Contacts of the helix formed by residues 16 - 28 (chain E) in PDB entry 4PJO
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 GLN 16 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E MET* 3.8 29.8 + - + +
15E VAL* 1.3 77.4 - - - +
17E PRO* 1.4 74.0 - - + +
18E ILE* 4.2 10.1 - - + +
19E ASN* 3.0 42.8 + - - +
20E LEU* 3.2 10.2 + - - +
34G PHE 4.5 2.0 - - - +
35G ASP* 5.2 4.3 - - + -
41G VAL* 4.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 17 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E VAL 3.6 1.5 - - - +
16E GLN* 1.4 79.0 - - + +
18E ILE* 1.3 62.3 + - + +
20E LEU 3.6 0.7 + - - +
21E ILE* 3.3 28.4 + - + +
54E MET* 5.8 0.7 - - + -
34G PHE* 3.7 22.4 - - - +
35G ASP* 3.9 13.7 - - + +
39G ASN* 3.5 46.0 - - + +
40G LEU 4.2 1.3 - - - -
41G VAL* 3.7 21.8 - - + -
61G VAL* 4.0 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 18 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1271 U 5.8 2.5 - - - +
16E GLN* 3.1 8.4 - - + +
17E PRO* 1.3 80.5 - - + +
19E ASN* 1.3 62.2 + - - +
21E ILE* 3.2 14.4 + - + +
22E PHE* 3.0 24.9 + - + +
50E PHE* 4.1 25.5 - - + -
51E ASP 5.4 6.3 - - - +
52E GLU* 5.6 8.1 - - - +
54E MET* 5.8 7.0 - - + -
35G ASP* 4.7 13.0 - - + +
39G ASN* 5.6 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 19 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E MET 5.3 1.4 - - - +
15E VAL* 4.8 6.4 - - + +
16E GLN* 3.0 42.3 + - - +
18E ILE* 1.3 82.3 - - - +
20E LEU* 1.3 51.9 + - - +
22E PHE* 2.7 16.1 + - - +
23E ARG* 2.6 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 20 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E VAL* 4.3 9.1 - - + +
16E GLN 3.2 9.4 + - - +
17E PRO 4.1 5.8 - - - +
18E ILE 3.4 0.2 - - - -
19E ASN* 1.3 78.8 - - - +
21E ILE* 1.3 56.9 + - - +
23E ARG* 3.5 28.3 - - + +
24E TYR* 2.9 50.1 + - + +
41G VAL* 3.6 22.7 - - + -
59G MET* 3.2 50.5 - - + +
60G VAL 3.8 1.8 - - - +
61G VAL* 3.8 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 21 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E PRO 3.3 17.3 + - - +
18E ILE* 3.2 14.9 + - + +
19E ASN 3.1 0.8 - - - -
20E LEU* 1.3 75.4 - - - +
22E PHE* 1.3 58.2 + - - +
24E TYR* 3.1 12.2 + - + +
25E LEU* 2.9 25.8 + - - +
47E ILE* 4.3 17.6 - - + +
50E PHE* 3.7 38.1 - - + -
54E MET* 4.2 25.1 - - + -
56E LEU* 4.9 2.9 - - + -
87E LEU* 4.0 27.4 - - + -
61G VAL* 4.1 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 22 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E ILE* 3.0 12.1 + - + +
19E ASN* 2.7 23.0 + - - +
21E ILE* 1.3 68.8 - - - +
23E ARG* 1.3 63.0 + - - +
25E LEU* 3.0 31.4 + - + +
26E GLN* 2.9 54.7 + - + +
50E PHE* 4.1 16.5 - + + -
4F PRO* 5.8 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 23 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E VAL* 3.5 29.3 - - - +
19E ASN* 2.6 18.2 + - - +
20E LEU* 3.5 34.7 - - + +
22E PHE* 1.3 70.1 - - - +
24E TYR* 1.3 64.7 + - + +
26E GLN* 3.0 13.5 + - - +
27E ASN* 2.9 46.1 + - - +
59G MET* 4.6 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 24 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E LEU* 2.9 43.0 + - + +
21E ILE* 3.1 17.2 + - + +
23E ARG* 1.3 72.5 - - + +
25E LEU* 1.3 64.1 + - - +
27E ASN* 4.6 6.3 - - - -
28E ARG* 3.3 14.0 + - - -
29E SER* 3.4 16.8 + - - +
31E ILE* 3.4 35.7 - - + -
47E ILE* 4.4 13.8 + - + +
87E LEU* 3.9 22.6 + - + -
88E GLN 4.8 2.1 - - - -
89E SER* 3.7 20.2 + - - -
58G GLY 4.5 0.5 + - - -
59G MET* 2.2 34.6 + - + -
60G VAL* 3.6 9.2 - - - -
61G VAL* 4.0 8.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ILE 2.9 12.2 + - - +
22E PHE* 3.0 29.4 + - + +
24E TYR* 1.3 75.5 - - - +
26E GLN* 1.3 70.4 + - + +
28E ARG* 3.1 17.8 + - - +
47E ILE* 3.2 26.4 - - + +
48E ILE 3.2 24.9 - - - +
49E GLY* 3.7 15.5 - - - -
50E PHE* 3.9 20.2 - - + -
3F LEU 5.8 0.4 - - - +
4F PRO* 4.3 18.6 - - + -
6F ASN* 5.1 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 26 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E PHE* 2.9 58.7 + - + +
23E ARG* 3.6 11.4 - - - +
25E LEU* 1.3 81.4 - - + +
27E ASN* 1.3 68.7 + - - +
28E ARG* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 27 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E ARG* 2.9 37.6 + - - +
24E TYR* 4.1 4.6 - - - +
26E GLN* 1.3 81.2 - - - +
28E ARG* 1.3 69.3 + - - +
29E SER* 3.2 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E TYR 3.3 1.9 + - - -
25E LEU 3.1 13.2 + - - +
26E GLN 3.0 19.3 + - - +
27E ASN* 1.3 79.8 - - - +
29E SER* 1.3 65.3 + - - +
30E ARG 3.9 0.2 + - - -
46E CYS* 3.7 17.6 - - + -
47E ILE 6.0 1.6 - - - +
3F LEU 6.1 1.0 - - - +
----------------------------------------------------------
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