - +
47A TYR* 3.1 0.8 - - - +
48A ILE* 1.4 76.3 - - - +
50A PHE* 1.3 67.7 + - - +
52A ARG* 3.1 4.7 + - - +
53A GLN* 2.9 46.6 + - - +
86A CYS* 4.0 23.4 - - - +
18B LYS* 2.8 39.1 + - - -
46B ALA 4.7 10.7 + - - +
47B TYR* 5.8 0.4 - - - -
49B ASP* 5.7 8.0 - - + +
50B PHE* 4.5 14.7 + - - +
53B GLN* 5.1 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LYS* 3.5 58.3 - - + -
21A LEU* 4.0 21.3 - - + -
22A GLY* 3.8 15.0 - - - -
25A ILE* 3.9 13.9 - - + -
46A ALA 5.4 0.6 + - - +
47A TYR* 3.6 35.1 + + + +
48A ILE 3.6 0.2 - - - -
49A ASP* 1.3 81.0 - - - +
51A ALA* 1.4 62.6 + - - +
53A GLN* 3.3 10.8 + - - +
54A LYS* 3.2 52.4 + - + +
49B ASP* 4.6 9.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TRP* 4.7 5.4 - - + -
21A LEU* 5.5 0.2 - - + -
25A ILE* 4.1 19.5 - - + +
43A PRO* 3.6 26.2 - - + -
47A TYR* 3.0 20.8 + - + +
48A ILE 4.2 2.0 - - - +
50A PHE* 1.4 76.3 - - + +
52A ARG* 1.3 59.7 + - - +
54A LYS* 3.0 3.5 + - - +
55A LEU* 2.9 35.9 + - + +
61A VAL* 4.5 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ILE 3.3 17.6 + - - +
49A ASP 3.1 2.5 + - - +
51A ALA* 1.3 77.3 - - - +
53A GLN* 1.3 66.8 + - + +
55A LEU* 3.1 38.0 + - - +
56A ASP 3.3 9.3 + - - -
57A PRO* 3.5 10.7 + - - +
59A ILE 2.8 30.5 + - - -
60A ALA* 3.5 4.2 - - - +
61A VAL* 3.3 35.2 - - + +
86A CYS 3.3 24.0 - - - +
87A GLY* 3.5 24.7 + - - +
89A THR* 5.5 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ASP* 2.9 43.5 + - - +
50A PHE* 3.4 11.9 + - - +
52A ARG* 1.3 81.4 - - + +
54A LYS* 1.3 60.3 + - + +
55A LEU 4.8 1.0 - - - +
18B LYS* 6.0 0.2 - - - -
53B GLN* 5.2 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LYS 5.5 1.2 + - - -
22A GLY* 4.8 8.7 - - - +
25A ILE* 3.4 25.0 - - + +
29A ASN* 3.2 18.9 + - - -
50A PHE* 3.2 42.8 + - + +
51A ALA 3.0 3.2 + - - -
53A GLN* 1.3 75.5 - - + +
55A LEU* 1.3 59.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TRP* 4.7 10.5 - - + -
25A ILE* 3.3 18.6 - - + +
28A LEU* 4.1 20.6 - - + -
29A ASN* 3.3 23.1 - - - +
41A CYS* 4.4 13.5 - - + -
43A PRO* 5.8 0.2 - - + -
51A ALA* 2.9 18.1 + - + +
52A ARG* 3.1 22.5 + - - +
53A GLN 3.5 2.1 - - - +
54A LYS* 1.3 79.8 - - - +
56A ASP* 1.3 65.0 + - - +
57A PRO* 3.4 4.3 - - - +
59A ILE* 4.1 28.5 - - + -
61A VAL* 3.7 24.9 - - + -
----------------------------------------------------------
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