Contacts of the helix formed by residues 6 - 24 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ARG* 1.3 78.5 - - - +
7A PRO* 1.3 75.0 - - - +
8A ALA* 3.5 6.9 + - - +
9A ALA* 2.9 22.4 + - - +
10A GLU 3.2 9.0 + - - -
80A ILE 2.9 11.4 + - - -
81A VAL* 2.6 35.1 + - - -
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Residues in contact with PRO 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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5A ARG* 3.7 18.8 - - - +
6A SER* 1.3 86.4 - - - +
8A ALA* 1.3 61.6 + - - +
10A GLU* 3.4 6.5 + - + +
11A GLY* 3.1 17.3 + - - -
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Residues in contact with ALA 8 (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 SER* 3.1 9.0 + - - +
7A PRO* 1.3 78.2 - - - +
9A ALA* 1.3 59.2 + - - +
11A GLY* 3.0 4.4 + - - -
12A ASP* 2.8 33.2 + - - +
81A VAL 4.5 0.2 - - - +
82A ARG* 3.7 28.0 - - - +
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Residues in contact with ALA 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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5A ARG* 4.4 4.5 - - + -
6A SER* 2.9 24.1 + - - +
8A ALA* 1.3 76.4 - - - +
10A GLU* 1.3 62.5 + - - +
12A ASP* 3.1 21.8 + - - +
13A LEU* 3.1 21.1 + - + +
80A ILE* 3.8 16.6 - - + +
81A VAL 3.5 10.3 + - - +
83A ILE* 3.6 21.1 - - + +
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Residues in contact with GLU 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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5A ARG* 2.4 62.5 + - - +
6A SER 3.2 5.3 + - - -
7A PRO* 3.7 6.3 - - - +
8A ALA 3.2 0.2 - - - -
9A ALA* 1.3 77.4 - - - +
11A GLY* 1.3 64.8 + - - +
13A LEU* 3.2 11.0 + - - +
14A VAL* 3.0 26.2 + - + +
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Residues in contact with GLY 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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7A PRO 3.1 10.7 + - - -
8A ALA* 3.0 8.0 + - - -
10A GLU* 1.3 79.0 - - - +
12A ASP* 1.3 62.2 + - - +
14A VAL* 2.9 26.1 - - - +
15A ASP* 3.0 20.6 + - - -
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Residues in contact with ASP 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 ALA 2.8 15.2 + - - +
9A ALA* 3.1 8.1 + - - +
11A GLY* 1.3 78.0 - - - +
13A LEU* 1.3 53.1 + - - +
15A ASP* 3.3 7.5 + - - +
16A ILE* 2.7 40.4 + - + +
82A ARG* 2.7 44.4 + - - +
83A ILE* 2.7 51.3 + - + +
84A VAL* 5.0 0.9 - - - -
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Residues in contact with LEU 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 ALA* 3.1 16.2 + - + +
10A GLU* 3.2 9.2 + - - +
12A ASP* 1.3 76.7 - - - +
14A VAL* 1.3 58.9 + - - +
16A ILE* 3.6 5.6 - - + +
17A TRP* 2.7 30.1 + - - +
32A LEU* 3.8 18.5 - - + +
35A ILE* 3.8 43.5 - - + -
39A ILE* 5.2 6.7 - - + -
80A ILE* 6.4 0.2 - - + -
83A ILE* 4.2 26.9 - - + -
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Residues in contact with VAL 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 GLU* 3.0 18.8 + - + +
11A GLY* 2.9 28.3 - - - +
13A LEU* 1.3 73.5 - - - +
15A ASP* 1.3 64.8 + - - +
17A TRP* 3.1 7.0 + - + +
18A LEU* 2.8 48.5 + - + +
32A LEU* 5.5 0.4 - - - -
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Residues in contact with ASP 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 GLY* 3.0 24.1 + - - +
12A ASP* 3.5 6.7 - - - +
14A VAL* 1.3 83.0 - - - +
16A ILE* 1.3 62.5 - - + +
18A LEU* 3.8 11.9 - - - +
19A ALA* 3.0 24.1 + - - +
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Residues in contact with ILE 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 ASP* 2.7 25.9 + - - +
13A LEU* 3.6 11.4 - - + +
15A ASP* 1.3 74.1 - - + +
17A TRP* 1.3 63.7 + - - +
19A ALA* 3.3 5.2 + - - +
20A ILE* 3.2 29.3 + - + +
31A PHE* 4.0 28.3 - - + -
32A LEU* 4.3 7.0 - - + -
35A ILE* 4.6 5.6 - - + -
67A TYR* 4.1 32.1 - - + +
83A ILE* 3.7 35.2 - - + +
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Residues in contact with TRP 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 LEU 2.7 21.0 + - - +
14A VAL* 3.5 9.2 - - + +
16A ILE* 1.3 75.1 - - - +
18A LEU* 1.3 78.0 + - + +
20A ILE* 3.3 2.0 + - - -
21A ALA* 2.8 50.1 + - + +
25A PRO* 3.7 28.0 - - + -
28A ALA* 3.2 21.6 - - + +
29A ASP* 2.9 28.2 + - - +
32A LEU* 3.4 39.7 - - + -
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Residues in contact with LEU 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 VAL* 2.8 39.6 + - + +
15A ASP* 3.8 11.7 - - - +
17A TRP* 1.3 94.2 - - + +
19A ALA* 1.3 65.1 + - - +
21A ALA* 3.0 11.7 + - + +
22A ASN* 3.0 19.3 + - - +
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Residues in contact with ALA 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 ASP 3.0 13.3 + - - +
16A ILE* 3.6 11.2 - - - +
18A LEU* 1.3 76.8 - - - +
20A ILE* 1.3 65.7 + - + +
22A ASN* 3.3 20.5 + - - +
23A ASP* 4.2 1.6 + - - +
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Residues in contact with ILE 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 ILE* 3.2 21.5 + - + +
17A TRP 3.9 0.4 - - - +
19A ALA* 1.3 78.6 - - + +
21A ALA* 1.3 63.2 + - - +
23A ASP* 3.0 12.3 + - + +
24A SER 3.0 18.7 + - - +
27A ALA* 3.8 14.1 - - + -
28A ALA* 3.5 31.6 - - + +
31A PHE* 3.8 40.8 - - + -
32A LEU* 5.1 1.1 - - + -
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Residues in contact with ALA 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 TRP* 2.8 53.4 + - + +
18A LEU* 3.0 7.5 + - + +
20A ILE* 1.3 78.1 - - - +
22A ASN* 1.4 62.8 + - - +
23A ASP 3.4 0.3 + - - -
24A SER 3.5 16.2 + - - -
25A PRO* 3.6 18.0 - - + +
28A ALA* 3.9 1.1 - - + +
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Residues in contact with ASN 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 LEU* 3.0 17.5 + - - +
19A ALA* 3.4 12.0 + - - +
20A ILE 3.1 0.2 - - - -
21A ALA* 1.4 77.1 - - - +
23A ASP* 1.3 62.2 + - - +
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Residues in contact with ASP 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 ALA 4.2 0.8 + - - +
20A ILE* 3.0 12.6 + - + +
21A ALA 3.8 0.4 - - - -
22A ASN* 1.3 83.4 - - - +
24A SER* 1.3 66.9 + - - +
25A PRO* 4.6 1.9 - - - +
27A ALA* 5.3 4.3 - - - +
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Residues in contact with SER 24 (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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20A ILE 3.0 11.5 + - - +
21A ALA* 3.5 1.8 + - - -
23A ASP* 1.3 90.1 - - - +
25A PRO* 1.3 70.6 - - - +
26A ARG* 3.6 11.8 + - - +
27A ALA* 3.1 33.3 + - - +
28A ALA 3.2 8.7 + - - -
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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