Contacts of the helix formed by residues 8 - 26 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D LEU 6.0 0.2 - - - -
6D GLU 3.4 3.5 + - - -
7D GLU* 1.3 73.7 - - - +
9D ALA* 1.3 56.7 + - - -
10D GLU 3.3 2.5 - - - -
11D GLU* 2.8 20.5 + - - -
12D ARG* 2.7 35.9 + - - +
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Residues in contact with ALA 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D GLY* 1.3 70.4 - - - +
10D GLU* 1.3 65.9 + - + +
12D ARG* 3.3 10.3 + - - +
13D GLN* 3.1 28.9 + - + +
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Residues in contact with GLU 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D GLY 3.3 0.6 - - - -
9D ALA* 1.3 78.8 - - + +
11D GLU* 1.3 64.1 + - + +
13D GLN* 3.5 29.1 + - - +
14D VAL* 3.6 14.4 + - - +
70D LEU* 4.8 3.1 - - + +
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Residues in contact with GLU 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D GLU* 3.2 11.5 - - + -
8D GLY* 2.8 32.3 + - - +
10D GLU* 1.3 78.0 - - + +
12D ARG* 1.3 60.3 + - - +
14D VAL* 3.2 3.8 + - - +
15D LEU* 2.9 37.2 + - + +
67D SER* 4.8 0.3 + - - -
69D ARG* 2.6 53.4 + - - +
70D LEU* 4.1 28.5 + - + +
73D ARG* 3.4 13.9 + - - -
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Residues in contact with ARG 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B ARG* 5.2 3.4 - - - +
6D GLU* 4.5 20.2 + - - +
7D GLU* 2.7 44.5 + - + +
8D GLY 2.7 24.0 + - - +
9D ALA* 3.8 7.6 - - - +
11D GLU* 1.3 70.4 - - - +
13D GLN* 1.3 64.7 + - - +
15D LEU* 3.9 2.2 - - - +
16D GLY* 3.0 23.1 + - - +
17D PRO* 4.2 0.5 - - - +
19D ARG* 5.8 0.2 - - - +
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Residues in contact with GLN 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ALA* 3.1 19.3 + - - +
10D GLU* 3.6 23.5 - - - +
11D GLU 3.2 0.2 - - - -
12D ARG* 1.3 76.6 - - - +
14D VAL* 1.3 61.1 + - + +
17D PRO* 3.0 24.8 - - - +
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Residues in contact with VAL 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D GLU 3.7 13.0 - - - +
11D GLU 3.2 5.7 + - - +
12D ARG 3.2 0.4 - - - -
13D GLN* 1.3 79.5 - - + +
15D LEU* 1.3 60.7 + - - +
16D GLY 3.5 0.2 + - - -
17D PRO* 3.5 4.2 - - - +
18D PHE* 3.1 32.1 + - + +
50D PHE* 5.2 13.3 - - + +
66D LEU* 5.4 8.3 - - + -
70D LEU* 4.1 21.5 - - + -
74D MET* 4.1 26.5 - - + -
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Residues in contact with LEU 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D GLU* 2.9 35.9 - - + +
11D GLU* 2.9 22.1 + - + +
12D ARG* 4.5 0.7 - - - +
14D VAL* 1.3 75.5 - - - +
16D GLY* 1.3 66.8 + - - +
18D PHE* 4.0 9.9 - - + -
19D ARG* 2.9 49.5 + - - +
70D LEU* 4.1 9.2 - - + -
73D ARG* 3.7 25.4 - - + +
74D MET* 3.7 37.9 - - + +
77D ALA* 5.1 3.6 - - + -
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Residues in contact with GLY 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ARG* 3.0 16.0 + - - +
15D LEU* 1.3 79.4 - - - +
17D PRO* 1.3 66.9 - - - +
19D ARG* 3.7 10.4 - - - +
20D GLU* 3.3 25.8 + - - +
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Residues in contact with PRO 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ARG 4.2 0.7 - - - +
13D GLN 3.0 28.5 - - - +
14D VAL 3.5 4.7 - - - +
16D GLY* 1.3 84.7 - - - +
18D PHE* 1.3 63.0 + - - +
20D GLU* 3.4 18.9 + - - +
21D PHE* 3.1 22.3 + - - +
50D PHE* 4.2 11.4 - - + -
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Residues in contact with PHE 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D VAL* 3.1 22.4 + - + +
15D LEU* 3.7 9.2 - - + +
16D GLY 3.2 0.2 - - - -
17D PRO* 1.3 77.4 - - - +
19D ARG* 1.3 57.9 + - - +
21D PHE* 3.1 9.3 + + - +
22D LEU* 2.9 43.6 + - + +
47D LEU* 3.9 15.7 - - + -
50D PHE* 3.6 34.5 - + + -
52D VAL* 3.6 32.1 - - + -
74D MET* 3.7 44.4 - - + -
77D ALA* 4.3 7.6 - - + -
78D ILE* 3.7 24.0 - - + -
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Residues in contact with ARG 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D GLU* 2.3 45.8 + - - -
12D ARG* 5.8 0.4 - - - +
15D LEU* 2.9 39.1 + - + +
16D GLY* 3.7 8.4 - - - +
18D PHE* 1.3 72.9 - - + +
20D GLU* 1.3 66.8 + - + +
22D LEU* 3.3 9.2 + - + +
23D LYS* 3.0 42.9 + - - +
73D ARG* 5.5 2.0 + - - +
77D ALA* 4.7 22.3 - - + +
81D TYR* 4.8 6.0 + - + +
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Residues in contact with GLU 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D GLY 3.3 12.7 + - - +
17D PRO* 3.6 22.4 - - - +
18D PHE 3.3 0.6 - - - -
19D ARG* 1.3 78.8 - - + +
21D PHE* 1.3 62.4 + - - +
23D LYS* 3.5 12.3 + - + +
24D ALA* 3.2 25.1 + - - +
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Residues in contact with PHE 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D PRO 3.1 13.9 + - - +
18D PHE* 3.1 10.1 + + - +
20D GLU* 1.3 78.2 - - - +
22D LEU* 1.3 69.0 + - + +
24D ALA* 3.3 2.6 + - - -
25D GLU* 2.8 66.6 + - + +
26D VAL* 4.2 6.7 - - + -
43D LEU* 4.5 6.5 - - + -
46D LYS* 3.4 39.3 - - + -
47D LEU* 3.6 28.3 - - + -
50D PHE* 3.6 32.1 - + + -
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Residues in contact with LEU 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D PHE* 2.9 31.8 + - + +
19D ARG* 3.3 11.6 + - - +
21D PHE* 1.3 94.4 - - + +
23D LYS* 1.3 63.5 + - - +
26D VAL* 2.9 38.1 + - + +
27D ALA* 3.0 11.1 + - - +
47D LEU* 4.3 2.0 - - + -
77D ALA* 3.3 47.3 - - + +
78D ILE* 3.8 20.6 - - + +
81D TYR* 3.7 18.3 - - + -
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Residues in contact with LYS 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ARG* 3.0 32.2 + - - +
20D GLU* 3.9 10.1 - - + +
22D LEU* 1.3 76.5 - - - +
24D ALA* 1.3 62.4 + - - +
27D ALA* 3.5 12.8 - - - +
28D PRO* 3.4 14.4 - - - +
81D TYR* 3.1 30.7 - - + +
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Residues in contact with ALA 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D GLU 3.2 15.6 + - - +
21D PHE* 4.0 2.7 - - - +
23D LYS* 1.3 80.8 - - - +
25D GLU* 1.3 73.8 + - + +
28D PRO* 3.4 16.5 - - - +
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Residues in contact with GLU 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D PHE* 2.8 54.1 + - + +
24D ALA* 1.3 89.1 - - + +
26D VAL* 1.3 60.6 + - - +
28D PRO* 3.8 9.6 - - - +
29D GLY 4.9 1.4 + - - -
33D ARG* 5.0 1.0 + - - -
42D ASP* 4.7 1.6 - - - +
43D LEU* 3.7 17.6 - - + +
46D LYS* 3.0 29.8 + - + +
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Residues in contact with VAL 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D PHE* 4.2 11.7 - - + -
22D LEU* 2.9 42.3 + - + +
25D GLU* 1.3 75.6 - - - +
27D ALA* 1.3 65.5 + - - +
28D PRO* 3.4 0.4 - - - -
29D GLY 3.4 5.0 + - - -
30D ALA* 3.4 0.7 + - - +
33D ARG* 2.8 32.0 + - - +
43D LEU* 4.0 18.2 - - + -
47D LEU* 5.1 2.5 - - + -
78D ILE* 5.2 3.1 - - + +
81D TYR* 4.2 9.4 - - + -
82D ASP* 3.6 30.5 - - + +
85D LEU* 3.8 15.7 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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