Contacts of the helix formed by residues 16 - 32 (chain D) in PDB entry 5TJ4
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 16 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ILE* 5.2 2.6 - - - +
15D LYS* 1.3 72.2 - - - +
17D TYR* 1.3 64.0 + - - -
19D GLY 3.5 1.0 + - - -
20D LEU* 3.1 19.1 + - - +
293D VAL* 3.6 19.8 - - - +
296D ASP* 3.2 26.9 - - - -
297D LYS* 3.7 20.1 + - - +
299D LEU* 5.9 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 17 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ILE* 3.7 26.9 - - + +
12D ASN 4.3 1.6 - - - -
13D GLY* 3.3 29.8 - - - -
15D LYS 3.0 10.0 + - - -
16D GLY* 1.3 70.1 - - - +
18D ASN* 1.3 104.9 + - - +
20D LEU* 3.2 5.7 + - - +
21D ALA* 2.9 27.5 + - - +
37D VAL* 3.8 14.0 - - + +
39D HIS* 3.5 49.9 + + - +
296D ASP* 3.5 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 18 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D TYR* 1.3 105.0 + - - +
19D GLY* 1.3 61.2 + - - +
21D ALA* 3.1 9.9 + - - +
22D GLU* 2.9 27.8 + - - +
296D ASP* 3.1 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 19 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D GLY 3.9 3.1 - - - -
17D TYR 3.3 0.2 - - - -
18D ASN* 1.3 76.6 - - - +
20D LEU* 1.3 60.8 + - - +
22D GLU* 3.3 14.0 - - - +
23D VAL* 3.2 23.2 + - - +
292D ALA* 3.7 22.8 - - - +
293D VAL* 4.1 7.4 - - - -
296D ASP* 3.0 18.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ILE* 3.9 25.4 - - + -
11D ILE* 3.8 26.0 - - + -
16D GLY 3.1 14.5 + - - +
17D TYR* 3.2 10.3 + - - +
19D GLY* 1.3 74.4 - - - +
21D ALA* 1.3 59.1 + - - +
23D VAL* 3.0 9.7 + - + +
24D GLY* 2.8 23.2 + - - -
37D VAL* 4.3 16.8 - - + +
61D PHE* 4.1 9.2 - - + -
279D PHE* 4.1 20.5 - - + -
284D LEU* 4.0 33.2 - - + -
293D VAL* 4.0 10.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 21 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D TYR 2.9 14.0 + - - +
18D ASN* 3.1 12.1 + - - +
20D LEU* 1.3 73.1 - - - +
22D GLU* 1.3 53.6 + - - +
24D GLY* 2.9 3.8 + - - +
25D LYS* 2.7 35.7 + - - +
35D VAL 5.6 3.2 - - - +
37D VAL* 4.0 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D ASN 2.9 11.3 + - - +
19D GLY* 3.3 16.3 - - - +
21D ALA* 1.3 76.6 - - - +
23D VAL* 1.3 62.0 + - - +
25D LYS* 3.3 8.7 + - - +
26D LYS* 3.1 21.1 + - - +
292D ALA* 4.0 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D GLY 3.2 13.2 + - - +
20D LEU* 3.0 10.9 + - + +
22D GLU* 1.3 75.1 - - - +
24D GLY* 1.3 64.1 + - - +
26D LYS* 3.3 9.0 + - + +
27D PHE* 3.0 20.6 + - - +
279D PHE* 3.8 21.1 - - + -
283D TYR* 3.8 29.1 - - + +
284D LEU* 4.0 6.5 - - + +
289D GLY* 3.5 30.3 - - - +
292D ALA* 3.9 7.9 - - + -
293D VAL* 4.2 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LEU 2.8 13.8 + - - -
21D ALA* 2.9 7.8 + - - -
23D VAL* 1.3 75.6 - - - +
25D LYS* 1.3 56.5 + - - +
27D PHE* 3.1 4.9 + - - +
28D GLU* 2.9 26.0 + - - +
35D VAL* 3.3 37.3 - - - +
279D PHE* 4.2 6.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ALA 2.7 16.5 + - - +
22D GLU* 3.3 8.7 + - - +
24D GLY* 1.3 71.6 - - - +
26D LYS* 1.3 56.5 + - - +
28D GLU* 3.2 21.3 + - + +
29D LYS* 2.9 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D GLU 3.1 11.4 + - - +
23D VAL* 3.3 11.6 + - + +
25D LYS* 1.3 76.4 - - - +
27D PHE* 1.3 60.8 + - - +
29D LYS* 3.5 9.1 - - + +
30D ASP* 3.4 30.8 + - - +
283D TYR* 3.7 9.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D LEU* 4.2 13.5 - - + -
23D VAL 3.0 12.3 + - - +
24D GLY 3.2 9.4 - - - +
26D LYS* 1.3 74.5 - - - +
28D GLU* 1.3 59.6 + - - +
30D ASP* 3.2 1.2 + - - -
31D THR* 2.8 68.6 + - + +
33D ILE* 4.1 17.7 - - + -
35D VAL* 3.7 19.3 - - + -
275D LEU* 3.9 27.6 - - + -
278D GLU* 4.5 7.2 - - + -
279D PHE* 3.7 32.1 - + + -
283D TYR* 3.5 36.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D GLY 2.9 15.6 + - - +
25D LYS* 3.5 22.8 - - + +
27D PHE* 1.3 72.3 - - - +
29D LYS* 1.3 58.7 + - - +
32D GLY* 2.8 31.9 + - - -
33D ILE 3.3 29.9 + - - +
34D LYS* 3.3 29.5 - - - +
35D VAL* 3.9 5.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D LYS* 2.9 15.3 + - + +
26D LYS* 3.5 13.5 - - + +
27D PHE 3.3 0.2 - - - -
28D GLU* 1.3 77.9 - - - +
30D ASP* 1.3 79.9 + - - +
32D GLY* 4.4 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D LYS* 3.4 12.9 + - - +
27D PHE 3.2 2.4 + - - +
29D LYS* 1.3 96.2 - - - +
31D THR* 1.3 61.5 + - - +
32D GLY 3.8 0.2 + - - -
283D TYR* 3.1 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D PHE* 2.8 59.3 + - + +
30D ASP* 1.3 77.0 - - - +
32D GLY* 1.3 61.8 + - - +
33D ILE* 3.3 37.5 - - + +
275D LEU* 4.9 1.9 - - - +
283D TYR* 5.1 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D GLU* 2.8 27.0 + - - -
29D LYS 4.4 1.3 + - - -
30D ASP 3.5 1.8 - - - -
31D THR* 1.3 74.8 - - - +
33D ILE* 1.3 61.3 + - - +
34D LYS 4.4 0.3 + - - -
----------------------------------------------------------
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