Contacts of the helix formed by residues 14 - 26 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E GLY 3.6 6.2 - - - +
12E ALA 3.5 0.2 - - - -
13E SER* 1.3 90.6 + - - +
15E GLY* 1.3 70.3 - - - +
16E PHE 3.5 1.2 + - - -
17E GLY 3.6 3.8 + - - -
18E ARG* 3.2 16.1 + - - -
39E ARG* 4.4 5.9 - - - +
40E ASN* 6.0 4.6 - - - +
201E ASP* 2.9 34.5 + - - +
805E NAP 2.7 80.3 + - - +
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Residues in contact with GLY 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E ARG* 1.3 75.0 - - - +
16E PHE* 1.3 64.0 + - - -
18E ARG* 3.2 5.2 + - - +
19E THR* 3.2 22.3 + - - -
200E THR* 3.7 16.4 - - - -
201E ASP* 5.6 0.4 + - - -
231E CYS* 4.2 3.8 - - - -
805E NAP 3.5 17.0 - - - -
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Residues in contact with PHE 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E GLY* 1.3 70.1 - - - -
17E GLY* 1.3 56.1 + - - +
19E THR* 3.2 2.8 + - - -
20E LEU* 2.9 39.3 + - + +
97E ASN* 3.5 21.5 - - - +
152E ILE* 3.9 28.9 - - + -
193E TYR* 4.3 3.4 - + - -
195E PRO* 4.3 8.7 - - + -
198E LEU* 3.6 30.5 - - + -
200E THR* 4.0 3.6 - - - +
231E CYS* 4.0 15.9 - - + -
234E SER* 3.7 17.3 - - - -
235E ALA* 3.6 39.9 - - + -
238E LEU* 4.1 16.6 - - + -
805E NAP 2.9 18.1 + - - +
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Residues in contact with GLY 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E LEU* 3.4 15.8 - - - +
11E GLY 3.2 20.2 - - - -
12E ALA* 4.0 4.7 - - - -
14E ARG 3.6 1.6 + - - -
15E GLY 3.4 0.8 - - - -
16E PHE* 1.3 77.8 - - - +
18E ARG* 1.3 56.5 + - - +
20E LEU* 4.2 5.8 - - - -
21E ALA* 2.9 28.6 + - - +
97E ASN* 3.5 17.8 - - - +
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Residues in contact with ARG 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E ALA 3.3 20.7 + - - +
13E SER 3.7 12.3 - - - +
14E ARG* 3.2 27.3 + - - -
15E GLY 3.2 4.1 + - - +
17E GLY* 1.3 75.0 - - - +
19E THR* 1.3 59.0 + - - +
21E ALA* 4.2 1.2 - - - +
22E PRO* 3.1 23.7 - - - +
43E ALA 5.2 2.0 - - - -
47E LEU* 4.0 25.6 - - - -
50E GLU* 5.0 6.1 - - - -
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Residues in contact with THR 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E GLY 3.2 10.2 + - - -
16E PHE 3.8 4.3 - - - -
18E ARG* 1.3 75.8 - - - +
20E LEU* 1.3 65.0 + - - +
22E PRO* 3.3 10.7 - - - +
23E LEU* 3.6 17.8 - - + +
231E CYS* 3.5 25.1 - - + +
232E LYS* 3.6 38.6 - - + +
235E ALA* 4.7 0.9 - - + -
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Residues in contact with LEU 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E LEU* 3.9 17.0 - - + -
16E PHE* 2.9 28.1 + - + +
17E GLY* 3.2 5.1 + - - +
19E THR* 1.3 76.7 - - - +
21E ALA* 1.3 54.7 + - - +
23E LEU* 3.1 5.4 + - + +
24E LEU* 2.8 41.6 + - + +
95E ILE* 3.8 29.8 - - + -
235E ALA* 3.8 27.8 - - + +
238E LEU* 4.1 18.4 - - + -
239E LEU* 4.1 31.2 - - + -
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Residues in contact with ALA 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E LEU* 3.9 17.0 - - + +
12E ALA* 5.1 1.6 - - + -
17E GLY 2.9 17.4 + - - +
18E ARG* 4.2 0.9 - - - +
20E LEU* 1.3 74.1 - - - +
22E PRO* 1.4 58.7 - - + +
24E LEU* 3.2 5.1 + - - +
25E ALA* 2.7 36.8 + - - +
34E LEU* 4.4 5.5 - - + +
36E LEU* 4.1 16.6 - - + -
47E LEU* 3.8 21.3 - - + -
51E LEU* 4.6 2.7 - - + -
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Residues in contact with PRO 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E ARG* 3.1 21.1 - - - +
19E THR* 3.3 12.8 - - - +
21E ALA* 1.4 92.5 - - + +
23E LEU* 1.3 61.7 + - + +
25E ALA* 3.4 1.6 + - - +
26E SER* 3.2 24.9 + - - -
47E LEU* 4.2 12.8 - - + -
50E GLU* 5.3 9.9 - - + +
51E LEU* 3.7 19.3 - - + -
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Residues in contact with LEU 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E THR* 3.6 18.2 - - + +
20E LEU* 3.1 6.8 + - - +
22E PRO* 1.3 79.7 - - + +
24E LEU* 1.3 62.0 + - - +
26E SER* 3.0 19.8 + - - +
27E LEU* 3.6 14.6 - - - +
232E LYS* 4.1 19.5 - - + +
235E ALA* 3.8 25.1 - - + -
236E GLN* 4.3 17.9 - - + +
239E LEU* 3.8 16.1 - - + +
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Residues in contact with LEU 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E LEU* 3.7 28.7 - - + -
7E CYS* 3.4 27.6 - - - -
9E LEU* 4.7 13.2 - - + -
20E LEU* 2.8 25.4 + - + +
21E ALA 3.4 4.3 - - - +
23E LEU* 1.3 74.0 - - - +
25E ALA* 1.3 66.0 + - - +
27E LEU* 2.9 17.4 + - - +
28E LEU* 3.4 16.7 + - + +
34E LEU* 4.4 10.1 - - + -
93E LEU* 3.8 14.8 - - + -
95E ILE* 3.9 18.6 - - + -
239E LEU* 3.8 20.1 - - + +
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Residues in contact with ALA 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E ALA 2.7 20.3 + - - +
22E PRO 3.7 5.8 - - - +
24E LEU* 1.3 72.1 - - - +
26E SER* 1.3 57.7 + - - +
28E LEU* 3.1 38.4 + - - +
34E LEU* 4.0 13.7 - - + +
51E LEU* 3.9 22.2 - - + -
58E LEU* 4.0 18.3 - - + +
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Residues in contact with SER 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-3E PHE 5.7 2.1 + - - -
1E MET* 3.6 17.9 - - - +
22E PRO 3.2 10.0 + - - -
23E LEU* 3.0 18.0 + - - +
25E ALA* 1.3 78.1 - - - +
27E LEU* 1.3 62.5 + - - +
28E 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