Contacts of the helix formed by residues 25 - 35 (chain D) in PDB entry 4GUN
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 SER 25 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D LEU 4.3 0.9 - - - -
21D GLU* 3.8 11.7 - - - -
24D ILE* 1.3 78.5 - - - +
26D LYS* 1.4 63.1 + - - +
27D GLU* 3.3 18.5 + - - +
28D ILE* 3.2 29.3 + - - +
29D ASN* 3.1 22.5 + - - -
178D LEU* 5.4 1.0 - - - +
179D GLN* 3.1 22.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
17D LEU* 3.3 39.8 + - + +
18D ASP* 3.8 26.6 + - + +
21D GLU* 2.9 21.5 + - - +
25D SER* 1.4 72.3 - - - +
27D GLU* 1.3 67.7 + - - +
29D ASN* 3.3 0.5 + - - +
30D ASP* 2.8 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D GLU* 4.1 3.6 - - - +
25D SER* 3.2 13.6 + - - +
26D LYS* 1.3 100.9 + - - +
28D ILE* 1.3 62.2 + - - +
30D ASP* 3.7 4.7 + - - +
31D LEU* 3.4 25.4 + - + +
178D LEU* 4.3 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ILE* 3.9 14.6 - - + -
25D SER* 3.2 18.7 + - - +
27D GLU* 1.3 73.8 - - - +
29D ASN* 1.4 53.3 + - - +
31D LEU* 3.2 5.6 + - - +
32D HIS* 2.8 44.3 + - + +
174D HIS 3.9 16.3 - - - +
175D ALA* 3.5 20.6 - - - +
176D TYR* 3.8 19.3 - - - +
178D LEU* 3.9 24.9 - - + +
179D GLN* 3.7 40.2 - - + +
180D TYR* 5.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D TRP* 3.7 25.7 - - + -
17D LEU* 3.0 39.1 + - + +
20D LEU* 3.8 20.9 - - - +
24D ILE* 3.3 23.4 + - - +
25D SER 3.1 18.7 + - - +
26D LYS 3.8 1.1 - - - +
28D ILE* 1.4 76.1 - - - +
30D ASP* 1.3 57.5 + - - +
32D HIS* 4.2 5.9 + - - +
33D ILE* 2.9 37.4 + - + +
83D PHE* 6.1 0.5 - - - -
84D TRP* 5.0 7.4 - - - -
87D LEU* 5.5 0.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
17D LEU* 4.0 23.3 - - + +
26D LYS* 2.8 28.3 + - + +
27D GLU* 4.0 5.6 - - - +
29D ASN* 1.3 72.7 - - - +
31D LEU* 1.3 59.1 + - + +
34D ASN* 3.0 51.2 + - - +
35D LYS* 4.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C TYR* 3.8 20.6 - - - +
181C GLN* 3.8 30.3 - - + +
182C ASN* 3.5 23.8 - - - +
27D GLU* 3.4 9.3 + - + +
28D ILE* 3.2 6.3 + - - +
30D ASP* 1.3 78.5 - - + +
32D HIS* 1.3 60.2 + - - +
35D LYS* 2.9 41.1 + - + +
36D HIS* 2.9 15.7 + - + -
178D LEU* 3.6 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ILE* 6.2 0.2 - - - +
28D ILE* 2.8 31.9 + - + +
29D ASN* 3.8 8.0 + - - +
31D LEU* 1.3 71.8 - - - +
33D ILE* 1.3 57.9 + - - +
36D HIS* 3.3 13.6 - - + +
37D HIS* 3.0 26.9 + - - +
80D HIS* 3.0 10.0 + + - -
83D PHE* 3.8 16.1 - + - -
84D TRP* 3.4 24.3 - + + -
170D ASP* 3.0 15.9 - - - -
174D HIS* 3.0 21.0 + + - +
175D ALA* 4.0 14.9 + - + -
301D MN 2.1 30.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D LEU* 3.7 18.2 - - + +
13D ILE* 3.6 33.9 - - + -
15D TRP* 4.0 26.7 - - + -
17D LEU* 3.9 19.1 - - + -
29D ASN* 2.9 21.3 + - + +
32D HIS* 1.3 75.5 - - - +
34D ASN* 1.4 74.3 + - - +
37D HIS* 3.3 20.7 - - - +
38D VAL 3.3 10.7 + - - -
84D TRP* 3.5 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 34 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D LEU* 3.9 12.3 - - - +
17D LEU* 4.6 10.9 - - - +
30D ASP* 3.0 42.0 + - - +
33D ILE* 1.4 88.6 - - - +
35D LYS* 1.3 70.1 + - + +
38D VAL* 3.3 25.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C ASN* 3.5 37.2 - - + +
30D ASP 4.8 1.1 - - - +
31D LEU* 2.9 37.0 + - + +
34D ASN* 1.3 88.9 + - + +
36D HIS* 1.4 64.2 + - - +
37D HIS 3.7 0.2 - - - -
38D VAL* 3.6 3.9 + - - +
39D ALA* 3.1 23.4 + - - +
----------------------------------------------------------
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