Contacts of the helix formed by residues 18 - 34 (chain W) in PDB entry 5IY8
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 18 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16W TYR* 6.4 1.6 - + - -
17W ILE* 1.3 96.4 - - + +
19W PRO* 1.4 72.2 - - + +
20W GLU* 4.0 15.3 - - + +
21W GLN* 3.0 20.7 + - + +
22W PHE* 3.2 12.8 + - - +
50W VAL* 3.6 31.2 + - + +
51W SER* 4.1 21.3 - - - -
54W ALA* 3.5 23.6 - - + -
90W LEU* 3.7 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 19 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17W ILE 4.2 3.1 - - - +
18W TYR* 1.4 79.4 - - + +
20W GLU* 1.3 57.9 - - - +
22W PHE* 3.5 12.0 - - + +
23W SER* 2.7 33.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 20 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18W TYR* 3.2 10.9 - - + +
19W PRO* 1.3 76.9 - - - +
21W GLN* 1.3 64.5 + - - +
23W SER* 3.2 6.1 + - - -
24W TYR* 3.2 40.4 + - + +
51W SER* 3.8 21.8 + - - -
480W THR 4.2 3.7 - - - +
481W PHE* 3.4 19.1 - - - +
482W THR* 2.8 32.1 + - - +
671W LYS* 3.0 23.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 21 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17W ILE* 3.5 30.2 - - + +
18W TYR* 3.0 21.5 + - + +
20W GLU* 1.3 79.8 - - - +
22W PHE* 1.3 63.9 + - - +
24W TYR* 3.8 0.6 - - - -
25W MET* 3.0 60.2 + - - +
54W ALA* 3.0 36.8 + - + +
55W LEU* 3.9 18.1 - - + +
57W MET* 3.8 16.2 - - - +
58W ALA* 4.5 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 22 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17W ILE* 5.8 2.2 - - + +
18W TYR 3.2 8.8 + - - +
19W PRO* 3.5 15.7 - - + +
21W GLN* 1.3 84.8 + - - +
23W SER* 1.3 71.6 + - - +
24W TYR 3.4 0.2 + - - -
25W MET* 3.8 10.2 + - - +
26W ARG* 4.9 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 23 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19W PRO 2.7 23.6 + - - -
20W GLU* 3.2 8.9 + - - -
22W PHE* 1.3 84.0 - - - +
24W TYR* 1.3 75.1 + - - +
25W MET 3.8 0.2 + - - -
26W ARG* 4.9 11.0 + - - +
27W GLU* 5.6 1.7 + - - +
482W THR* 5.3 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 24 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20W GLU* 3.2 32.7 + - + +
21W GLN* 4.1 1.8 - - - +
23W SER* 1.3 87.0 - - - +
25W MET* 1.3 62.2 + - - +
26W ARG 3.4 2.2 - - - -
27W GLU* 3.1 8.6 + - + +
28W LEU* 3.0 20.2 + - - +
55W LEU* 4.4 7.0 - - + -
478W MET* 3.5 23.2 - - + +
479W ALA 3.5 15.9 - - - -
480W THR* 3.5 22.9 - - - +
481W PHE 3.4 30.6 + - - -
482W THR* 3.6 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 25 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21W GLN* 3.0 39.8 + - - +
22W PHE* 3.8 7.8 + - - +
23W SER 3.6 2.2 - - - -
24W TYR* 1.3 72.7 - - - +
26W ARG* 1.3 71.9 + - + +
28W LEU* 3.4 1.8 + - + +
29W LYS* 2.8 34.9 + - + +
55W LEU* 4.0 12.3 - - + +
58W ALA* 3.3 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 26 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22W PHE* 4.9 20.1 + - - -
23W SER* 4.9 9.5 + - - +
24W TYR 3.4 0.8 - - - -
25W MET* 1.3 91.3 - - + +
27W GLU* 1.3 57.2 + - - +
29W LYS* 3.4 7.1 + - - +
30W ARG* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 27 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23W SER 5.6 1.7 + - - +
24W TYR* 3.1 13.2 + - + +
26W ARG* 1.3 78.1 - - - +
28W LEU* 1.3 49.0 + - - +
30W ARG* 2.8 50.0 + - - +
31W THR* 2.6 41.0 + - - -
478W MET* 3.5 23.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24W TYR 3.0 13.7 + - - +
25W MET* 3.8 4.7 - - + +
27W GLU* 1.3 73.6 - - - +
29W LYS* 1.4 56.0 + - - +
31W THR* 3.2 4.4 + - - -
32W LEU* 2.8 43.9 + - + +
40W LEU* 3.4 39.5 - - + -
52W LEU* 5.7 3.1 - - + -
55W LEU* 3.9 48.0 - - + +
56W ILE* 5.3 5.6 - - + -
58W ALA* 6.3 0.4 - - + -
455W ILE* 6.4 0.2 - - + -
478W MET* 3.3 16.7 - - + -
480W THR* 4.1 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 29 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25W MET* 2.8 28.1 + - + +
26W ARG* 3.7 7.2 - - - +
28W LEU* 1.4 74.0 - - - +
30W ARG* 1.3 56.7 + - - +
32W LEU* 3.3 12.7 + - - +
33W ASP* 3.0 33.3 + - + +
58W ALA* 5.0 11.4 - - + +
59W TYR* 4.2 34.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 30 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26W ARG 3.0 14.5 + - - +
27W GLU* 2.8 40.2 + - - +
29W LYS* 1.3 73.9 - - - +
31W THR* 1.3 61.1 + - - +
33W ASP* 3.0 29.0 + - + +
34W ALA* 4.1 3.5 + - - +
476W VAL* 4.6 22.1 - - - +
477W THR 5.3 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 31 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27W GLU* 2.6 32.5 + - - -
28W LEU* 3.5 7.9 - - - -
30W ARG* 1.3 72.9 + - - +
32W LEU* 1.3 59.5 + - - +
33W ASP 3.8 0.2 + - - -
34W ALA* 4.3 1.9 + - - +
37W HIS 4.1 8.8 - - - +
38W GLY* 4.9 3.8 - - - -
39W VAL 4.3 2.5 - - - +
40W LEU* 4.2 14.8 - - + -
455W ILE* 6.1 2.9 - - + +
476W VAL* 3.8 52.5 - - + +
477W THR 4.3 1.3 + - - -
478W MET* 3.2 40.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28W LEU* 2.8 19.3 + - + +
29W LYS* 3.3 15.3 - - + +
30W ARG 3.1 0.2 - - - -
31W THR* 1.3 75.6 - - - +
33W ASP* 1.4 61.3 + - - +
34W ALA* 3.3 2.6 + - - -
35W LYS* 3.6 10.4 + - - +
56W ILE* 4.4 20.4 - - + -
59W TYR* 4.4 34.8 - - + -
230W VAL* 4.6 28.0 - - + -
453W SER* 6.2 3.1 - - - -
454W VAL 5.8 0.9 - - - +
455W ILE* 4.8 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 33 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29W LYS* 3.0 21.8 + - + +
30W ARG* 3.0 21.6 + - + +
32W LEU* 1.4 70.3 - - - +
34W ALA* 1.3 57.6 + - - +
35W LYS* 3.0 17.3 + - - +
59W TYR* 5.1 4.0 + - - -
63W TYR* 4.4 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 34 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30W ARG 4.1 3.0 + - - +
31W THR 4.3 4.5 - - - +
32W LEU 3.3 1.0 + - - +
33W ASP* 1.3 76.7 - - - +
35W LYS* 1.4 67.1 + - - +
36W GLY* 3.4 2.6 + - - +
37W HIS 4.3 7.9 - - - +
476W VAL* 3.5 31.9 - - + -
----------------------------------------------------------
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