Contacts of the helix formed by residues 6 - 22 (chain E) in PDB entry 6X0A
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 SER 6 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5E ARG* 1.3 81.6 - - - +
7E PRO* 1.3 67.9 - - - +
8E ALA* 3.4 8.0 + - - +
9E ALA* 2.6 42.9 + - - +
10E GLU 3.1 10.4 + - - -
80E ILE 3.2 9.0 + - - -
81E VAL* 2.7 25.6 + - - -
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Residues in contact with PRO 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ARG* 3.6 19.5 - - - +
6E SER* 1.3 85.1 - - - +
8E ALA* 1.3 60.6 + - - +
10E GLU* 3.2 23.1 - - + +
11E GLY* 3.2 4.9 + - - -
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Residues in contact with ALA 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E SER* 3.1 8.4 + - - +
7E PRO* 1.3 78.1 - - - +
9E ALA* 1.3 55.3 + - - +
11E GLY* 3.0 4.8 + - - +
12E ASP* 2.7 36.3 + - - +
82E ARG* 3.6 24.2 - - - +
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Residues in contact with ALA 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ARG* 4.1 8.5 - - + -
6E SER* 2.6 37.2 + - - +
8E ALA* 1.3 73.8 - - - +
10E GLU* 1.3 61.1 + - - +
12E ASP* 3.2 11.4 + - - +
13E LEU* 3.0 28.3 + - + +
80E ILE* 3.7 7.2 - - + +
81E VAL 3.5 11.0 + - - +
83E ILE* 4.0 17.6 - - + +
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Residues in contact with GLU 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ARG* 3.3 44.1 + - - +
6E SER 3.1 6.5 + - - -
7E PRO* 3.2 17.1 - - - +
9E ALA* 1.3 77.6 - - - +
11E GLY* 1.3 58.5 + - - +
13E LEU* 3.1 10.6 + - + +
14E VAL* 2.7 48.4 + - + +
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Residues in contact with GLY 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E PRO 3.2 5.8 + - - -
8E ALA* 3.0 8.7 + - - -
10E GLU* 1.3 85.8 - - - +
12E ASP* 1.3 55.1 + - - +
14E VAL* 4.5 5.2 - - - -
15E ASP* 2.8 41.7 + - - +
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Residues in contact with ASP 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E ALA 2.7 22.9 + - - +
9E ALA* 3.2 7.6 + - - +
11E GLY* 1.3 76.2 - - - +
13E LEU* 1.3 58.2 + - - +
15E ASP* 3.3 6.4 + - - +
16E ILE* 2.8 36.9 + - + +
82E ARG* 2.4 50.0 + - - -
83E ILE* 3.3 35.5 + - + +
84E VAL* 4.1 1.9 - - - +
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Residues in contact with LEU 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ARG* 6.1 5.6 - - + -
9E ALA* 3.0 20.3 + - + +
10E GLU* 3.7 12.3 - - + +
12E ASP* 1.3 76.5 - - - +
14E VAL* 1.3 59.7 + - + +
16E ILE* 3.8 5.5 - - + +
17E TRP* 3.0 28.1 + - - +
32E LEU* 3.8 23.5 - - + +
35E ILE* 4.2 30.3 - - + -
39E ILE* 5.2 9.4 - - + -
80E ILE* 6.3 0.4 - - + -
83E ILE* 3.9 32.5 - - + -
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Residues in contact with VAL 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E GLU* 2.7 35.9 + - + +
11E GLY* 3.9 4.7 - - - +
13E LEU* 1.3 71.8 - - + +
15E ASP* 1.3 68.0 + - - +
17E TRP* 3.2 6.6 + - + +
18E LEU* 3.0 41.6 + - + +
32E LEU* 5.7 0.2 - - - -
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Residues in contact with ASP 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E GLY* 2.8 26.6 + - - +
12E ASP* 3.6 6.8 + - - +
14E VAL* 1.3 80.4 - - - +
16E ILE* 1.3 62.6 + - + +
18E LEU* 3.3 12.2 + - - +
19E ALA* 2.9 24.8 + - - +
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Residues in contact with ILE 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E ASP* 2.8 27.0 + - - +
13E LEU* 3.8 9.6 - - + +
15E ASP* 1.3 72.1 - - + +
17E TRP* 1.3 64.5 + - - +
19E ALA* 3.3 7.4 + - - +
20E ILE* 3.0 28.4 + - + +
31E PHE* 3.7 32.3 - - + -
32E LEU* 4.4 7.0 - - + -
35E ILE* 4.9 4.7 - - + -
67E TYR* 4.1 28.9 - - + +
83E ILE* 3.7 37.7 - - + +
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Residues in contact with TRP 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E LEU 3.0 18.1 + - - +
14E VAL* 3.2 7.8 + - + +
16E ILE* 1.3 76.3 - - - +
18E LEU* 1.3 70.5 + - + +
20E ILE* 3.2 2.2 + - - -
21E ALA* 2.6 57.9 + - + +
25E PRO* 3.4 32.3 - - + -
28E ALA* 3.2 36.1 - - + +
29E ASP* 2.8 29.8 + - - +
32E LEU* 3.8 23.6 - - + -
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Residues in contact with LEU 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E VAL* 3.0 36.0 + - + +
15E ASP* 3.7 9.9 - - - +
17E TRP* 1.3 93.3 - - + +
19E ALA* 1.3 64.9 + - - +
21E ALA* 3.0 14.0 + - + +
22E ASN* 3.1 19.8 + - - +
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Residues in contact with ALA 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ASP 2.9 17.0 + - - +
16E ILE* 3.5 8.3 - - - +
18E LEU* 1.3 77.8 - - - +
20E ILE* 1.3 63.9 + - + +
22E ASN* 3.6 16.8 + - - +
23E ASP* 4.5 0.9 + - - +
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Residues in contact with ILE 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ILE* 3.0 22.3 + - + +
17E TRP* 3.8 3.4 - - - +
19E ALA* 1.3 77.4 - - + +
21E ALA* 1.3 63.3 + - - +
23E ASP* 3.0 19.8 + - + +
24E SER 3.2 8.0 + - - +
27E ALA* 4.0 13.5 - - + +
28E ALA* 3.7 26.9 - - + +
31E PHE* 3.5 43.5 - - + -
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Residues in contact with ALA 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E TRP* 2.6 56.9 + - + +
18E LEU* 3.0 8.6 + - + +
20E ILE* 1.3 70.5 - - - +
22E ASN* 1.3 66.4 + - - +
23E ASP 3.2 0.7 + - - -
24E SER 3.3 18.5 + - - -
25E PRO* 3.6 15.8 - - + +
28E ALA* 3.9 0.9 - - - +
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Residues in contact with ASN 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E LEU* 3.1 15.9 + - - +
19E ALA* 3.7 12.7 + - - +
21E ALA* 1.3 76.8 - - - +
23E ASP* 1.3 61.8 + - - +
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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