Contacts of the helix formed by residues 6 - 20 (chain A) in PDB entry 1E8O
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 THR 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A TYR* 3.5 2.0 - - - +
5A GLN* 1.3 92.4 - - + +
7A TRP* 1.3 62.6 + - - +
8A GLU* 3.1 10.8 + - - +
9A GLU* 3.4 35.0 + - + +
10A PHE* 3.5 12.8 + - - +
51A TYR* 4.2 6.5 - - - -
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Residues in contact with TRP 7 (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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6A THR* 1.3 72.7 - - - +
8A GLU* 1.3 68.4 + - - +
10A PHE* 3.4 31.6 - + - -
11A SER* 2.9 32.3 + - - -
40A VAL* 4.6 3.1 - - + -
51A TYR* 3.3 51.4 + + + +
58A ASP* 5.0 0.2 - - - +
61A LYS* 3.5 58.4 + - + +
62A ILE* 3.8 24.5 - - + -
65A PHE* 3.4 48.0 - + + -
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Residues in contact with GLU 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A THR* 3.1 11.4 - - - +
7A TRP* 1.3 84.9 - - - +
9A GLU* 1.3 75.2 + - - +
11A SER* 3.2 14.6 - - - -
12A ARG* 3.7 15.7 + - - +
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Residues in contact with GLU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TYR* 3.8 20.8 - - + -
6A THR* 3.4 20.0 + - + +
8A GLU* 1.3 85.5 - - - +
10A PHE* 1.3 67.2 + - - +
11A SER 2.9 1.9 + - - -
12A ARG* 2.8 41.4 + - - +
13A ALA* 2.9 22.9 + - - +
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Residues in contact with PHE 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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4A TYR* 3.7 30.2 - + + -
6A THR 3.5 8.6 + - - +
7A TRP* 3.4 44.6 - + - +
8A GLU 3.5 0.2 - - - -
9A GLU* 1.3 78.7 - - - +
11A SER* 1.3 53.8 + - - +
13A ALA* 3.8 6.5 - - - -
14A ALA* 2.6 47.0 + - + +
40A VAL* 4.0 29.4 - - + -
42A VAL* 4.2 13.2 - - + -
49A LEU* 3.6 39.0 - - + -
50A VAL 4.2 2.2 - - - -
51A TYR* 3.6 19.3 - - + -
65A PHE* 5.1 3.1 - + - -
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Residues in contact with SER 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TRP* 2.9 30.5 + - - -
8A GLU* 3.2 13.2 - - - -
9A GLU 2.9 1.2 + - - -
10A PHE* 1.3 80.3 - - - +
12A ARG* 1.3 54.2 + - - -
14A ALA* 3.3 1.9 - - - +
15A GLU* 2.7 38.8 + - - +
65A PHE* 3.9 21.4 - - - -
68A GLN* 5.1 4.3 + - - -
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Residues in contact with ARG 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 GLU* 4.0 14.8 + - - +
9A GLU* 2.8 52.9 + - - +
11A SER* 1.3 76.2 + - - +
13A ALA* 1.3 77.4 + - + +
15A GLU* 4.0 16.8 - - - +
16A LYS* 2.6 32.1 + - + +
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Residues in contact with ALA 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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4A TYR* 3.7 28.7 - - + +
9A GLU 2.9 16.9 + - - +
10A PHE* 3.4 10.8 - - - +
12A ARG* 1.3 83.1 - - + +
14A ALA* 1.3 61.5 + - - +
16A LYS* 3.7 8.4 - - - +
17A LEU* 3.1 22.0 + - - +
49A LEU* 3.8 8.1 - - + +
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Residues in contact with ALA 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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10A PHE* 2.6 40.3 + - + +
11A SER 3.3 2.7 - - - +
13A ALA* 1.3 70.6 - - - +
15A GLU* 1.3 66.5 + - - +
17A LEU* 3.1 4.3 + - - +
18A TYR* 2.9 22.4 + - - +
42A VAL* 4.0 14.9 - - + +
49A LEU* 3.5 10.9 - - + +
65A PHE* 3.5 23.1 - - + -
69A LEU* 6.2 0.4 - - - -
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Residues in contact with GLU 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 SER* 2.7 22.1 + - - +
12A ARG* 3.7 15.8 + - - +
14A ALA* 1.3 72.7 - - - +
16A LYS* 1.3 59.8 + - - +
18A TYR* 3.3 8.6 + - - +
19A LEU* 2.9 42.8 + - + +
65A PHE* 4.5 11.1 - - + -
69A LEU* 5.3 5.6 - - + -
72A LEU* 5.5 9.0 - - + +
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Residues in contact with LYS 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 ARG* 2.6 22.9 + - + +
13A ALA* 3.7 7.0 - - - +
15A GLU* 1.3 75.5 - - - +
17A LEU* 1.3 66.0 + - - +
19A LEU* 2.9 21.3 + - + +
20A ALA* 3.0 16.3 + - + +
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Residues in contact with LEU 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 ALA 3.1 10.0 + - - +
14A ALA 3.3 9.2 - - - +
16A LYS* 1.3 81.8 - - - +
18A TYR* 1.3 65.3 + - - +
20A ALA* 3.4 15.2 + - - +
21A ASP* 3.8 8.5 + - - +
25A ALA* 4.6 8.1 - - + -
42A VAL* 4.5 11.9 - - + +
43A THR 4.8 2.7 - - - +
44A ASP* 3.3 32.7 - - + +
47A VAL* 3.7 23.6 - - + -
49A LEU* 3.1 36.3 - - + -
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Residues in contact with TYR 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 ALA 2.9 12.0 + - - +
15A GLU 3.5 8.1 - - - +
17A LEU* 1.3 77.3 - - - +
19A LEU* 1.3 73.5 + - + +
21A ASP 3.0 23.9 - - - -
22A PRO* 3.1 39.6 - - + +
25A ALA* 4.0 29.4 - - + -
42A VAL* 5.6 5.4 - - + -
69A LEU* 3.8 22.7 - - + -
72A LEU* 3.7 36.8 - - + +
73A MET* 3.8 37.4 + - + +
32B LYS* 3.7 19.2 + - + +
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Residues in contact with LEU 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 GLU* 2.9 27.6 + - + +
16A LYS* 3.1 16.8 - - - +
18A TYR* 1.3 94.1 - - + +
20A ALA* 1.3 55.3 + - - +
21A ASP 3.0 5.4 + - - -
22A PRO* 3.3 13.5 - - + +
72A LEU* 4.4 15.9 - - + -
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Residues in contact with ALA 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 LYS* 3.0 15.5 + - + +
17A LEU* 3.9 9.2 - - - +
18A TYR 3.3 1.0 - - - -
19A LEU* 1.3 73.3 - - - +
21A ASP* 1.3 63.9 + - - +
22A PRO* 4.2 0.7 - - - -
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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