Contacts of the helix formed by residues 27 - 38 (chain A) in PDB entry 1TF6
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 ASN 27 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TYR* 3.0 44.1 - - + +
26A LYS* 1.3 68.0 - - - +
28A TRP* 1.3 50.6 + - - +
30A LEU* 3.0 6.8 + - - +
31A GLN* 2.7 67.7 + - - +
35C G 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS* 2.7 33.0 + - + +
27A ASN* 1.3 78.5 - - - +
29A LYS* 1.3 89.5 + - + +
31A GLN* 3.1 11.1 + - - +
32A ALA* 2.8 37.4 + - + +
55A THR 5.6 4.0 - - - -
56A SER* 6.1 4.0 - - - -
26B G 3.8 24.7 - + - -
27B A 3.3 31.6 - - - -
28B G 3.7 11.8 + - - -
35C G 4.3 8.5 + + - -
36C T 3.2 34.0 - - + +
37C C 4.4 5.8 - - - -
38C T 5.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.3 26.9 - - + +
25A ASN* 2.8 32.9 + - - +
26A LYS* 2.5 36.9 + - + +
28A TRP* 1.3 98.0 - - + +
30A LEU* 1.3 63.7 + - - +
32A ALA* 3.1 5.6 + - - +
33A HIS* 3.0 20.1 + - - +
26B G 3.7 20.2 + - + +
27B A 2.5 49.2 + - - +
28B G 5.1 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TYR* 3.7 16.6 - - + -
14A ILE 3.0 48.2 - - - +
15A CYS* 4.0 9.0 - - - +
16A SER* 4.8 2.7 - - - +
24A TYR* 3.2 21.6 - - + -
26A LYS 3.4 1.8 + - - -
27A ASN* 3.0 10.3 + - - +
29A LYS* 1.3 79.1 - - - +
31A GLN* 1.3 59.8 + - - +
33A HIS* 2.8 8.3 + - + +
34A LEU* 2.6 69.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASN* 2.7 51.2 + - - +
28A TRP* 3.2 17.0 - - - +
30A LEU* 1.3 82.6 - - - +
32A ALA* 1.3 55.8 - - - +
34A LEU* 3.0 32.2 - - - +
35A CYS* 3.0 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TRP* 2.8 25.6 + - + +
29A LYS* 3.1 7.8 + - - +
31A GLN* 1.3 71.7 - - - +
33A HIS* 1.3 66.7 + - - +
35A CYS* 3.2 17.1 + - - +
36A LYS* 3.5 4.7 + - - +
55A THR* 4.0 37.8 + - - +
25B G 6.4 1.8 - - + -
26B G 6.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A CYS* 2.9 17.2 - - + -
20A CYS* 3.1 11.7 - - - -
22A ALA* 3.6 5.6 - - + -
24A TYR* 3.2 41.5 + + + +
29A LYS 3.0 5.3 + - - +
30A LEU* 2.8 15.0 + - + +
32A ALA* 1.3 77.8 - - - +
34A LEU* 1.3 60.2 + - - +
36A LYS* 2.8 45.4 + - + +
37A HIS* 2.9 11.0 + + - -
201A ZN 2.0 37.3 - - - -
26B G 4.4 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A SER* 3.7 34.5 - - - +
17A PHE* 4.3 19.3 - - + -
30A LEU* 2.6 39.5 + - + +
31A GLN* 3.0 34.5 - - - +
32A ALA 3.2 0.2 - - - -
33A HIS* 1.3 79.3 - - + +
35A CYS* 1.3 54.7 + - - +
36A LYS 2.7 0.9 + - - -
37A HIS* 2.6 29.2 + - + +
38A THR* 2.9 15.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLN 3.0 24.5 - - - -
32A ALA* 3.2 2.6 + - - +
34A LEU* 1.3 78.0 - - - +
36A LYS* 1.3 57.8 + - - +
38A THR* 3.0 11.7 - - - -
39A GLY* 2.7 29.6 + - - +
40A GLU* 3.6 17.1 + - - +
42A PRO* 3.8 19.5 - - - -
55A THR* 3.2 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ALA 3.5 3.5 + - - +
33A HIS* 2.8 33.2 + - + +
34A LEU 2.7 1.0 + - - -
35A CYS* 1.3 80.8 - - - +
37A HIS* 1.3 66.5 + - + +
38A THR 4.1 0.2 - - - -
39A GLY* 4.0 4.2 + - - -
25B G 3.0 43.7 + - - +
26B G 4.8 9.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A CYS* 3.4 10.5 - - - -
17A PHE* 3.0 52.7 - + + -
20A CYS* 3.8 5.8 - - + -
33A HIS* 2.9 22.4 + + - -
34A LEU* 2.6 13.5 + - - +
36A LYS* 1.3 80.9 - - + +
38A THR* 1.3 65.3 + - - +
201A ZN 1.8 39.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 4.9 12.1 - - + -
34A LEU* 2.9 17.1 + - + +
35A CYS* 3.0 16.8 + - - -
36A LYS 4.1 0.4 - - - -
37A HIS* 1.3 81.5 - - - +
39A GLY* 1.3 57.4 + - - -
40A GLU* 4.0 26.8 + - + +
----------------------------------------------------------
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