Contacts of the helix formed by residues 17 - 25 (chain F) in PDB entry 1R4N
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 TRP 17 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E GLY 4.9 6.7 - - - -
12F ASP 3.7 15.6 - - - +
13F TRP 5.1 0.4 + - - -
15F GLY 3.5 0.4 - - - -
16F ARG* 1.3 124.5 - - + +
18F ASN* 1.3 64.7 + - - +
19F HIS 3.2 3.4 - - - -
20F VAL* 3.0 18.4 + - + -
21F LYS* 3.0 28.9 + - + +
42F LEU* 3.5 29.8 - - + -
46F LEU* 4.0 23.7 - - + +
68F ALA 3.4 19.7 - - - -
69F LEU* 3.6 15.7 - - + -
71F GLY* 3.3 35.2 - - - -
72F PHE 5.4 0.4 - - - -
73F ARG* 4.1 9.6 - - - +
115F VAL* 5.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 18 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LYS* 4.1 19.6 - - - +
266B GLU* 5.0 0.8 + - - -
68E GLU* 3.8 25.4 + - + +
15F GLY* 2.8 39.5 - - - +
16F ARG 3.2 3.6 + - - -
17F TRP* 1.3 76.8 + - - +
19F HIS* 1.3 60.2 + - - +
20F VAL 2.8 5.9 + - - -
21F LYS* 3.5 20.9 + - - +
22F LYS* 3.6 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 19 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E GLU* 3.3 57.2 + - + +
69E ASP* 5.6 2.1 + - - -
71E GLY 6.0 0.2 - - - -
72E ASN* 3.0 34.3 + - + -
487E ALA 5.5 0.8 + - - -
488E ALA* 4.2 11.0 - - + -
489E GLU* 3.1 44.3 + - - +
490E PRO* 4.2 11.1 - - + +
491E HIS 5.4 0.7 - - - +
16F ARG 4.5 2.7 + - - +
17F TRP 3.2 1.4 - - - -
18F ASN* 1.3 76.9 + - + +
20F VAL* 1.3 65.5 + - + +
22F LYS* 5.4 3.6 + - - -
23F PHE* 3.8 19.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F TRP* 3.6 29.2 - - + +
18F ASN 2.8 1.0 + - - -
19F HIS* 1.3 90.1 - - + +
21F LYS* 1.3 68.3 + - - +
22F LYS 3.1 1.6 - - - -
23F PHE* 2.9 19.6 + - - +
24F LEU* 3.3 22.0 + - + +
42F LEU* 4.5 8.7 - - + -
69F LEU 4.2 9.0 - - - +
70F SER* 3.4 29.6 - - - +
308F PHE* 3.6 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 21 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F TRP* 3.0 27.3 + - - +
18F ASN* 3.5 14.3 + - - +
20F VAL* 1.3 76.4 - - - +
22F LYS* 1.3 55.5 + - + +
24F LEU* 2.8 11.3 + - - +
25F GLU* 2.5 72.0 + - + +
39F THR* 5.8 1.3 + - - -
42F LEU* 3.9 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 22 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E GLU* 4.3 16.0 + - - -
445E VAL* 3.6 29.0 + - - +
447E ASN* 4.6 4.0 - - - +
484E ARG* 4.0 17.7 + - - +
485E TYR 3.8 19.1 - - - +
486E GLY* 3.8 14.2 + - - +
487E ALA 5.3 0.2 - - - -
488E ALA* 3.8 12.1 - - + +
18F ASN* 3.6 31.5 + - - +
19F HIS* 5.4 3.2 + - - -
20F VAL 3.1 0.8 - - - -
21F LYS* 1.3 77.7 - - + +
23F PHE* 1.3 68.0 + - + +
25F GLU* 5.1 0.2 - - - -
26F ARG* 3.3 51.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 23 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157E GLY* 4.3 10.1 - - - -
158E LEU* 3.9 24.7 - - + -
484E ARG* 3.0 27.5 + - + +
485E TYR* 4.4 12.8 - + - -
488E ALA* 4.2 14.6 - - + -
490E PRO* 3.3 35.7 - - + -
19F HIS 3.8 16.2 - - - -
20F VAL* 2.9 14.9 + - - +
22F LYS* 1.3 83.8 - - + +
24F LEU* 1.3 61.4 + - - +
26F ARG 4.2 1.3 - - - -
35F PHE* 3.5 10.0 - - - -
308F PHE* 4.5 15.5 - + + -
314F ALA* 3.6 15.0 - - + +
315F TYR* 3.6 28.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F VAL* 3.4 29.8 - - + +
21F LYS* 2.8 6.1 + - - +
23F PHE* 1.3 84.3 - - - +
25F GLU* 1.3 62.2 + - + +
26F ARG 3.4 0.4 - - - -
35F PHE* 3.5 17.3 - - + -
38F SER 3.2 23.6 + - - +
41F SER* 3.9 20.0 + - - -
42F LEU* 3.9 34.3 - - + +
45F LEU* 4.5 3.1 - - + -
308F PHE* 3.6 11.7 - - + -
312F THR* 3.4 41.1 - - + +
314F ALA* 4.4 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 25 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447E ASN* 2.9 28.1 + - - +
21F LYS* 2.5 61.8 + - + +
24F LEU* 1.3 73.9 - - + +
26F ARG* 1.3 62.3 + - + +
37F PRO* 3.8 14.9 - - - +
38F SER 3.7 17.2 - - - +
39F THR* 3.6 25.8 + - - +
42F LEU* 6.4 1.3 - - + -
----------------------------------------------------------
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