Contacts of the helix formed by residues 14 - 26 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F GLY 3.6 6.8 - - - +
13F SER* 1.3 89.4 + - - +
15F GLY* 1.3 69.0 + - - +
16F PHE 3.5 1.4 + - - -
17F GLY 3.6 3.1 + - - -
18F ARG* 3.3 16.2 + - - -
39F ARG* 4.3 5.9 - - - +
40F ASN* 6.0 4.5 - - - +
43F ALA* 5.8 1.3 - - + -
201F ASP* 2.9 34.5 + - - +
806F NAP 2.7 84.4 + - - +
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Residues in contact with GLY 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F ARG* 1.3 75.0 - - - +
16F PHE* 1.3 63.2 + - - -
18F ARG* 3.2 5.4 + - - +
19F THR* 3.2 23.4 + - - -
200F THR* 3.7 17.0 - - - -
231F CYS* 4.3 4.5 - - - -
806F NAP 3.4 17.0 - - - -
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Residues in contact with PHE 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F GLY* 1.3 70.5 - - - -
17F GLY* 1.3 56.6 + - - +
19F THR* 3.2 2.9 + - - -
20F LEU* 2.9 41.2 + - + +
97F ASN* 3.5 21.5 - - - +
152F ILE* 3.9 29.2 - - + -
193F TYR* 4.3 2.5 - + - -
195F PRO* 4.3 9.4 - - + -
198F LEU* 3.6 28.9 - - + -
200F THR* 4.0 3.2 - - - +
231F CYS* 3.9 17.5 - - + -
234F SER* 3.8 16.8 - - - -
235F ALA* 3.6 40.8 - - + -
238F LEU* 4.2 15.5 - - + -
806F NAP 2.9 18.8 + - - +
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Residues in contact with GLY 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F LEU* 3.3 19.8 - - - +
11F GLY 3.2 19.3 - - - -
12F ALA* 3.9 4.0 - - - +
14F ARG 3.6 1.6 + - - -
15F GLY 3.4 0.6 - - - -
16F PHE* 1.3 78.2 - - - +
18F ARG* 1.3 57.2 + - - +
20F LEU* 4.2 3.6 - - - -
21F ALA* 2.9 27.4 + - - +
97F ASN* 3.5 17.6 - - - +
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Residues in contact with ARG 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F ALA 3.3 20.2 + - - +
13F SER 3.2 18.3 + - - +
14F ARG* 3.3 28.2 + - - -
15F GLY 3.2 3.7 + - - +
17F GLY* 1.3 76.8 - - - +
19F THR* 1.3 57.9 + - - +
21F ALA* 4.2 1.2 - - - +
22F PRO* 3.1 24.5 - - - +
43F ALA* 3.7 18.0 + - - +
46F GLN* 3.5 33.7 + - - +
47F LEU* 3.8 32.3 - - - +
50F GLU* 5.7 3.4 - - - +
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Residues in contact with THR 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F GLY 3.2 10.8 + - - -
16F PHE 3.8 5.4 - - - -
18F ARG* 1.3 74.9 - - - +
20F LEU* 1.3 64.7 + - - +
22F PRO* 3.3 10.4 - - - +
23F LEU* 3.6 15.7 - - + +
231F CYS* 3.5 23.8 - - + +
232F LYS* 3.5 47.8 - - + +
235F ALA* 4.6 1.1 - - + -
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Residues in contact with LEU 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F LEU* 3.9 16.8 - - + -
16F PHE* 2.9 26.8 + - + +
17F GLY* 3.8 5.4 - - - +
18F ARG 3.3 0.6 - - - -
19F THR* 1.3 76.9 - - - +
21F ALA* 1.3 66.6 - - - +
23F LEU* 3.1 5.0 + - + +
24F LEU* 2.8 30.6 + - + +
95F ILE* 3.8 29.6 - - + -
235F ALA* 3.8 28.5 - - + +
238F LEU* 4.1 17.0 - - + -
239F LEU* 4.1 30.3 - - + -
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Residues in contact with ALA 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F LEU* 3.8 16.8 - - + +
17F GLY 2.9 17.4 + - - +
18F ARG 4.2 0.2 - - - +
20F LEU* 1.3 75.4 - - - +
22F PRO* 1.4 58.3 - - + +
24F LEU* 3.3 5.0 + - - +
25F ALA* 2.7 36.0 + - - +
34F LEU* 4.3 5.1 - - + +
36F LEU* 4.1 11.0 - - + -
47F LEU* 3.8 29.4 - - + -
51F LEU* 4.6 2.9 - - + -
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Residues in contact with PRO 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F ARG* 3.1 21.1 - - - +
19F THR* 3.3 11.4 - - - +
21F ALA* 1.4 92.1 - - + +
23F LEU* 1.3 62.6 + - + +
25F ALA* 3.4 1.4 + - - +
26F SER* 3.2 24.6 + - - -
47F LEU* 4.2 12.3 - - + -
50F GLU* 5.5 7.6 - - + +
51F LEU* 3.7 18.1 - - + +
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Residues in contact with LEU 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F THR* 3.6 20.4 - - + +
20F LEU* 3.1 6.4 + - - +
22F PRO* 1.3 79.3 - - + +
24F LEU* 1.3 62.0 + - - +
26F SER* 3.0 20.4 + - - +
27F LEU* 3.6 15.8 - - - +
232F LYS* 4.1 21.8 - - + +
235F ALA* 3.7 28.9 - - + -
236F GLN* 4.3 18.6 - - + +
239F LEU* 3.8 14.8 - - + +
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Residues in contact with LEU 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F LEU* 3.7 29.4 - - + -
7F CYS* 3.4 28.0 - - - -
9F LEU* 4.7 11.7 - - + -
20F LEU* 2.8 26.3 + - + +
21F ALA 3.4 4.0 - - - +
23F LEU* 1.3 73.6 - - - +
25F ALA* 1.3 68.1 + - - +
27F LEU* 2.9 17.4 + - - +
28F LEU* 3.4 16.0 - - + +
34F LEU* 4.4 10.3 - - + -
93F LEU* 3.9 12.8 - - + -
95F ILE* 3.9 19.7 - - + -
239F LEU* 3.8 19.9 - - + +
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Residues in contact with ALA 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F ALA 2.7 21.2 + - - +
22F PRO 3.4 5.6 + - - +
24F LEU* 1.3 72.1 - - - +
26F SER* 1.3 57.6 + - - +
28F LEU* 3.1 36.1 + - - +
34F LEU* 4.0 13.9 - - + +
51F LEU* 3.9 22.7 - - + -
58F LEU* 3.6 25.6 - - + +
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Residues in contact with SER 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-3F PHE 5.9 2.5 - - - -
-1F GLY 5.6 0.7 + - - -
1F MET* 3.7 16.6 - - - +
22F PRO 3.2 9.9 + - - -
23F LEU* 3.0 17.8 + - - +
25F ALA* 1.3 77.7 - - - +
27F LEU* 1.3 65.8 + - - +
28F LEU 3.4 1.5 + - - +
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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