Contacts of the helix formed by residues 8 - 24 (chain A) in PDB entry 2DZQ
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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6A SER* 2.9 2.8 - - - -
7A GLY* 1.3 81.0 - - - +
9A ARG* 1.3 56.5 + - - +
11A GLN* 2.6 18.9 + - - +
12A VAL* 2.5 36.8 + - - +
63A ILE* 3.1 45.8 - - + +
66A LEU* 3.2 27.1 - - + -
67A ARG* 3.3 37.9 - - + +
70A LEU* 3.6 20.4 - - + -
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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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6A SER* 3.6 27.8 + - - +
8A LEU* 1.3 76.9 - - - +
10A LYS* 1.3 63.7 + - + +
12A VAL* 3.2 2.3 + - - +
13A GLU* 2.8 38.2 + - + +
58A PRO* 2.7 37.2 - - + +
59A ASN* 3.5 34.5 - - - +
66A LEU* 4.2 9.4 - - + +
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Residues in contact with LYS 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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7A GLY* 3.4 13.8 + - - +
8A LEU 3.1 0.6 - - - -
9A ARG* 1.3 83.6 - - + +
11A GLN* 1.3 64.5 + - + +
13A GLU* 3.3 23.0 + - + +
14A LEU* 3.1 21.0 + - - +
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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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7A GLY 3.0 18.7 + - - +
8A LEU* 2.6 23.4 + - - +
10A LYS* 1.3 70.4 - - + +
12A VAL* 1.3 65.2 + - - +
14A LEU* 3.0 12.6 + - - +
15A LEU* 2.9 19.1 + - - +
70A LEU* 3.5 31.9 - - + +
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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 2.5 22.1 + - - +
9A ARG 3.5 6.1 - - - +
11A GLN* 1.3 71.4 - - - +
13A GLU* 1.3 55.3 + - - +
15A LEU* 2.6 25.2 + - - +
16A PHE* 2.7 55.3 + - + -
58A PRO* 3.4 15.9 - - + -
61A PHE* 6.3 0.2 - - + -
66A LEU* 3.5 33.0 - - + +
69A ILE* 4.5 6.1 - - + -
70A LEU* 3.8 25.4 - - + -
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Residues in contact with GLU 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* 2.8 26.6 + - - +
10A LYS* 3.4 27.5 + - - +
12A VAL* 1.3 72.4 - - - +
14A LEU* 1.3 54.7 + - - +
16A PHE* 4.5 4.5 - - - -
17A ASN* 2.6 53.9 + - - +
34A TYR* 3.9 16.9 + - - -
58A PRO* 3.5 18.8 - - + +
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Residues in contact with LEU 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 LYS 3.1 7.9 + - - +
11A GLN* 3.0 13.7 + - - +
13A GLU* 1.3 78.3 - - - +
15A LEU* 1.3 51.0 - - - +
17A ASN* 4.3 2.7 - - - -
18A THR* 2.4 62.5 + - + +
29A PRO* 3.3 25.4 - - + -
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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 2.9 10.4 + - - +
12A VAL* 2.6 15.3 + - - +
14A LEU* 1.3 72.5 - - - +
16A PHE* 1.3 58.6 + - + +
18A THR* 3.5 3.6 - - - -
19A ARG* 2.6 73.7 + - + +
69A ILE* 3.4 48.5 - - + +
70A LEU* 4.1 12.6 - - + -
73A SER* 3.2 30.3 - - - +
76A ILE* 3.6 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* 2.7 38.2 + - + -
13A GLU* 3.7 6.3 - - - +
15A LEU* 1.3 77.8 - - + +
17A ASN* 1.3 57.3 + - - +
19A ARG* 3.1 3.6 + - - +
20A TYR* 2.8 33.1 + - - +
32A VAL* 3.8 5.4 - - + -
34A TYR* 3.9 25.8 - + - +
46A VAL* 5.9 0.2 - - + -
49A LEU* 4.6 3.8 - - + -
54A SER 4.8 7.0 - - - -
55A LEU* 4.1 15.7 - - + -
56A ARG 3.4 24.5 - - - -
58A PRO* 4.8 2.5 - - + -
61A PHE* 5.2 1.3 - + - -
69A ILE* 3.5 37.0 - - + -
76A ILE* 4.2 8.1 - - + -
78A PHE* 3.2 31.5 - + + -
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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 GLU* 2.6 45.0 + - - +
14A LEU* 4.3 0.4 - - - -
16A PHE* 1.3 75.5 - - - +
18A THR* 1.3 65.3 + - - +
20A TYR* 2.9 19.1 + - - +
21A ALA 3.0 5.9 + - - -
29A PRO* 3.6 16.3 + - + +
30A VAL* 2.7 39.6 + - - +
31A LYS* 3.5 14.2 - - - +
32A VAL* 4.0 9.6 + - - +
34A TYR* 5.0 3.1 + - - -
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Residues in contact with THR 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 LEU* 2.4 51.8 + - + +
15A LEU* 3.5 4.5 - - - -
17A ASN* 1.3 72.2 - - - +
19A ARG* 1.3 79.7 + - - +
21A ALA* 3.0 19.4 + - - +
22A LYS* 3.5 4.2 + - - +
27A SER 5.1 10.3 - - - +
29A PRO* 3.2 14.5 - - + +
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Residues in contact with ARG 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* 2.6 44.5 + - + +
16A PHE 3.3 0.9 - - - +
18A THR* 1.3 98.3 + - - +
20A TYR* 1.3 63.8 + - - +
22A LYS* 2.9 26.1 + - - +
23A ALA* 3.2 8.0 + - - +
73A SER* 2.9 45.9 + - - -
74A ASN* 3.9 7.6 + - - +
76A ILE* 3.5 29.9 + - + -
77A GLN* 4.1 6.7 - - - +
78A PHE* 3.1 29.9 + - + +
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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 2.8 8.3 + - - -
17A ASN 3.0 13.0 - - - +
19A ARG* 1.3 72.5 - - - +
21A ALA* 1.3 53.6 + - - +
23A ALA* 2.5 36.7 + - + +
24A ILE* 2.9 24.0 + - + +
30A VAL* 3.6 21.8 - - + -
31A LYS 2.7 23.8 - - - -
32A VAL* 3.3 26.2 - - + -
33A PRO* 3.1 27.2 - - + +
37A PHE* 3.7 16.6 - + - -
78A PHE* 3.8 15.2 - + - -
80A ILE* 4.5 5.2 - - + -
86A LEU* 2.8 33.3 - - + +
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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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17A ASN 3.0 8.4 + - - +
18A THR 3.1 14.6 - - - +
20A TYR* 1.3 75.9 - - - +
22A LYS* 1.3 47.5 - - - +
24A ILE* 2.6 17.3 + - - +
25A GLY 2.5 16.3 + - - -
26A ILE* 2.5 42.8 + - + +
27A SER 4.4 1.1 - - - -
28A GLU 2.6 33.2 - - - +
29A PRO* 4.4 0.2 - - + -
30A VAL* 4.5 1.3 - - - +
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Residues in contact with LYS 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 THR 3.5 3.3 + - - +
19A ARG* 2.9 20.1 + - - +
21A ALA* 1.3 78.8 - - - +
23A ALA* 1.3 59.4 + - - +
25A GLY* 3.3 11.8 + - - +
26A ILE 3.6 6.8 + - - +
77A GLN* 5.3 23.2 + - + +
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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 ARG 3.2 3.0 + - - -
20A TYR* 2.5 30.4 + - + +
22A LYS* 1.3 72.7 - - - +
24A ILE* 1.3 59.9 + - + +
25A GLY 3.5 0.2 - - - -
78A PHE* 3.2 29.2 - - + +
80A ILE* 3.3 33.5 - - + +
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Residues in contact with ILE 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* 3.3 30.5 - - + +
21A ALA* 2.6 24.2 + - - +
23A ALA* 1.3 82.8 - - + +
25A GLY* 1.3 62.4 + - - +
26A ILE* 3.4 34.9 - - + +
30A VAL* 3.6 31.0 - - + -
80A ILE* 5.8 1.6 - - + -
86A LEU* 5.3 6.3 - - + -
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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