Contacts of the helix formed by residues 18 - 28 (chain A) in PDB entry 1XTR
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 GLY 18 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A SER 3.2 0.8 - - - -
17A VAL* 1.3 80.2 - - - +
19A LYS* 1.3 66.7 + - - +
20A SER 3.2 2.9 - - - -
21A SER* 3.9 0.2 - - - -
22A LEU* 2.9 29.6 + - - +
84A VAL* 5.1 1.8 - - - -
119A ASN* 3.8 3.3 + - - -
179A GNP 3.0 40.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 3.7 22.7 - - + +
12A LEU* 3.4 27.6 - - - -
13A GLY* 3.1 13.8 + - - +
14A TYR 2.8 21.6 + - - -
17A VAL* 3.7 2.6 - - + +
18A GLY* 1.3 76.5 - - - +
20A SER* 1.3 53.7 + - - +
22A LEU* 3.9 3.3 - - - +
23A THR* 2.5 36.6 + - - -
60A ASP* 3.4 12.3 - - - +
61A THR* 3.3 24.0 - - - -
63A GLY* 3.7 4.0 - - - +
84A VAL* 3.4 24.0 - - + -
179A GNP 2.7 45.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LYS* 1.3 76.2 - - - +
21A SER* 1.3 58.1 + - - +
23A THR* 2.8 2.5 + - - -
24A ILE* 2.6 50.1 + - - +
32A VAL* 6.2 1.6 - - - -
36A ASP 5.9 0.9 - - - -
38A THR* 3.3 5.5 + - - -
41A ASN* 5.5 1.1 - - - -
60A ASP* 2.5 22.3 + - - -
178A MG 2.3 31.5 - - - -
179A GNP 3.2 11.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLY 3.9 0.9 - - - -
20A SER* 1.3 72.0 - - - +
22A LEU* 1.3 57.7 + - - +
24A ILE* 3.9 4.7 - - - +
25A GLN* 2.9 32.7 + - - +
30A GLN 4.8 1.0 - - - +
31A PHE* 4.2 9.4 - - - -
32A VAL* 4.2 16.2 + - - +
150A ALA* 3.4 22.7 - - - +
179A GNP 2.6 56.0 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
11A ILE* 6.1 2.5 - - + -
18A GLY 2.9 18.0 + - - +
19A LYS* 3.9 4.3 - - - +
21A SER* 1.3 76.8 - - - +
23A THR* 1.3 60.6 + - - +
25A GLN* 3.8 2.2 - - - +
26A PHE* 3.4 19.2 + - - +
82A ILE* 6.0 1.6 - - + -
84A VAL* 4.4 11.0 - - + -
117A VAL* 4.1 13.9 - - + -
119A ASN* 3.8 17.5 - - - +
148A SER* 3.4 23.8 - - - +
150A ALA* 3.6 13.6 - - + +
156A ALA* 3.5 30.7 - - + +
159A VAL* 4.3 10.3 - - + -
160A PHE* 3.8 15.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 3.9 19.2 - - + +
19A LYS 2.5 20.9 + - - -
20A SER* 2.8 11.7 + - - -
22A LEU* 1.3 75.4 - - - +
24A ILE* 1.3 60.7 + - - +
26A PHE* 3.3 2.4 + - - +
27A VAL* 2.8 40.2 + - + +
43A PHE* 3.9 31.9 - - + -
58A LEU* 4.3 15.9 - - + -
60A ASP* 4.3 10.3 + - + -
160A PHE* 4.1 8.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A SER* 2.6 49.0 + - - +
21A SER* 4.0 4.5 - - - +
23A THR* 1.3 70.7 - - - +
25A GLN* 1.3 63.4 - - - +
27A VAL* 4.3 5.4 - - - -
28A GLU* 2.6 66.1 + - + +
29A GLY 3.1 3.8 + - - -
30A GLN* 3.9 14.1 - - + +
32A VAL* 4.6 26.5 - - + -
41A ASN* 6.0 1.1 - - - +
43A PHE* 3.8 26.7 - - + -
60A ASP* 4.9 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A SER 2.9 19.1 + - - +
22A LEU 3.8 5.2 - - - +
24A ILE* 1.3 78.7 - - - +
26A PHE* 1.3 57.7 + - - +
29A GLY* 3.0 37.0 + - - +
30A GLN 3.3 22.1 + - - +
31A PHE* 4.1 2.6 - - - +
150A ALA 3.0 29.6 + - - +
151A LYS* 3.7 18.8 + - - +
153A ASN* 3.3 43.0 + - - +
156A ALA* 3.8 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU 3.4 7.7 + - - +
23A THR 3.3 5.3 + - - +
24A ILE 3.1 0.2 - - - -
25A GLN* 1.3 84.0 - - - +
27A VAL* 1.3 65.9 + - + +
29A GLY* 4.4 1.0 + - - -
45A LYS* 3.4 29.3 + - + -
47A ILE* 3.3 42.0 - - + -
56A LEU* 4.2 4.7 - - + -
58A LEU* 3.7 25.6 - - + -
153A ASN* 4.7 6.4 + - - +
156A ALA* 4.4 7.6 - - + +
157A VAL* 3.9 30.8 - - + +
160A PHE* 3.4 50.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A THR* 2.8 31.2 + - + +
24A ILE* 4.0 4.3 - - - +
26A PHE* 1.3 79.4 - - + +
28A GLU* 1.3 67.6 + - + +
43A PHE* 3.8 36.8 - - + -
44A THR 5.7 0.7 - - - -
45A LYS* 2.9 43.7 + - + +
58A LEU* 3.9 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 2.6 41.9 + - + +
27A VAL* 1.3 85.6 - - + +
29A GLY* 1.3 57.8 + - - +
30A GLN* 3.5 15.7 + - + +
32A VAL* 5.4 3.5 - - - +
43A PHE* 3.8 21.7 - - + -
----------------------------------------------------------
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