Contacts of the helix formed by residues 6 - 24 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5G ARG* 1.3 79.7 - - - +
7G PRO* 1.3 78.8 - - - +
8G ALA* 3.4 12.1 + - - +
9G ALA* 2.9 12.8 + - - +
10G GLU 3.1 9.7 + - - -
80G ILE 2.8 11.0 + - - -
81G VAL* 3.2 32.0 + - - +
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Residues in contact with PRO 7 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G ARG* 3.7 18.6 - - - +
6G SER* 1.3 89.4 - - - +
8G ALA* 1.3 61.0 + - - +
10G GLU* 3.3 9.8 - - + +
11G GLY* 3.1 17.3 + - - -
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Residues in contact with ALA 8 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G SER* 3.1 10.7 + - - +
7G PRO* 1.3 77.8 - - - +
9G ALA* 1.3 53.4 + - - +
11G GLY* 3.0 4.6 + - - +
12G ASP* 2.7 39.7 + - - +
82G ARG* 4.1 31.4 - - + +
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Residues in contact with ALA 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G ARG* 4.4 3.6 - - + -
6G SER 2.9 11.5 + - - +
8G ALA* 1.3 78.1 - - - +
10G GLU* 1.3 63.4 + - - +
12G ASP* 3.1 14.8 + - - +
13G LEU* 3.0 27.1 + - + +
80G ILE* 3.7 13.7 - - + +
81G VAL 3.3 26.9 + - - +
83G ILE* 3.8 16.8 - - + +
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Residues in contact with GLU 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G ARG* 2.8 47.3 + - - +
6G SER 3.1 7.7 + - - -
7G PRO* 3.3 14.6 - - - +
9G ALA* 1.3 76.2 - - - +
11G GLY* 1.3 62.7 + - - +
13G LEU* 3.1 9.8 + - - +
14G VAL* 2.9 41.8 + - + +
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Residues in contact with GLY 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G PRO 3.1 5.3 + - - -
8G ALA* 3.0 8.9 + - - -
10G GLU* 1.3 84.7 - - - +
12G ASP* 1.3 63.2 + - - +
14G VAL* 3.5 5.4 + - - +
15G ASP* 3.0 33.4 + - - +
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Residues in contact with ASP 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G ALA 2.7 21.9 + - - +
9G ALA 3.3 7.2 - - - +
11G GLY* 1.3 74.1 - - - +
13G LEU* 1.3 57.9 + - - +
15G ASP* 3.2 8.3 + - - +
16G ILE* 2.8 34.1 + - - +
82G ARG* 2.7 47.5 + - - +
83G ILE* 2.8 45.1 + - + +
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Residues in contact with LEU 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G ARG* 6.6 0.7 - - + -
9G ALA 3.0 18.9 + - - +
10G GLU* 3.1 10.3 + - - +
12G ASP* 1.3 75.1 - - - +
14G VAL* 1.3 59.3 + - + +
16G ILE* 3.6 10.1 - - + +
17G TRP* 2.7 30.0 + - - +
32G LEU* 4.0 23.6 - - + +
35G ILE* 4.0 27.6 - - + -
39G ILE* 5.3 4.9 - - + -
80G ILE* 6.3 0.4 - - + -
83G ILE* 4.0 37.0 - - + -
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Residues in contact with VAL 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G GLU* 2.9 30.6 + - + +
11G GLY* 3.9 6.5 - - - +
13G LEU* 1.3 74.8 - - + +
15G ASP* 1.3 62.4 - - - +
17G TRP* 3.1 7.2 + - + +
18G LEU* 2.8 48.4 + - + +
32G LEU* 5.8 0.4 - - - -
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Residues in contact with ASP 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G GLY* 3.0 21.4 + - - +
12G ASP* 3.5 6.1 - - - +
14G VAL* 1.3 77.6 - - - +
16G ILE* 1.3 65.2 - - + +
18G LEU* 3.3 11.0 + - - +
19G ALA* 3.0 25.5 + - - +
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Residues in contact with ILE 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G ASP 2.8 22.5 + - - +
13G LEU* 3.6 14.8 - - + +
15G ASP* 1.3 74.0 - - + +
17G TRP* 1.3 67.0 + - - +
19G ALA* 3.4 5.8 + - - +
20G ILE* 3.3 23.5 + - + +
31G PHE* 3.8 33.2 - - + -
32G LEU* 4.2 9.6 - - + -
35G ILE* 5.4 0.9 - - + -
67G TYR* 4.0 31.2 - - + +
83G ILE* 3.5 36.6 - - + +
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Residues in contact with TRP 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G LEU 2.7 21.2 + - - +
14G VAL* 3.1 8.9 + - + +
16G ILE* 1.3 76.2 - - - +
18G LEU* 1.3 84.4 + - + +
20G ILE* 3.3 0.7 + - - -
21G ALA* 3.0 38.3 + - + -
25G PRO* 3.6 29.4 - - + -
28G ALA* 3.3 23.7 - - + +
29G ASP* 2.8 29.1 + - - +
32G LEU* 3.3 40.8 - - + -
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Residues in contact with LEU 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G VAL* 2.8 39.4 + - + +
15G ASP* 3.9 11.0 - - - +
17G TRP* 1.3 95.7 - - + +
19G ALA* 1.3 63.8 + - - +
21G ALA* 2.9 14.3 + - + +
22G ASN* 3.1 17.7 + - - +
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Residues in contact with ALA 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G ASP 3.0 17.7 + - - +
16G ILE* 3.6 7.9 - - - +
17G TRP 3.3 0.2 - - - -
18G LEU* 1.3 77.8 - - - +
20G ILE* 1.3 64.3 + - + +
22G ASN* 3.4 19.4 + - - +
23G ASP* 4.3 1.4 + - - +
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Residues in contact with ILE 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G ILE* 3.3 17.9 + - + +
17G TRP* 3.3 1.5 + - - +
18G LEU 3.3 0.2 - - - -
19G ALA* 1.3 78.9 - - + +
21G ALA* 1.3 59.1 + - - +
23G ASP* 3.1 12.6 + - + +
24G SER 3.0 21.5 + - - -
27G ALA* 3.8 13.2 - - + -
28G ALA* 3.5 33.7 - - + +
31G PHE* 3.6 42.4 - - + -
32G LEU* 5.3 0.2 - - + -
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Residues in contact with ALA 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G TRP* 3.0 44.8 + - + +
18G LEU* 2.9 14.8 + - + +
20G ILE* 1.3 75.2 - - - +
22G ASN* 1.3 66.0 + - - +
23G ASP 3.2 0.7 + - - -
24G SER 3.4 16.8 + - - -
25G PRO* 3.6 16.5 - - + +
28G ALA* 4.2 1.3 - - + -
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Residues in contact with ASN 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G LEU* 3.1 14.9 + - - +
19G ALA* 3.5 12.2 + - - +
21G ALA* 1.3 77.5 - - - +
23G ASP* 1.3 62.0 + - - +
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Residues in contact with ASP 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G ALA 4.3 0.8 + - - +
20G ILE* 3.1 12.1 + - + +
21G ALA 3.6 1.1 - - - +
22G ASN* 1.3 82.5 - - - +
24G SER* 1.3 68.0 + - - +
25G PRO* 4.5 1.7 - - - +
27G ALA* 5.2 5.0 - - - +
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Residues in contact with SER 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G ILE 3.0 10.0 + - - +
21G ALA* 3.4 4.1 + - - -
23G ASP* 1.3 91.2 - - - +
25G PRO* 1.3 70.0 - - - +
26G ARG* 3.5 9.7 + - - +
27G ALA* 3.4 26.2 + - - +
28G ALA 3.2 16.1 + - - -
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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