Contacts of the helix formed by residues 8 - 26 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B LEU 5.8 0.9 - - - -
6B GLU 3.3 3.8 + - - -
7B GLU* 1.3 75.6 - - - +
9B ALA* 1.3 60.7 + - - -
10B GLU 3.4 2.2 - - - -
11B GLU* 2.8 21.2 + - - -
12B ARG* 3.0 29.0 + - - +
69B ARG* 4.6 0.6 - - - +
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Residues in contact with ALA 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLY* 1.3 72.9 - - - +
10B GLU* 1.3 63.8 + - + +
12B ARG* 3.9 7.8 - - - +
13B GLN* 3.0 39.5 + - - +
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Residues in contact with GLU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLY 3.4 0.2 - - - -
9B ALA* 1.3 77.5 - - + +
11B GLU* 1.3 66.8 + - + +
13B GLN* 3.5 15.8 + - - +
14B VAL* 3.3 26.2 + - - +
70B LEU* 4.7 4.6 - - + +
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Residues in contact with GLU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLU* 3.3 6.8 - - + -
8B GLY* 2.8 33.1 + - - +
9B ALA 3.3 0.2 - - - -
10B GLU* 1.3 79.2 - - + +
12B ARG* 1.3 52.9 + - - +
14B VAL* 3.1 3.3 + - - +
15B LEU* 2.7 47.3 + - + +
67B SER* 4.8 1.0 + - - -
69B ARG* 2.6 52.9 + - - +
70B LEU* 4.0 33.5 + - + +
73B ARG* 3.5 10.0 + - - -
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Residues in contact with ARG 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLU* 4.3 24.4 + - - +
7B GLU* 2.6 48.1 + - + +
8B GLY 3.0 19.4 + - - +
9B ALA* 3.9 7.0 - - - +
11B GLU* 1.3 74.1 - - - +
13B GLN* 1.3 60.2 + - + +
15B LEU 4.3 0.7 - - - +
16B GLY* 2.8 32.6 + - - +
17B PRO* 4.1 0.3 - - - +
19B ARG* 6.0 0.2 - - - +
316D ARG* 5.7 0.8 - - - +
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Residues in contact with GLN 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ALA* 3.0 30.0 + - - +
10B GLU* 3.8 15.8 - - - +
11B GLU 3.3 0.2 - - - -
12B ARG* 1.3 77.5 - - + +
14B VAL* 1.3 58.9 + - + +
17B PRO* 3.4 19.7 - - - +
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Residues in contact with VAL 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLU 3.3 11.6 + - - +
11B GLU 3.1 7.7 + - - +
12B ARG 3.0 0.4 - - - -
13B GLN* 1.3 81.3 - - + +
15B LEU* 1.3 66.6 + - - +
16B GLY 3.4 0.6 + - - -
17B PRO* 3.6 4.5 - - - +
18B PHE* 3.2 19.7 + - + +
50B PHE* 5.4 4.3 - - + +
66B LEU* 5.2 9.2 - - + -
70B LEU* 4.1 21.8 - - + -
74B MET* 4.0 34.5 - - + -
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Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLU* 3.5 32.3 - - + +
11B GLU 2.7 24.2 + - - +
12B ARG 4.4 0.7 - - - +
14B VAL* 1.3 71.9 - - - +
16B GLY* 1.3 65.9 + - - +
18B PHE* 4.0 10.3 - - + -
19B ARG* 2.9 52.8 + - + +
70B LEU* 3.9 11.2 - - + -
73B ARG* 3.7 26.0 - - + +
74B MET* 3.8 42.0 - - + +
77B ALA* 4.9 1.8 - - + -
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Residues in contact with GLY 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ARG* 2.8 21.5 + - - +
15B LEU* 1.3 76.3 - - - +
17B PRO* 1.3 66.2 - - - +
19B ARG* 3.5 8.4 + - - +
20B GLU* 3.4 26.8 + - - +
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Residues in contact with PRO 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ARG 4.1 0.2 - - - +
13B GLN* 3.4 24.5 - - - +
14B VAL 3.6 4.3 - - - +
16B GLY* 1.3 87.8 - - - +
18B PHE* 1.3 64.6 + - - +
20B GLU* 3.3 15.4 + - + +
21B PHE* 3.1 22.2 + - - +
50B PHE* 4.4 11.2 - - + -
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Residues in contact with PHE 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B VAL 3.2 21.3 + - - +
15B LEU* 3.7 9.2 - - + +
17B PRO* 1.3 76.7 - - - +
19B ARG* 1.3 57.9 + - + +
21B PHE* 3.1 10.1 + + - +
22B LEU* 3.0 47.5 + - + +
47B LEU* 3.9 18.2 - - + -
50B PHE* 3.9 31.3 - + + -
52B VAL* 3.6 29.6 - - + -
74B MET* 3.8 46.4 - - + -
77B ALA* 4.3 7.6 - - + -
78B ILE* 3.7 20.9 - - + -
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Residues in contact with ARG 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLU* 2.4 46.2 + - - -
15B LEU* 2.9 43.2 + - + +
16B GLY* 3.9 6.7 - - - +
18B PHE* 1.3 74.1 - - + +
20B GLU* 1.3 66.0 + - + +
22B LEU* 3.3 10.3 + - + +
23B LYS* 3.0 40.6 + - - +
73B ARG* 5.4 4.4 + - - +
77B ALA* 4.5 23.7 - - + +
81B TYR* 4.7 5.6 - - + +
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Residues in contact with GLU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B GLY 3.4 18.1 + - - +
17B PRO* 3.3 16.8 + - + +
18B PHE 3.3 0.6 - - - -
19B ARG* 1.3 76.4 - - + +
21B PHE* 1.3 63.0 + - - +
23B LYS* 3.5 13.5 + - + +
24B ALA* 3.2 24.6 + - - +
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Residues in contact with PHE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PRO 3.1 13.2 + - - +
18B PHE* 3.2 13.0 - + - +
20B GLU* 1.3 78.0 - - - +
22B LEU* 1.3 64.2 + - + +
24B ALA* 3.4 1.3 + - - -
25B GLU* 2.8 64.1 + - + +
26B VAL* 4.2 8.5 - - + -
43B LEU* 4.4 9.0 - - + -
46B LYS* 3.5 39.5 - - + -
47B LEU* 3.3 29.8 - - + -
50B PHE* 3.7 33.7 - + + -
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B PHE* 3.0 30.2 + - + +
19B ARG* 3.3 11.6 + - + +
21B PHE* 1.3 86.4 - - + +
23B LYS* 1.3 58.1 + - - +
26B VAL* 2.9 49.8 + - + +
27B ALA* 3.0 11.1 + - - +
47B LEU* 4.1 13.0 - - + -
77B ALA* 3.5 45.3 - - + +
78B ILE* 3.8 15.3 - - + +
81B TYR* 3.7 17.0 - - + -
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Residues in contact with LYS 23 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B ARG* 3.0 31.5 + - - +
20B GLU* 3.9 11.0 - - + +
22B LEU* 1.3 77.0 - - - +
24B ALA* 1.3 62.0 + - + +
27B ALA* 3.5 11.6 - - - +
28B PRO* 3.5 16.3 - - - +
81B TYR* 2.9 31.6 - - + +
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Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLU 3.2 14.5 + - - +
21B PHE* 4.2 2.0 - - - +
23B LYS* 1.3 81.6 - - - +
25B GLU* 1.3 70.6 + - + +
28B PRO* 3.4 16.6 - - - +
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Residues in contact with GLU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B PHE* 2.8 49.7 + - + +
24B ALA* 1.3 86.8 - - + +
26B VAL* 1.3 62.7 + - - +
28B PRO* 3.9 5.7 - - - +
29B GLY 5.0 2.4 + - - -
33B ARG* 5.0 1.0 + - - -
43B LEU* 3.7 20.8 - - + +
46B LYS* 3.3 28.9 + - + +
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Residues in contact with VAL 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B PHE* 3.8 9.8 + - + -
22B LEU* 2.9 38.9 + - + +
25B GLU* 1.3 80.2 - - - +
27B ALA* 1.3 66.1 + - - +
28B PRO 3.4 0.9 - - - -
29B GLY 3.4 5.2 + - - -
30B ALA* 3.5 1.2 + - - +
33B ARG* 2.8 30.2 + - - +
43B LEU* 4.0 17.3 - - + -
47B LEU* 4.7 2.7 - - + -
78B ILE* 5.1 2.7 - - + +
81B TYR* 4.0 11.7 - - + -
82B ASP* 3.7 28.9 - - + +
85B LEU* 4.0 15.0 - - + -
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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