Contacts of the helix formed by residues 15 - 23 (chain A) in PDB entry 1TQ6
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 ASP 15 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASN* 2.9 20.6 + - - +
14A ASN* 1.3 78.7 - - - +
16A LEU* 1.3 57.9 + - - +
17A PRO* 3.5 16.0 - - - +
18A SER* 2.9 32.1 + - - -
19A SER* 2.8 31.8 + - - -
379A PRO* 4.3 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASN 4.0 2.4 + - - -
15A ASP* 1.3 67.6 + - - +
17A PRO* 1.3 78.5 - - + +
18A SER 3.1 1.1 - - - -
19A SER* 2.9 4.7 + - - -
20A PHE* 2.7 24.9 + - - +
46A MET* 4.4 19.5 - - + -
287A PHE* 3.5 21.3 - - + -
291A LEU* 3.2 37.9 - - + -
378A LEU* 4.6 5.4 - - + -
379A PRO* 4.8 6.7 - - + +
382A SER* 5.4 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASP* 3.5 17.9 - - - +
16A LEU* 1.3 96.7 - - + +
18A SER* 1.3 61.5 + - - +
20A PHE* 3.3 2.9 + - - +
21A THR* 3.3 22.2 + - - -
43A GLU* 3.6 28.5 - - + +
46A MET* 3.9 25.1 - - + +
47A ARG* 4.0 34.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASN* 3.1 20.8 + - - -
15A ASP* 2.9 22.2 + - - -
17A PRO* 1.3 82.9 - - - +
19A SER* 1.3 56.5 + - - +
21A THR* 3.5 5.8 + - - -
22A GLY* 2.9 26.9 + - - -
43A GLU* 4.0 5.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASN* 2.7 25.4 + - - +
15A ASP 2.8 15.0 + - - -
16A LEU* 2.9 5.2 + - - -
18A SER* 1.3 73.4 - - - +
20A PHE* 1.3 67.9 + - - +
22A GLY* 4.0 2.4 - - - -
23A TYR* 3.4 13.9 + - - +
283A TRP* 3.6 11.1 - - - -
377A LEU 5.7 1.6 - - - -
378A LEU* 5.1 7.6 - - - -
379A PRO* 3.2 28.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU 2.7 15.3 + - - +
17A PRO 3.5 4.0 - - - +
18A SER 3.2 0.2 - - - -
19A SER* 1.3 79.4 - - - +
21A THR* 1.3 73.7 + - + +
23A TYR* 3.3 4.9 - - - +
24A PHE* 3.7 14.9 - + - -
39A LEU* 3.6 23.3 - - + -
42A ILE* 3.6 27.6 - - + -
43A GLU* 5.1 2.0 - - + -
46A MET* 3.8 17.5 - - + -
58A ILE* 5.0 1.3 - - + -
283A TRP* 3.0 38.6 + + - +
284A LEU* 4.1 18.6 - - + -
287A PHE* 3.4 59.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PRO 3.3 9.5 + - - -
18A SER* 3.5 5.0 + - - -
20A PHE* 1.3 90.3 - - + +
22A GLY* 1.3 63.5 + - - +
23A TYR 3.0 6.4 + - - -
24A PHE* 3.4 20.0 + - - +
25A LYS* 4.2 10.3 + - - +
36A GLN* 6.0 1.6 - - - -
39A LEU* 3.8 28.1 - - + +
40A ASN* 6.0 0.7 - - - +
43A GLU* 3.6 39.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A SER 2.9 19.0 + - - -
19A SER* 3.5 3.6 + - - -
20A PHE 3.3 0.6 - - - -
21A THR* 1.3 78.1 + - - +
23A TYR* 1.3 61.3 + - - +
24A PHE 3.4 0.4 + - - -
25A LYS* 3.7 34.3 + - - +
26A LYS* 4.5 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A SER 3.4 4.9 + - - +
20A PHE 3.3 2.9 - - - +
21A THR 3.0 0.2 - - - -
22A GLY* 1.3 79.5 - - - +
24A PHE* 1.3 66.9 + + - +
26A LYS* 3.2 52.1 + - + +
27A PHE* 3.4 24.5 - + - -
279A LYS* 3.2 25.1 + - - +
280A GLN* 4.5 3.1 - - - -
283A TRP* 3.2 74.9 - + + +
377A LEU* 5.2 9.5 - - + +
392A TYR* 3.1 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