Contacts of the helix formed by residues 8 - 24 (chain A) in PDB entry 1ZY3
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 ASP 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ALA 4.1 1.0 + - - -
7A PRO* 1.3 73.0 - - - +
9A THR* 1.3 68.5 + - - +
10A ARG* 2.7 67.7 + - - +
11A ALA* 2.9 26.4 + - + +
12A LEU* 3.3 7.8 - - - +
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Residues in contact with THR 9 (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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7A PRO 3.8 1.2 + - - -
8A ASP* 1.3 77.5 + - - +
10A ARG* 1.3 64.9 + - - +
12A LEU* 3.1 13.5 + - + +
13A VAL* 3.0 30.4 + - + +
45A MET* 4.4 17.5 - - + -
143A TRP* 4.9 17.3 - - + +
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Residues in contact with ARG 10 (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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8A ASP* 2.7 47.3 + - - +
9A THR* 1.3 76.5 - - - +
11A ALA* 1.3 56.2 + - - +
13A VAL* 3.2 11.1 + - + +
14A ALA* 2.9 29.3 + - - +
122A GLN* 5.8 8.1 - - + -
126A VAL* 4.4 32.7 - - + +
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Residues in contact with ALA 11 (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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7A PRO* 4.7 9.6 - - + -
8A ASP* 2.9 22.3 + - + +
10A ARG* 1.3 78.4 - - - +
12A LEU* 1.3 58.0 + - + +
14A ALA* 3.4 8.0 + - - +
15A ASP* 2.9 27.7 + - - +
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Residues in contact with LEU 12 (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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7A PRO* 3.9 29.6 - - + +
8A ASP 3.3 26.2 - - - +
9A THR* 3.1 11.8 + - + +
11A ALA* 1.3 78.2 - - - +
13A VAL* 1.3 58.4 - - - +
15A ASP* 3.1 8.6 + - - +
16A PHE* 2.9 28.8 + - - +
39A ASP* 5.5 0.7 - - - +
41A LEU* 3.8 37.9 - - + -
42A HIS* 3.9 29.4 + - + +
45A MET* 3.6 26.3 - - + +
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Residues in contact with VAL 13 (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 THR* 3.0 23.3 + - + +
10A ARG* 3.2 12.1 + - + +
12A LEU* 1.3 75.9 - - - +
14A ALA* 1.3 56.6 + - - +
16A PHE* 3.2 7.5 + - + +
17A VAL* 2.8 46.9 + - + +
45A MET* 4.0 15.0 - - + -
99A PHE* 4.8 16.6 - - + -
103A ALA* 6.2 2.7 - - + -
122A GLN* 5.0 20.6 - - + +
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Residues in contact with ALA 14 (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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10A ARG 2.9 16.7 + - - +
11A ALA* 3.6 8.7 - - - +
13A VAL* 1.3 76.9 - - - +
15A ASP* 1.3 54.3 + - - +
17A VAL* 4.0 5.0 - - - +
18A GLY* 2.7 32.2 + - - -
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Residues in contact with ASP 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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11A ALA 2.9 14.7 + - - +
12A LEU* 3.1 11.8 + - - +
14A ALA* 1.3 78.3 - - - +
16A PHE* 1.3 53.3 + - - +
18A GLY 3.7 0.2 - - - -
19A TYR* 2.8 41.1 + - - +
22A ARG* 3.9 16.8 + - - +
42A HIS* 3.4 27.1 + - + -
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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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12A LEU 2.9 13.2 + - - +
13A VAL* 3.5 10.8 - - + +
15A ASP* 1.3 75.8 - - - +
17A VAL* 1.3 64.9 + - + +
19A TYR* 3.2 11.7 + + + +
20A LYS* 2.9 61.7 + - + +
42A HIS* 5.7 0.9 - - - +
45A MET* 3.3 42.4 - - + -
46A ARG* 3.8 16.8 - - + -
49A GLY* 4.6 16.2 - - - -
99A PHE* 3.9 27.8 - + - -
100A VAL* 6.4 0.4 - - + -
103A ALA* 4.1 20.2 - - + -
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Residues in contact with VAL 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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13A VAL* 2.8 36.3 + - + +
14A ALA* 4.0 4.9 - - - +
16A PHE* 1.3 78.4 - - + +
18A GLY* 1.3 60.1 + - - +
20A LYS* 3.3 7.4 + - - +
21A LEU* 2.9 29.4 + - + +
103A ALA* 4.6 19.1 - - + +
106A CYS* 4.7 8.1 - - + -
107A ALA* 3.7 29.6 - - - +
110A VAL* 4.4 18.4 - - + -
122A GLN* 6.0 0.7 - - - +
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Residues in contact with GLY 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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14A ALA 2.7 22.7 + - - -
15A ASP 3.9 0.4 - - - -
17A VAL* 1.3 76.6 - - - +
19A TYR* 1.3 55.3 + - - +
21A LEU* 3.2 11.4 + - - +
22A ARG* 2.9 51.3 + - - +
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Residues in contact with TYR 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 ASP* 2.8 29.1 + - - +
16A PHE* 3.2 13.0 + + + +
18A GLY* 1.3 72.1 - - - +
20A LYS* 1.3 54.8 + - + +
22A ARG* 3.0 20.1 + - + +
23A GLN* 2.7 73.9 + - + +
27A VAL* 4.6 6.6 - - - +
28A CYS 3.2 28.5 + - - -
29A GLY* 4.9 2.5 - - - -
30A ALA 4.4 12.8 + - - -
46A ARG* 6.0 7.2 - - + -
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Residues in contact with LYS 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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16A PHE* 2.9 48.2 + - + +
17A VAL* 3.7 7.2 - - - +
19A TYR* 1.3 78.9 - - + +
21A LEU* 1.3 61.0 + - - +
23A GLN* 3.4 23.3 + - + +
24A LYS* 3.5 15.1 + - - +
49A GLY 5.0 7.1 + - - +
60A PHE* 4.3 26.1 - - - -
107A ALA* 5.1 9.9 - - + -
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Residues in contact with LEU 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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17A VAL* 2.9 20.1 + - + +
18A GLY* 3.4 11.2 - - - +
20A LYS* 1.3 75.9 - - - +
22A ARG* 1.3 61.7 + - + +
24A LYS* 3.2 50.0 - - - +
25A GLY* 4.3 2.9 + - - -
107A ALA* 4.3 13.2 - - + +
110A VAL* 4.5 18.4 - - + -
111A ASN* 4.1 24.0 - - + +
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Residues in contact with ARG 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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15A ASP* 3.9 21.4 + - - +
18A GLY* 2.9 31.6 + - - +
19A TYR* 3.5 33.0 - - + +
21A LEU* 1.3 77.9 - - + +
23A GLN* 1.3 59.2 + - - +
24A LYS 3.1 2.2 - - - -
25A GLY* 2.9 4.3 + - - -
26A TYR* 2.7 45.3 + - + +
28A CYS* 4.6 20.2 + - + +
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Residues in contact with GLN 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 TYR* 2.7 68.6 + - + +
20A LYS* 3.4 22.0 + - + +
22A ARG* 1.3 73.1 - - - +
24A LYS* 1.3 56.1 + - - +
25A GLY 3.2 3.5 + - - -
26A TYR 4.7 0.7 - - - -
27A VAL* 3.5 45.5 - - - +
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Residues in contact with LYS 24 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A LYS 3.5 9.3 + - - +
21A LEU* 3.2 38.3 - - - +
22A ARG 3.1 0.2 - - - -
23A GLN* 1.3 77.0 - - - +
25A GLY* 1.3 55.5 + - - +
107A ALA 5.5 0.8 + - - -
108A GLU* 6.2 0.8 - - - +
111A ASN* 3.8 30.6 + - - +
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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