Contacts of the helix formed by residues 8 - 26 (chain A) in PDB entry 2CX9
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 GLY 8 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU 5.8 1.1 - - - -
6A GLU 3.4 2.9 + - - -
7A GLU* 1.3 76.1 - - - +
9A ALA* 1.3 62.0 + - - -
10A GLU 3.4 2.5 - - - -
11A GLU* 2.6 21.0 + - - -
12A ARG* 2.8 30.5 + - - +
69A ARG* 4.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLY* 1.3 71.6 - - - +
10A GLU* 1.3 60.8 + - + +
12A ARG* 3.2 18.0 + - - +
13A GLN* 3.0 42.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLY 3.4 0.2 - - - -
9A ALA* 1.3 76.0 - - + +
11A GLU* 1.3 65.9 + - + +
13A GLN* 3.5 17.9 + - - +
14A VAL* 3.4 25.8 + - - +
70A LEU* 4.7 3.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLU* 3.1 10.5 - - + -
8A GLY* 2.6 34.1 + - - +
9A ALA 3.3 0.2 - - - -
10A GLU* 1.3 77.1 - - + +
12A ARG* 1.3 56.3 + - - +
14A VAL* 3.0 4.0 + - - +
15A LEU* 2.8 47.1 + - + +
67A SER* 5.0 0.5 + - - -
69A ARG* 2.5 49.8 + - - +
70A LEU* 4.1 29.8 + - + +
73A ARG* 3.6 11.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 6.0 3.4 - - - +
7A GLU* 3.0 40.1 + - + +
8A GLY 2.8 9.0 + - - +
9A ALA* 3.2 29.6 + - - +
11A GLU* 1.3 74.9 - - - +
13A GLN* 1.3 57.8 + - + +
15A LEU 4.4 0.7 - - - +
16A GLY* 2.8 33.2 + - - +
17A PRO* 4.0 0.5 - - - +
19A ARG* 6.0 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA* 3.0 37.8 + - - +
10A GLU* 3.6 19.0 - - - +
11A GLU 3.2 0.2 - - - -
12A ARG* 1.3 76.0 - - + +
14A VAL* 1.3 60.2 + - + +
17A PRO* 3.2 22.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLU 3.4 13.0 + - - +
11A GLU 3.0 6.7 + - - +
13A GLN* 1.3 79.4 - - + +
15A LEU* 1.3 66.4 + - - +
17A PRO* 3.3 6.3 - - - +
18A PHE* 3.1 24.3 + - + +
50A PHE* 5.4 10.7 - - + +
66A LEU* 5.0 9.4 - - + -
70A LEU* 4.0 21.8 - - + -
74A MET* 4.1 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLU* 3.1 39.0 - - + +
11A GLU* 2.8 24.4 + - + +
12A ARG 4.4 0.2 - - - +
14A VAL* 1.3 72.4 - - - +
16A GLY* 1.3 65.3 + - - +
18A PHE* 4.0 11.9 - - + -
19A ARG* 2.9 46.0 + - - +
70A LEU* 3.9 10.1 - - + -
73A ARG* 3.7 27.1 - - + +
74A MET* 3.8 40.8 - - + +
77A ALA* 4.9 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 2.8 25.2 + - - +
15A LEU* 1.3 75.8 - - - +
17A PRO* 1.3 64.3 - - - +
19A ARG* 3.7 9.3 + - - +
20A GLU* 3.5 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG 4.0 0.7 - - - +
13A GLN* 3.2 25.8 - - - +
14A VAL 3.3 5.8 - - - +
16A GLY* 1.3 88.2 - - - +
18A PHE* 1.3 64.3 + - - +
20A GLU* 3.3 9.7 + - + +
21A PHE* 3.1 22.0 + - - +
50A PHE* 4.3 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 3.1 22.7 + - + +
15A LEU* 3.3 10.3 + - + +
17A PRO* 1.3 77.5 - - - +
19A ARG* 1.3 57.4 + - + +
21A PHE* 3.2 8.2 + + - +
22A LEU* 3.0 47.0 + - + +
47A LEU* 4.0 22.7 - - + -
50A PHE* 3.7 44.1 - + + -
52A VAL* 4.2 13.7 - - + -
74A MET* 3.7 43.3 - - + -
77A ALA* 4.3 7.6 - - + -
78A ILE* 3.8 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLU* 2.9 39.1 + - - -
12A ARG* 5.9 2.0 - - - +
15A LEU* 2.9 42.4 + - + +
16A GLY* 4.1 6.7 - - - +
18A PHE* 1.3 74.5 - - + +
20A GLU* 1.3 66.0 + - - +
22A LEU* 3.2 9.8 + - + +
23A LYS* 2.9 38.1 + - - +
73A ARG* 5.5 1.8 + - - +
77A ALA* 4.1 26.0 - - + +
81A TYR* 4.7 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLY 3.5 13.3 + - - +
17A PRO* 3.3 12.9 + - + +
18A PHE 3.3 0.4 - - - -
19A ARG* 1.3 77.7 - - - +
21A PHE* 1.3 63.3 + - - +
23A LYS* 3.2 28.7 + - - +
24A ALA* 3.2 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PRO 3.1 8.1 + - - +
18A PHE* 3.3 12.6 - + - +
20A GLU* 1.3 78.3 - - - +
22A LEU* 1.3 67.0 + - + +
24A ALA* 4.9 2.5 - - - -
25A GLU* 2.9 61.6 + - + +
26A VAL* 4.2 2.9 - - + -
43A LEU* 4.4 7.9 - - + -
46A LYS* 3.6 40.4 - - + -
47A LEU* 3.3 30.1 - - + -
50A PHE* 3.5 39.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE* 3.0 30.9 + - + +
19A ARG* 3.2 11.6 + - - +
21A PHE* 1.3 87.8 - - + +
23A LYS* 1.3 59.2 + - - +
26A VAL* 3.0 32.9 + - + +
27A ALA* 3.0 26.9 + - - +
47A LEU* 4.2 12.6 - - + -
77A ALA* 3.5 46.7 - - + +
78A ILE* 3.7 14.1 - - + +
81A TYR* 3.7 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ARG* 2.9 29.3 + - - +
20A GLU* 3.2 31.8 + - - +
22A LEU* 1.3 74.7 - - - +
24A ALA* 1.3 61.5 + - + +
27A ALA* 3.5 22.4 - - + +
28A PRO* 3.5 5.7 - - - +
81A TYR* 2.9 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU 3.2 14.0 + - - +
21A PHE* 4.2 2.5 - - - +
23A LYS* 1.3 82.1 - - + +
25A GLU* 1.3 69.9 + - + +
28A PRO* 3.2 18.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 2.9 49.9 + - + +
24A ALA* 1.3 86.2 - - + +
26A VAL* 1.3 62.8 + - - +
28A PRO* 3.7 7.0 - - - +
29A GLY 4.9 1.7 + - - -
33A ARG* 4.9 1.0 + - - -
43A LEU* 3.7 18.3 - - + +
46A LYS* 3.1 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 3.8 13.0 + - + -
22A LEU* 3.0 39.2 + - + +
25A GLU* 1.3 76.2 - - - +
27A ALA* 1.3 68.1 + - - +
28A PRO* 3.2 3.6 - - - -
29A GLY 3.4 5.5 + - - -
30A ALA* 3.6 1.0 + - - +
33A ARG* 2.9 27.9 + - - +
43A LEU* 4.2 8.3 - - + -
47A LEU* 4.8 3.1 - - + -
78A ILE* 5.1 2.9 - - + +
81A TYR* 3.9 13.2 - - + -
82A ASP* 3.7 29.6 - - + -
85A LEU* 4.1 17.7 - - + -
----------------------------------------------------------
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