Contacts of the helix formed by residues 10 - 25 (chain D) in PDB entry 2ZPN
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 PRO 10 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D GLU 4.5 2.2 - - - +
9D TYR* 1.3 90.1 - - + +
11D PHE* 1.3 57.2 + - - +
12D GLU* 3.4 4.9 - - + +
13D LYS* 2.7 47.9 + - + +
14D ARG* 3.3 5.1 + - - +
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Residues in contact with PHE 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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6D LYS* 6.4 0.2 - - - -
10D PRO* 1.3 69.5 - - - +
12D GLU* 1.3 61.5 + - + +
14D ARG* 2.6 57.7 + - - +
15D LYS* 2.9 28.3 + - + -
100D ASP* 4.6 1.6 - - - -
101D LYS* 3.6 30.7 - - + -
102D ASP* 3.5 25.1 - - + -
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Residues in contact with GLU 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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10D PRO* 3.2 5.3 + - + +
11D PHE* 1.3 86.7 - - + +
13D LYS* 1.3 60.9 + - - +
15D LYS* 4.2 3.5 - - - +
16D ALA* 3.4 19.9 + - - +
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Residues in contact with LYS 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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9D TYR* 4.5 12.6 - - + -
10D PRO* 2.7 42.6 + - + +
12D GLU* 1.3 74.5 - - - +
14D ARG* 1.3 56.0 + - - +
16D ALA* 3.1 21.6 - - - +
17D GLU* 3.7 9.2 + - - +
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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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5D PHE* 3.8 20.1 + - + -
6D LYS* 2.6 55.9 + - - +
9D TYR* 3.1 25.4 + - + -
10D PRO* 3.6 8.0 - - - +
11D PHE* 2.6 40.7 + - - +
13D LYS* 1.3 67.9 - - - +
15D LYS* 1.3 58.4 + - - +
16D ALA 2.8 10.3 + - - -
17D GLU* 3.2 13.1 + - - -
18D SER* 3.1 14.4 + - - -
102D ASP* 3.4 41.8 + - + +
104D PHE* 3.4 16.2 - - + -
106D TYR* 3.7 7.2 - - - -
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Residues in contact with LYS 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 PHE* 2.9 39.3 + - + +
12D GLU* 4.2 4.9 - - - +
14D ARG* 1.3 75.2 - - - +
16D ALA* 1.3 62.9 + - - +
18D SER* 3.5 11.5 - - - -
19D GLU* 3.3 23.5 - - - +
101D LYS 5.2 1.3 - - - +
102D ASP* 3.6 15.8 + - - +
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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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12D GLU 3.4 12.2 + - - +
13D LYS* 3.1 16.2 - - - +
14D ARG 2.8 1.2 + - - -
15D LYS* 1.3 80.0 - - - +
17D GLU* 1.3 68.5 + - + +
18D SER 3.0 1.0 + - - -
19D GLU* 3.2 4.7 + - - +
20D ARG* 3.0 30.2 + - - +
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Residues in contact with GLU 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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5D PHE* 4.4 13.2 - - - -
9D TYR* 6.0 2.4 - - - -
13D LYS 3.7 7.6 + - - +
14D ARG* 3.2 8.7 + - - +
16D ALA* 1.3 78.6 - - + +
18D SER* 1.3 54.3 + - - +
20D ARG* 2.8 34.5 + - - +
21D ILE* 2.5 44.4 + - + +
48D LYS* 5.3 6.4 + - - +
104D PHE* 3.9 14.7 - - + -
1H TRP* 3.0 33.4 + - - +
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Residues in contact with SER 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 3.1 7.4 + - - -
15D LYS* 3.5 10.1 - - - -
16D ALA 3.1 0.2 - - - -
17D GLU* 1.3 79.1 - - - +
19D GLU* 1.3 54.8 + - - +
21D ILE* 3.0 5.1 + - - +
22D ALA* 2.5 37.1 + - - +
30D PRO* 5.2 5.7 - - - +
102D ASP 2.5 29.7 + - - -
103D GLY* 3.5 19.8 - - - -
104D PHE* 3.6 13.8 - - - -
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Residues in contact with GLU 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 LYS* 3.3 21.8 - - - +
16D ALA* 3.2 6.5 + - - +
18D SER* 1.3 79.1 - - - +
20D ARG* 1.3 57.8 + - - +
22D ALA* 3.3 11.0 - - + +
23D ASP* 2.6 38.6 + - - +
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Residues in contact with ARG 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 20.6 + - - +
17D GLU* 2.8 44.0 + - - +
19D GLU* 1.3 77.5 - - - +
21D ILE* 1.3 54.5 + - - +
23D ASP* 3.7 3.9 - - - +
24D ARG* 2.5 40.4 + - - +
1H TRP* 5.7 1.4 - - - +
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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 GLU* 2.5 29.9 + - + +
18D SER* 3.5 3.6 - - - +
20D ARG* 1.3 73.6 - - + +
22D ALA* 1.3 58.8 + - - +
23D ASP 3.0 2.2 - - - -
24D ARG* 3.9 1.1 - - - -
25D PHE* 2.7 62.1 + - + +
28D ARG* 5.1 5.3 - - + +
30D PRO* 4.3 19.7 - - + -
50D LEU* 3.6 22.0 - - + -
104D PHE* 4.7 0.9 - - + -
1H TRP* 3.3 47.8 - - + +
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Residues in contact with ALA 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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18D SER 2.5 22.4 + - - +
19D GLU* 3.3 14.1 - - + +
21D ILE* 1.3 73.1 - - - +
23D ASP* 1.3 57.0 + - - +
25D PHE 3.0 15.1 - - - +
26D LYS 4.9 1.6 - - - +
28D ARG 5.8 3.8 - - - -
30D PRO* 6.1 2.2 - - - +
95D TYR* 6.2 0.4 - - - +
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Residues in contact with ASP 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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19D GLU 2.6 19.5 + - - +
20D ARG* 3.7 3.8 - - - +
22D ALA* 1.3 74.3 - - - +
24D ARG* 1.3 59.0 + - - +
25D PHE* 2.9 14.0 + - - -
26D LYS* 5.5 0.2 - - - -
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Residues in contact with ARG 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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20D ARG* 2.5 29.1 + - + +
21D ILE* 3.9 0.2 - - - -
23D ASP* 1.3 72.3 - - - +
25D PHE* 1.3 91.4 + - + +
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Residues in contact with PHE 25 (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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21D ILE* 2.7 46.2 + - + +
22D ALA* 3.0 21.5 - - - +
23D ASP 2.9 4.6 + - - -
24D ARG* 1.3 96.7 - - + +
26D LYS* 1.3 67.0 + - - +
27D ASN* 4.9 0.2 - - - -
28D ARG* 4.1 32.1 + - + +
50D LEU* 4.0 26.9 - - + -
3H GLU* 5.3 1.3 - - - -
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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