Contacts of the helix formed by residues 8 - 24 (chain A) in PDB entry 2DZR
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 LEU 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLY* 1.3 67.0 - - - -
9A ARG* 1.3 57.2 + - - +
11A GLN* 2.5 37.8 + - - +
12A VAL* 3.0 12.9 + - - +
63A SER* 3.3 45.5 - - - +
66A LEU* 3.8 13.7 - - + -
67A GLU* 4.1 23.8 - - + +
70A LEU* 3.7 22.4 - - + -
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Residues in contact with ARG 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 GLY 5.1 0.2 - - - -
8A LEU* 1.3 78.4 - - - +
10A GLU* 1.3 52.6 + - - +
12A VAL* 3.1 1.3 + - - +
13A GLN* 2.5 68.6 + - - +
58A PRO* 4.1 14.1 - - + +
59A CYS* 3.6 35.8 - - - +
61A PHE 5.2 0.9 - - - +
66A LEU* 3.5 23.5 - - + +
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Residues in contact with GLU 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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4A GLY 4.5 5.3 - - - +
5A SER* 3.4 19.7 + - - +
6A SER* 3.8 25.0 + - - +
7A GLY* 2.8 14.1 + - - +
9A ARG* 1.3 78.9 - - - +
11A GLN* 1.3 62.8 + - - +
13A GLN* 3.6 10.3 - - + +
14A ASP* 2.9 30.5 + - - +
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Residues in contact with GLN 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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5A SER* 3.0 26.5 + - - +
7A GLY 2.7 11.2 + - - +
8A LEU* 2.5 25.8 + - - +
10A GLU* 1.3 72.9 - - - +
12A VAL* 1.3 49.3 + - - +
14A ASP* 3.2 4.7 + - - +
15A LEU* 2.7 31.5 + - - +
70A LEU* 3.4 32.5 - - + +
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Residues in contact with VAL 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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8A LEU 3.0 6.1 + - - +
9A ARG 3.6 4.0 - - - +
11A GLN* 1.3 71.7 - - - +
13A GLN* 1.3 54.4 + - - +
14A ASP 2.6 7.2 + - - -
15A LEU* 2.5 24.8 + - + -
16A PHE* 3.0 46.3 + - + -
58A PRO* 3.6 13.9 - - + -
66A LEU* 3.6 26.9 - - + -
69A ILE* 3.6 19.1 - - + -
70A LEU* 3.1 35.4 - - + -
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Residues in contact with GLN 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 ARG* 2.5 56.0 + - - +
10A GLU* 3.6 11.8 - - + +
12A VAL* 1.3 72.8 - - - +
14A ASP* 1.3 58.3 + - - +
16A PHE* 4.8 2.9 - - - +
17A ASN* 3.6 11.8 + - - +
34A TYR* 3.3 43.8 + - + +
57A LYS* 5.4 5.0 + - - -
58A PRO* 4.0 22.2 - - + +
59A CYS* 4.5 7.1 - - - -
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Residues in contact with ASP 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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3A SER* 4.2 14.9 + - - -
4A GLY 4.3 14.0 + - - +
5A SER* 4.8 5.9 - - - -
10A GLU* 2.9 23.6 + - - +
11A GLN* 3.4 6.1 - - - +
12A VAL 2.6 5.0 + - - -
13A GLN* 1.3 75.7 - - - +
15A LEU* 1.3 56.7 + - - +
16A PHE 3.4 0.2 - - - -
17A ASN* 2.7 16.2 + - - +
18A LYS* 2.5 44.9 + - - +
29A PRO* 5.7 4.2 - - - +
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Residues in contact with LEU 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 GLN 2.7 15.7 + - - +
12A VAL* 2.5 14.0 + - - +
14A ASP* 1.3 70.0 - - - +
16A PHE* 1.3 71.0 + - + +
17A ASN 2.7 1.9 + - - -
18A LYS* 2.9 6.0 + - + +
19A LYS* 2.7 49.3 + - + +
69A ILE* 3.7 28.5 - - + -
70A LEU* 4.0 9.9 - - + -
73A ALA* 3.2 42.2 - - + +
76A ILE* 3.9 7.9 - - + -
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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 VAL* 3.0 38.2 + - + +
13A GLN* 4.8 3.4 - - - +
15A LEU* 1.3 80.8 - - + +
17A ASN* 1.3 61.0 + - - +
19A LYS* 4.0 2.4 - - - +
20A TYR 3.3 12.1 + - - -
32A VAL* 3.2 17.1 - - + +
34A TYR* 5.4 7.2 - + + +
46A ILE* 4.4 9.0 - - + -
49A LEU* 4.4 11.2 - - + -
56A ARG 4.2 13.0 - - - -
57A LYS* 5.9 0.2 - - - -
58A PRO* 4.1 24.0 - - + -
61A PHE* 5.1 0.2 - + - -
69A ILE* 3.8 15.7 - - + -
76A ILE* 3.7 33.0 - - + -
78A PHE* 3.2 40.9 - + + -
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Residues in contact with ASN 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 GLN 3.6 11.3 + - - +
14A ASP* 2.7 25.1 + - - +
16A PHE* 1.3 77.0 - - - +
18A LYS* 1.3 60.9 + - - +
20A TYR* 2.6 29.3 - - - +
21A GLY 3.5 0.7 + - - -
29A PRO* 6.3 0.9 - - + -
30A VAL 3.4 19.7 + - - +
31A GLN* 4.0 9.7 - - - +
32A VAL* 2.8 35.3 + - - +
34A TYR* 3.3 16.0 + - - -
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Residues in contact with LYS 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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3A SER* 4.0 25.5 + - - +
14A ASP* 2.5 26.6 + - - +
15A LEU* 3.7 5.2 - - + +
17A ASN* 1.3 72.2 - - - +
19A LYS* 1.3 65.8 + - + +
21A GLY* 2.9 17.2 + - - -
22A GLU* 3.7 12.1 + - - +
28A TYR 5.3 1.0 - - - +
29A PRO* 4.6 25.4 - - + +
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Residues in contact with LYS 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 LEU* 2.7 42.5 + - + +
16A PHE* 4.0 7.4 - - - +
18A LYS* 1.3 72.7 - - + +
20A TYR* 1.3 54.4 + - - +
22A GLU* 2.5 69.0 + - + +
23A ALA* 3.1 4.9 + - - +
73A ALA 3.4 25.5 + - - +
74A ASP* 4.6 16.4 + - - +
76A ILE* 4.2 16.1 + - + +
77A LYS* 6.0 0.2 - - - -
78A PHE* 4.7 13.7 - - + +
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Residues in contact with TYR 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 3.3 7.0 + - - +
17A ASN* 2.6 23.3 + - - +
19A LYS* 1.3 72.9 - - - +
21A GLY* 1.3 63.1 + - - +
23A ALA* 2.7 21.4 + - - +
24A LEU* 2.9 48.9 + - + +
30A VAL* 4.0 14.1 - - + +
31A GLN 3.3 21.3 - - - -
32A VAL* 3.3 19.7 - - + -
33A PRO* 2.9 38.3 - - + +
44A VAL* 3.9 24.0 - - + +
78A PHE* 4.2 13.9 - + - -
80A VAL* 4.5 8.4 - - + +
82A ARG* 5.2 4.0 + - - -
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Residues in contact with GLY 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 ASN 3.5 1.2 + - - -
18A LYS 2.9 15.3 + - - -
20A TYR* 1.3 75.8 - - - +
22A GLU* 1.3 49.6 - - - +
24A LEU* 3.5 2.1 + - - -
25A GLY 2.6 11.1 + - - -
26A ILE* 2.5 52.8 + - - +
27A LYS 5.9 0.2 - - - -
28A TYR 4.1 12.6 - - - -
30A VAL* 4.2 8.8 - - - +
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Residues in contact with GLU 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 LYS* 4.3 9.8 - - + +
19A LYS* 2.5 62.8 + - + +
21A GLY* 1.3 68.9 - - - -
23A ALA* 1.3 58.3 + - - +
24A LEU 2.9 2.2 - - - -
25A GLY* 2.5 26.1 + - - +
26A ILE 4.5 3.6 - - - +
84A PHE* 6.1 0.2 - - - -
90A LYS 4.3 13.2 - - - +
92A ASP 5.7 0.7 + - - -
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Residues in contact with ALA 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 LYS 3.1 2.5 + - - +
20A TYR* 2.7 17.2 + - + +
22A GLU* 1.3 75.6 - - - +
24A LEU* 1.3 61.4 + - - +
78A PHE* 3.8 39.5 - - + +
80A VAL* 3.9 24.3 + - + +
84A PHE* 5.0 11.6 - - - -
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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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20A TYR* 2.9 47.7 + - + +
21A GLY 3.9 3.1 - - - +
22A GLU 2.9 1.0 - - - -
23A ALA* 1.3 76.8 - - - +
25A GLY* 1.3 58.3 + - - +
26A ILE* 3.4 28.2 + - + +
30A VAL* 4.8 2.9 - - + -
80A VAL* 3.0 50.9 - - + -
82A ARG* 3.6 20.6 - - - +
83A PRO 5.6 2.5 - - - +
84A PHE* 4.2 23.3 - - - +
85A GLN* 4.6 13.2 + - + +
86A GLY 5.7 0.2 + - - -
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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