Contacts of the helix formed by residues 8 - 23 (chain A) in PDB entry 2E3L
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 LEU 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLY* 1.3 73.1 - - - -
9A ARG* 1.3 71.2 - - - +
10A LYS 3.1 1.3 - - - -
11A ALA* 2.6 17.6 + - - +
12A VAL* 2.8 16.2 + - - +
63A LEU* 4.6 14.8 - - + -
66A LEU* 5.0 8.3 - - + -
67A LYS* 3.3 49.6 - - + +
70A LEU* 3.5 24.0 - - + -
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Residues in contact with ARG 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 1.3 77.6 - - - +
10A LYS* 1.3 81.0 + - - +
12A VAL* 3.1 6.4 + - - +
13A GLU* 3.1 49.3 + - - +
57A HIS* 4.8 3.2 - - - -
58A PRO* 4.1 6.0 - - + +
59A GLU* 3.6 44.7 - - - +
66A LEU* 4.1 22.1 - - + +
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Residues in contact with LYS 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 5.5 4.4 + - - +
3A SER 3.3 25.8 + - - +
4A GLY* 4.3 15.0 - - - -
6A SER 4.1 14.1 - - - +
7A GLY* 5.0 2.5 - - - -
8A LEU 3.1 1.2 - - - +
9A ARG* 1.3 93.2 - - - +
11A ALA* 1.3 54.9 + - - +
13A GLU* 2.6 19.4 + - + +
14A ASP* 2.5 39.2 + - + +
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Residues in contact with ALA 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A GLY 5.7 2.9 - - - -
5A SER 4.8 8.3 - - - +
6A SER 4.7 0.8 + - - -
7A GLY 3.2 18.4 + - - +
8A LEU* 2.6 19.6 + - - +
10A LYS* 1.3 74.4 - - - +
12A VAL* 1.3 54.5 + - - +
14A ASP* 3.2 9.0 + - - +
15A TYR* 2.8 31.6 + - - +
70A LEU* 4.5 16.7 - - + +
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Residues in contact with VAL 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU 2.8 18.0 + - - +
9A ARG 3.3 8.3 - - - +
11A ALA* 1.3 71.8 - - - +
13A GLU* 1.3 57.4 + - - +
15A TYR* 3.2 7.0 - - - +
16A PHE* 2.9 66.0 + - + -
58A PRO* 3.4 16.6 - - + -
66A LEU* 3.6 29.4 - - + +
69A ILE* 4.2 12.8 - - + -
70A LEU* 3.7 28.3 - - + -
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Residues in contact with GLU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ARG* 3.1 33.5 + - - +
10A LYS* 2.6 23.6 + - + +
12A VAL* 1.3 68.7 - - - +
14A ASP* 1.3 63.0 + - - +
15A TYR 2.9 5.2 + - - -
16A PHE* 3.2 8.3 + - - +
17A CYS* 3.1 31.2 + - - -
34A TYR* 3.0 20.4 + - - +
57A HIS* 2.7 37.7 + - - -
58A PRO* 3.2 21.0 - - + +
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Residues in contact with ASP 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A SER 4.2 0.7 - - - +
4A GLY* 2.9 46.3 + - - +
10A LYS* 2.5 19.3 + - + +
11A ALA* 3.5 11.7 - - - +
13A GLU* 1.3 72.8 - - - +
15A TYR* 1.3 63.0 + - - +
17A CYS* 3.8 2.0 - - - +
18A PHE* 3.5 18.5 + - - +
29A MET* 3.4 34.8 - - - +
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Residues in contact with TYR 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ALA 2.8 16.6 + - - +
12A VAL* 3.2 10.1 - - - +
13A GLU 2.9 0.6 - - - -
14A ASP* 1.3 77.4 + - - +
16A PHE* 1.3 81.5 + + - +
17A CYS 2.8 4.3 - - - -
18A PHE* 2.6 28.8 + + + +
19A CYS* 3.0 27.4 + - - -
69A ILE* 4.9 6.1 - - + -
70A LEU* 5.0 6.1 - - + -
73A LYS* 2.5 62.5 + - + -
74A ALA* 4.8 0.2 - - - -
76A ILE* 3.2 35.0 + - + +
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Residues in contact with PHE 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A VAL* 2.9 45.7 + - + +
13A GLU* 3.6 11.0 - - - +
15A TYR* 1.3 88.8 - + - +
17A CYS* 1.3 63.8 - - - +
19A CYS* 3.2 9.6 - - + +
20A TYR 3.2 13.9 + - - -
32A VAL* 3.3 21.3 - - + +
34A TYR* 4.3 10.3 - + - +
49A LEU* 5.3 2.5 - - + -
55A PHE* 3.2 39.9 - + + -
56A GLN 5.0 1.8 - - - -
58A PRO* 4.0 17.3 - - + -
61A TYR* 4.1 17.9 - + - -
69A ILE* 4.3 8.1 - - + -
76A ILE* 4.3 25.4 - - + -
78A PHE* 5.2 3.6 - + - -
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Residues in contact with CYS 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLU* 3.2 20.9 - - - +
14A ASP* 3.8 7.6 - - - +
15A TYR 2.6 4.6 + - - -
16A PHE* 1.3 72.3 - - - +
18A PHE* 1.3 55.4 + - - +
19A CYS 2.6 15.9 + - - -
20A TYR* 2.7 15.2 + - - +
21A GLY 2.8 10.7 + - - -
29A MET* 4.1 13.9 - - + -
30A VAL 3.0 37.1 - - - +
31A PRO* 4.2 3.6 - - - -
32A VAL* 3.8 15.5 - - - -
34A TYR* 5.4 4.0 - - - -
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Residues in contact with PHE 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ASP* 3.5 11.7 + - - +
15A TYR* 2.6 25.7 + + + +
17A CYS* 1.3 74.5 - - - +
19A CYS* 1.3 54.4 + - - +
21A GLY* 3.7 2.8 - - - +
22A LYS* 2.9 68.0 + - + +
27A THR 5.8 3.4 - - - -
28A VAL* 5.0 7.7 - - - +
29A MET* 3.7 30.4 - - + +
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Residues in contact with CYS 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TYR* 3.0 51.3 + - - -
16A PHE* 3.2 12.6 - - + +
17A CYS 2.6 4.4 + - - -
18A PHE* 1.3 71.9 - - - +
20A TYR* 1.3 54.5 + - - +
22A LYS* 2.6 29.2 + - - +
23A ALA* 2.7 18.9 + - - +
76A ILE* 4.4 13.5 - - + -
77A SER* 5.5 1.6 - - - -
78A PHE* 4.7 20.6 - - + +
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Residues in contact with TYR 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A PHE 3.2 1.4 + - - +
17A CYS 2.7 10.9 + - - +
19A CYS* 1.3 76.1 - - - +
21A GLY* 1.3 49.8 + - - +
23A ALA* 3.2 4.9 + - - +
24A LEU* 2.7 65.8 + - + +
30A VAL* 3.0 36.8 - - + +
31A PRO 4.4 0.2 - - - -
32A VAL* 3.8 22.0 - - + -
33A PRO* 3.1 32.9 - - + +
44A VAL* 3.9 21.3 - - + -
78A PHE* 3.8 22.9 - + + -
80A ILE* 4.4 9.0 - - + -
84A PHE* 3.1 27.2 - - - -
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Residues in contact with GLY 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A CYS 2.8 11.9 + - - -
18A PHE 3.7 1.3 - - - -
20A TYR* 1.3 78.9 - - - +
22A LYS* 1.3 59.1 + - - +
24A LEU* 3.7 5.3 - - - +
25A GLY 3.2 2.8 + - - -
26A THR* 2.9 53.8 + - - +
28A VAL 3.7 13.0 - - - -
30A VAL* 3.9 5.1 - - - +
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Residues in contact with LYS 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE* 2.9 52.7 + - + +
19A CYS* 2.6 13.5 + - - +
21A GLY* 1.3 73.2 - - - +
23A ALA* 1.3 61.0 + - - +
25A GLY* 3.8 8.4 + - - -
26A THR 4.6 6.7 - - - +
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Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A CYS 2.7 11.4 + - - +
20A TYR* 3.5 11.2 - - - +
22A LYS* 1.3 77.6 - - - +
24A LEU* 1.3 66.2 + - - +
25A GLY* 3.0 2.7 + - - -
78A PHE* 4.1 18.8 - - + +
80A ILE* 3.9 32.9 - - + +
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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