Contacts of the helix formed by residues 14 - 26 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLY 3.6 10.0 - - - +
13A SER* 1.3 88.0 + - - +
15A GLY* 1.3 70.5 + - - +
16A PHE 3.5 1.2 + - - -
17A GLY 3.6 0.3 + - - -
18A ARG* 3.3 15.9 + - - -
39A ARG* 4.3 6.5 - - - +
40A ASN* 6.1 3.9 - - - +
43A ALA* 5.8 1.3 - - + -
201A ASP* 2.9 34.4 + - - +
801A NAP 2.7 83.8 + - - +
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Residues in contact with GLY 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ARG* 1.3 74.6 - - - +
16A PHE* 1.3 65.0 + - - -
18A ARG* 3.2 5.2 + - - +
19A THR* 3.2 23.2 + - - -
200A THR* 3.7 16.2 - - - -
201A ASP* 5.7 0.4 + - - -
231A CYS* 4.3 4.3 - - - -
801A NAP 3.4 17.2 + - - -
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Residues in contact with PHE 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLY* 1.3 71.8 - - - -
17A GLY* 1.3 56.2 + - - +
19A THR* 3.2 4.2 + - - -
20A LEU* 2.9 40.0 + - + +
97A ASN* 3.6 22.2 - - - +
152A ILE* 3.9 29.2 - - + -
193A TYR* 4.3 2.9 - + - -
195A PRO* 4.3 8.3 - - + -
198A LEU* 3.6 30.5 - - + -
200A THR* 4.0 3.2 - - - +
231A CYS* 3.9 18.4 - - + -
234A SER* 3.8 16.4 - - - -
235A ALA* 3.6 40.2 - - + -
238A LEU* 4.2 16.2 - - + -
801A NAP 2.9 17.1 + - - +
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Residues in contact with GLY 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.4 19.8 - - - +
11A GLY 3.2 19.3 - - - -
12A ALA* 3.9 4.9 - - - +
14A ARG 3.6 2.0 + - - -
15A GLY 3.4 0.6 - - - -
16A PHE* 1.3 79.1 - - - +
18A ARG* 1.3 56.2 + - - +
20A LEU* 4.3 3.1 - - - -
21A ALA* 2.9 28.2 + - - +
97A ASN* 3.5 17.9 - - - +
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Residues in contact with ARG 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ALA 3.3 18.0 + - - +
13A SER 2.9 21.2 + - - +
14A ARG* 3.3 20.6 + - - -
15A GLY 3.2 11.2 + - - +
17A GLY* 1.3 76.3 - - - +
19A THR* 1.3 58.3 + - - +
21A ALA* 4.2 1.6 - - - +
22A PRO* 3.1 23.6 - - - +
43A ALA* 3.5 26.2 + - - +
46A GLN* 2.7 36.0 + - - +
47A LEU* 4.0 24.2 - - - +
50A GLU* 4.0 21.0 + - - -
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Residues in contact with THR 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLY 3.2 8.7 + - - -
16A PHE 3.2 6.1 + - - -
18A ARG* 1.3 75.1 - - - +
20A LEU* 1.3 64.3 + - - +
22A PRO* 3.3 11.8 - - - +
23A LEU* 3.6 15.9 - - + +
231A CYS* 3.5 25.2 - - + +
232A LYS* 3.6 43.1 - - + +
235A ALA* 4.7 0.7 - - + -
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Residues in contact with LEU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.9 17.5 - - + -
16A PHE* 2.9 27.4 + - + +
17A GLY* 3.3 5.1 + - - +
19A THR* 1.3 77.8 - - - +
21A ALA* 1.3 54.8 + - - +
23A LEU* 3.2 3.7 + - - +
24A LEU* 2.8 42.1 + - + +
95A ILE* 3.8 29.4 - - + -
235A ALA* 3.8 28.7 - - + +
238A LEU* 4.1 17.7 - - + -
239A LEU* 4.0 31.4 - - + -
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Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.9 15.9 - - + +
17A GLY 2.9 17.4 + - - +
18A ARG 4.2 0.2 - - - +
20A LEU* 1.3 75.6 - - - +
22A PRO* 1.4 58.9 - - + +
24A LEU* 3.3 4.9 + - - +
25A ALA* 2.8 36.0 + - - +
34A LEU* 4.3 4.9 - - + +
36A LEU* 4.1 9.6 - - + -
47A LEU* 3.8 30.3 - - + -
51A LEU* 4.5 2.2 - - + -
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Residues in contact with PRO 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ARG 3.1 20.0 - - - +
19A THR* 3.3 11.7 - - - +
21A ALA* 1.4 88.8 - - + +
23A LEU* 1.3 65.2 + - + +
25A ALA* 3.4 1.9 + - - +
26A SER* 3.2 24.6 + - - -
47A LEU* 4.2 11.9 - - + -
50A GLU* 4.7 13.2 - - + +
51A LEU* 3.7 17.9 - - + -
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A THR* 3.6 13.9 - - + +
20A LEU* 3.2 7.1 + - - +
22A PRO* 1.3 79.9 - - + +
24A LEU* 1.3 61.1 + - - +
26A SER* 3.0 20.7 + - - +
27A LEU* 3.6 15.4 - - - +
232A LYS* 4.0 32.8 - - + +
235A ALA* 3.7 28.5 - - + -
236A GLN* 4.3 15.0 - - + +
239A LEU* 3.8 14.9 - - + +
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Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LEU* 3.7 28.7 - - + -
7A CYS* 3.4 27.1 - - - -
9A LEU* 4.8 12.1 - - + -
20A LEU* 2.8 30.8 + - + +
21A ALA 3.5 3.6 - - - +
23A LEU* 1.3 70.9 - - - +
25A ALA* 1.3 67.6 + - - +
27A LEU* 2.9 16.8 + - - +
28A LEU* 3.4 16.8 + - + +
34A LEU* 4.4 9.6 - - + -
93A LEU* 3.9 13.0 - - + -
95A ILE* 3.9 19.5 - - + -
239A LEU* 3.8 19.7 - - + +
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ALA 2.8 21.0 + - - +
22A PRO 3.6 4.9 - - - +
24A LEU* 1.3 72.4 - - - +
26A SER* 1.3 56.6 + - - +
28A LEU* 3.1 40.1 + - - +
34A LEU* 4.0 5.3 - - + +
51A LEU* 3.9 20.0 - - + -
56A SER* 6.1 0.7 - - - -
58A LEU* 3.7 25.2 - - + +
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Residues in contact with SER 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.6 17.9 - - - +
22A PRO 3.2 10.1 + - - -
23A LEU* 3.0 18.5 + - - +
24A LEU 3.2 0.2 + - - -
25A ALA* 1.3 77.5 - - - +
27A LEU* 1.3 62.1 + - - +
28A 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