Contacts of the helix formed by residues 14 - 26 (chain D) in PDB entry 1Z6Z
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 ARG 14 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D GLY 3.6 9.7 - - - +
12D ALA 3.4 0.2 - - - -
13D SER* 1.3 87.2 + - - +
15D GLY* 1.3 68.8 + - - +
16D PHE 3.5 1.2 + - - -
17D GLY 3.6 0.5 + - - -
18D ARG* 3.3 15.9 + - - -
39D ARG* 4.4 6.7 - - - +
40D ASN* 6.0 4.6 - - - +
43D ALA* 5.8 1.6 - - + -
201D ASP* 3.0 34.5 + - - +
804D NAP 2.7 82.4 + - - +
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Residues in contact with GLY 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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14D ARG* 1.3 74.6 - - - +
16D PHE* 1.3 63.6 + - - -
18D ARG* 3.2 5.3 + - - +
19D THR* 3.2 23.2 + - - -
200D THR* 3.8 14.4 - - - -
201D ASP 5.7 0.2 - - - -
231D CYS* 4.2 6.7 - - - -
804D NAP 3.4 17.0 + - - -
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Residues in contact with PHE 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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15D GLY* 1.3 71.3 - - - -
17D GLY* 1.3 56.9 + - - +
19D THR* 3.2 4.2 + - - -
20D LEU* 2.9 38.6 + - + +
97D ASN* 3.5 22.2 - - - +
152D ILE* 3.9 29.6 - - + -
193D TYR* 4.3 3.8 - + - -
195D PRO* 4.3 11.4 - - + -
198D LEU* 3.6 29.6 - - + -
200D THR* 4.1 0.6 - - - +
231D CYS* 3.9 20.3 - - + -
234D SER* 3.8 13.2 - - - -
235D ALA* 3.6 39.9 - - + -
238D LEU* 4.1 16.6 - - + -
804D NAP 2.9 18.2 + - - +
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Residues in contact with GLY 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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9D LEU* 3.4 20.0 - - - +
11D GLY 3.2 19.1 - - - -
12D ALA* 3.9 4.2 - - - +
14D ARG 3.6 1.6 + - - -
15D GLY 3.4 0.4 - - - -
16D PHE* 1.3 78.4 - - - +
18D ARG* 1.3 56.9 + - - +
20D LEU* 4.2 3.4 - - - -
21D ALA* 3.0 28.1 + - - +
97D ASN* 3.5 18.2 - - - +
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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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12D ALA 3.3 20.5 + - - +
13D SER 3.6 15.9 + - - +
14D ARG* 3.3 21.1 + - - -
15D GLY 3.2 10.2 + - - +
17D GLY* 1.3 77.1 - - - +
19D THR* 1.3 58.4 + - - +
21D ALA* 4.2 1.6 - - - +
22D PRO* 3.1 23.8 - - - +
43D ALA* 3.6 21.4 + - - +
46D GLN* 3.1 33.7 + - - +
47D LEU* 4.0 28.6 - - - +
50D GLU* 5.5 4.8 - - - +
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Residues in contact with THR 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 GLY 3.2 8.5 + - - -
16D PHE 3.2 7.8 + - - -
18D ARG* 1.3 77.4 - - - +
20D LEU* 1.3 63.7 + - - +
22D PRO* 3.3 12.0 - - - +
23D LEU* 3.6 18.2 - - + +
231D CYS* 3.5 22.7 - - + +
232D LYS* 3.6 40.6 - - + +
235D ALA* 4.7 0.4 - - + -
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Residues in contact with LEU 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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9D LEU* 3.9 17.7 - - + -
16D PHE* 2.9 26.7 + - + +
17D GLY 3.3 5.1 + - - +
19D THR* 1.3 76.7 - - - +
21D ALA* 1.3 55.4 + - - +
23D LEU* 3.1 5.0 + - - +
24D LEU* 2.8 41.5 + - + +
95D ILE* 3.8 28.3 - - + -
235D ALA* 3.8 29.8 - - + +
238D LEU* 4.1 17.5 - - + -
239D LEU* 4.0 31.0 - - + -
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Residues in contact with ALA 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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9D LEU* 3.9 16.4 - - + +
17D GLY 3.0 16.8 + - - +
18D ARG 4.2 0.4 - - - +
20D LEU* 1.3 76.1 - - - +
22D PRO* 1.4 63.3 - - + +
24D LEU* 3.5 4.9 - - - +
25D ALA* 2.8 30.9 + - - +
34D LEU* 4.3 4.6 - - + +
36D LEU* 4.1 10.5 - - + -
47D LEU* 3.8 29.8 - - + -
51D LEU* 4.5 2.2 - - + -
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Residues in contact with PRO 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 ARG* 3.1 21.5 - - - +
19D THR* 3.3 13.2 - - - +
21D ALA* 1.4 92.7 - - + +
23D LEU* 1.3 62.8 + - + +
25D ALA* 3.3 1.6 + - - +
26D SER* 3.1 24.8 + - - -
47D LEU* 4.2 12.3 - - + -
50D GLU* 5.5 7.4 - - + +
51D LEU* 3.7 17.9 - - + +
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Residues in contact with LEU 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 THR* 3.6 13.7 - - + +
20D LEU* 3.1 6.2 + - - +
22D PRO* 1.3 80.3 - - + +
24D LEU* 1.3 60.8 + - - +
26D SER* 3.0 20.5 + - - +
27D LEU* 3.6 14.4 - - - +
232D LYS* 4.1 34.3 - - + +
235D ALA* 3.8 28.5 - - + -
236D GLN* 4.3 17.9 - - + +
239D LEU* 3.8 15.6 - - + +
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Residues in contact with LEU 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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2D LEU* 3.7 29.4 - - + -
7D CYS* 3.5 26.7 - - - -
9D LEU* 4.8 12.6 - - + -
20D LEU* 2.8 25.0 + - + +
21D ALA* 3.5 4.0 - - - +
23D LEU* 1.3 76.1 - - - +
25D ALA* 1.3 65.8 + - - +
27D LEU* 2.9 17.1 + - - +
28D LEU* 3.4 17.5 + - + +
34D LEU* 4.4 9.9 - - + -
93D LEU* 3.8 14.4 - - + -
95D ILE* 3.9 20.2 - - + -
239D LEU* 3.8 19.2 - - + +
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Residues in contact with ALA 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 ALA 2.8 21.0 + - - +
22D PRO 3.3 5.4 + - - +
24D LEU* 1.3 72.3 - - - +
26D SER* 1.3 57.1 + - - +
28D LEU* 3.1 37.8 + - - +
34D LEU* 4.0 7.6 - - + +
51D LEU* 3.8 20.9 - - + -
58D LEU* 3.8 26.5 - - + +
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Residues in contact with SER 26 (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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-3D PHE 5.1 8.1 + - - -
-2D GLN* 6.2 0.2 - - - -
1D MET* 3.6 18.1 - - - +
22D PRO 3.1 12.0 + - - -
23D LEU* 3.0 18.2 + - - +
25D ALA* 1.3 75.5 - - - +
27D LEU* 1.3 65.3 + - - +
28D LEU 3.4 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