Contacts of the helix formed by residues 9 - 24 (chain D) in PDB entry 4A12
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 LYS 9 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D LYS 3.9 5.5 + - - +
8D LEU* 1.3 74.1 - - - +
10D LYS* 1.4 59.0 + - - +
11D ASP* 3.4 2.9 - - + +
12D LYS* 3.1 17.0 + - + +
13D ARG* 2.8 31.1 + - - +
6F T 5.4 1.1 - - - -
39G G 4.9 5.3 + - - -
40G C 3.0 29.7 + - - -
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Residues in contact with LYS 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LYS* 1.4 70.8 - - - +
11D ASP* 1.3 75.8 + - - +
13D ARG* 3.5 15.5 + - - +
14D ARG* 3.1 71.4 + - - +
49D TYR* 5.7 4.0 - - - -
5F A 3.6 46.1 + - - +
6F T 3.9 26.4 + - - +
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Residues in contact with ASP 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LYS* 3.4 2.2 - - + +
10D LYS* 1.3 96.7 - - - +
12D LYS* 1.4 63.1 + - + +
14D ARG* 3.5 11.3 + - - +
15D GLU* 3.2 23.7 + - - +
49D TYR* 5.8 2.4 - - - -
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Residues in contact with LYS 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D LYS 6.1 0.2 - - - +
8D LEU* 3.8 24.3 - - + +
9D LYS* 3.1 21.5 + - + +
11D ASP* 1.4 76.0 - - + +
13D ARG* 1.4 64.6 + - - +
15D GLU* 3.5 13.7 + - - +
16D ALA* 3.2 21.5 + - - +
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Residues in contact with ARG 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 4.1 26.2 + - + +
9D LYS 2.8 18.9 + - - +
10D LYS* 3.5 20.9 + - - +
12D LYS* 1.4 70.9 - - - +
14D ARG* 1.3 54.8 + - - +
16D ALA* 3.1 4.3 + - - +
17D ILE* 2.8 49.5 + - + +
36D PHE* 3.7 24.0 - - + +
38D VAL* 4.0 29.1 - - - +
42D THR* 3.8 8.8 - - - +
43D ILE* 6.1 0.7 - - - -
46D ASP* 2.8 43.6 + - - -
6F T 2.8 43.4 + - - -
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Residues in contact with ARG 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D LYS* 3.1 60.9 + - - +
11D ASP* 3.8 10.6 + - - +
13D ARG* 1.3 78.1 - - - +
15D GLU* 1.4 55.8 + - - +
17D ILE* 3.2 5.0 + - - -
18D ARG* 2.9 26.2 + - - +
45D LEU* 4.2 13.5 + - - +
46D ASP* 2.8 42.0 + - + +
49D TYR* 3.4 51.9 - - - +
50D LEU* 3.1 28.4 - - + +
6F T 5.5 1.8 + - - -
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Residues in contact with GLU 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ASP 3.2 17.6 + - - +
12D LYS* 3.7 12.3 - - - +
13D ARG 3.3 0.2 - - - -
14D ARG* 1.4 75.0 - - - +
16D ALA* 1.3 59.5 + - - +
18D ARG* 4.2 9.9 + - - +
19D GLN* 3.1 48.5 + - - +
50D LEU* 5.7 1.1 - - - -
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Residues in contact with ALA 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 4.6 9.2 - - + -
12D LYS 3.2 12.4 + - - +
13D ARG* 3.1 10.4 + - - +
15D GLU* 1.3 75.7 - - - +
17D ILE* 1.4 59.1 + - - +
19D GLN* 3.5 8.9 + - - +
20D GLN* 3.0 28.9 + - - +
36D PHE* 3.5 20.0 - - + -
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Residues in contact with ILE 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ARG* 2.8 37.1 + - + +
14D ARG* 3.2 5.4 + - - +
16D ALA* 1.4 74.1 - - - +
18D ARG* 1.4 59.4 + - - +
20D GLN* 3.1 4.2 + - - +
21D ILE* 2.9 49.5 + - + +
32D LEU* 4.8 9.8 - - + +
36D PHE* 3.7 26.9 - - + -
43D ILE* 4.6 15.3 - - + -
46D ASP* 3.5 33.9 - - + +
47D ARG* 5.0 5.2 - - + -
50D LEU* 4.2 12.6 - - + -
52D ILE* 4.9 0.2 - - + -
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Residues in contact with ARG 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ARG 2.9 16.7 + - - +
15D GLU* 4.2 10.2 + - - +
17D ILE* 1.4 75.1 - - - +
19D GLN* 1.3 65.8 + - - +
21D ILE* 3.6 2.3 + - - +
22D ASP* 3.0 34.9 + - - +
50D LEU* 3.6 28.3 - - + -
52D ILE* 3.8 24.9 - - + +
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Residues in contact with GLN 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D GLU* 3.1 42.4 + - - +
16D ALA* 3.8 7.5 - - - +
17D ILE 3.3 0.4 - - - -
18D ARG* 1.3 86.6 - - - +
20D GLN* 1.4 59.8 + - - +
22D ASP* 3.4 8.7 + - - +
23D SER* 2.9 30.5 + - - -
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Residues in contact with GLN 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ALA 3.0 18.6 + - - +
17D ILE 3.1 5.6 + - - +
19D GLN* 1.4 74.7 - - - +
21D ILE* 1.3 59.6 + - - +
23D SER* 2.9 22.8 + - - -
24D ASN* 2.9 25.3 + - - +
27D ILE* 3.9 15.3 - - + +
32D LEU* 3.9 16.6 - - + -
35D LEU* 3.8 31.3 - - + +
36D PHE* 4.3 5.2 - - + -
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Residues in contact with ILE 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ILE* 2.9 36.8 + - + +
18D ARG 4.1 3.4 - - - +
20D GLN* 1.3 71.2 - - - +
22D ASP* 1.3 64.9 + - - +
24D ASN 3.6 5.6 - - - -
25D PRO* 3.1 26.4 - - + +
27D ILE* 3.9 18.4 - - + -
32D LEU* 3.9 13.0 - - + -
47D ARG* 3.9 15.9 - - + -
52D ILE* 3.8 32.3 - - + -
58D ARG* 3.6 33.4 - - - +
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Residues in contact with ASP 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C TYR* 5.5 2.1 - - - -
18D ARG* 3.0 26.2 + - + +
19D GLN* 3.5 10.3 - - - +
21D ILE* 1.3 78.3 - - - +
23D SER* 1.4 60.6 + - - +
24D ASN 3.6 0.2 + - - -
25D PRO* 4.4 8.5 - - - +
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Residues in contact with SER 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C TYR* 2.6 28.0 + - - -
19D GLN 2.9 15.5 + - - -
20D GLN* 2.9 32.9 + - - -
22D ASP* 1.4 78.4 - - - +
24D ASN* 1.3 51.7 + - - +
25D PRO* 4.3 0.7 - - - -
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Residues in contact with ASN 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C TYR* 4.0 7.4 + - - +
20D GLN* 2.9 19.6 + - - +
21D ILE 3.1 7.1 - - - +
22D ASP 3.4 0.2 - - - -
23D SER* 1.3 78.1 - - - +
25D PRO* 1.4 64.4 - - - +
26D PHE* 3.3 26.3 + - - +
27D ILE* 3.3 50.5 - - + +
31D GLU* 5.0 2.8 + - - -
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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