Contacts of the helix formed by residues 13 - 24 (chain A) in PDB entry 3O9Z
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 ILE 13 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 1.3 76.3 - - + +
14A ALA* 1.3 69.3 + - - +
15A PRO 3.2 1.1 - - - -
16A ARG* 2.9 63.7 + - + +
17A HIS* 3.5 8.8 - - + -
77A ALA* 3.8 20.6 - - + -
100A GLU* 3.5 18.8 - - - +
264A HIS* 3.8 5.8 - - - +
311A NAD 2.9 71.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 4.6 7.4 - - + +
8A GLY 3.4 19.0 + - - +
9A LEU* 3.2 35.2 - - + +
11A GLY 3.5 4.3 + - - +
12A TYR 3.4 0.2 - - - -
13A ILE* 1.3 83.5 - - - +
15A PRO* 1.3 69.2 - - + +
17A HIS* 2.9 21.5 + - - +
18A LEU* 3.0 15.7 + - + +
77A ALA* 4.9 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU 5.1 1.1 - - - +
11A GLY 3.4 11.2 - - - +
12A TYR 3.3 17.9 - - - +
13A ILE 3.3 1.1 - - - +
14A ALA* 1.3 91.8 - - + +
16A ARG* 1.3 56.4 + - - +
18A LEU* 3.6 14.2 - - + +
19A LYS* 3.0 28.6 + - - +
40A LEU* 3.9 29.2 - - + -
44A PHE* 4.4 8.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 3.6 24.4 + - - -
13A ILE* 2.9 34.2 + - + +
15A PRO* 1.3 79.1 - - - +
17A HIS* 1.3 58.7 + - - +
19A LYS* 3.6 13.6 + - + +
20A ALA* 3.0 27.4 + - - +
129A GLN* 4.2 4.0 + - - -
260A PHE* 4.1 4.2 + - - -
261A THR* 3.3 58.2 + - - +
264A HIS* 3.4 51.0 - - + +
265A THR* 5.0 0.5 + - - -
311A NAD 4.2 6.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 4.3 20.2 - - + +
13A ILE* 3.5 24.7 - - + -
14A ALA* 2.9 7.5 + - - +
16A ARG* 1.3 75.8 - - - +
18A LEU* 1.3 58.7 + - - +
20A ALA* 3.2 5.0 + - - +
21A ILE* 2.9 37.6 + - + +
75A SER* 4.4 7.4 - - - -
76A ILE 4.9 3.6 - - - -
77A ALA* 4.3 7.8 - - + +
98A LEU* 5.3 2.9 - - + -
100A GLU* 2.7 43.8 + - + +
127A VAL* 4.2 9.0 - - + -
264A HIS* 3.6 13.7 - + - -
268A TYR* 2.7 34.4 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 3.9 9.0 - - + -
9A LEU* 3.9 25.8 - - + +
14A ALA* 3.0 14.1 + - + +
15A PRO* 3.6 16.8 - - + +
16A ARG 3.4 0.2 - - - -
17A HIS* 1.3 77.8 - - - +
19A LYS* 1.3 62.9 + - - +
21A ILE* 3.5 5.1 + - + +
22A LYS* 3.1 23.4 + - - +
28A LEU* 3.7 30.5 - - + -
40A LEU* 4.9 4.7 - - + +
41A VAL* 4.3 14.1 - - + +
44A PHE* 3.7 38.7 - - + -
45A PHE* 3.8 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PRO 3.0 18.1 + - - +
16A ARG* 3.8 13.2 - - + +
18A LEU* 1.3 77.4 - - - +
20A ALA* 1.3 55.7 + - - +
22A LYS* 3.3 5.3 - - + +
23A GLU* 2.9 66.6 + - + +
44A PHE* 3.8 15.8 - - + -
262A ASP* 5.5 5.1 + - - -
265A THR* 4.5 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG 3.0 18.4 + - - +
17A HIS 3.2 4.2 + - - +
19A LYS* 1.3 73.5 - - - +
21A ILE* 1.3 65.8 + - - +
23A GLU* 3.3 0.9 + - - +
24A VAL* 2.9 30.9 + - - +
264A HIS* 4.0 2.2 - - + +
265A THR* 3.4 27.6 + - - +
268A TYR* 3.4 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 3.7 41.7 - - + -
6A LEU* 5.0 9.0 - - + -
17A HIS* 2.9 25.9 + - + +
18A LEU* 3.8 7.9 - - + +
20A ALA* 1.3 76.6 - - - +
22A LYS* 1.3 61.7 - - - +
24A VAL* 3.5 7.3 - - - +
25A GLY 3.4 1.7 + - - -
26A GLY 2.9 38.8 + - - -
27A VAL 4.1 5.4 - - - +
28A LEU* 4.1 17.3 - - + +
45A PHE* 3.6 20.4 - - + -
75A SER* 4.5 2.7 - - - +
268A TYR* 3.7 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU 3.1 13.9 + - - +
19A LYS* 3.3 13.2 - - + +
21A ILE* 1.3 76.9 - - - +
23A GLU* 1.3 62.6 + - + +
25A GLY* 2.8 27.2 + - - -
26A GLY 4.9 1.5 - - - +
44A PHE* 2.8 42.7 + - + +
45A PHE* 3.6 23.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LYS* 2.9 55.1 + - + +
22A LYS* 1.3 80.4 - - + +
24A VAL* 1.3 61.2 + - - +
25A GLY 3.3 1.0 + - - -
265A THR* 2.8 42.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A THR* 5.6 0.9 + - - -
4A PHE* 4.4 8.3 - - + -
20A ALA 2.9 24.2 + - - +
21A ILE* 3.5 14.6 - - - +
23A GLU* 1.3 78.2 - - - +
25A GLY* 1.3 59.2 + - - +
26A GLY* 4.1 4.0 - - - +
265A THR* 4.2 10.8 - - + +
268A TYR* 3.9 24.2 - - + -
269A ARG* 4.0 20.4 - - + +
272A LEU* 4.0 26.4 - - + +
----------------------------------------------------------
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