Contacts of the helix formed by residues 9 - 22 (chain A) in PDB entry 1WNA
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 ALA 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A MSE 3.2 28.8 + - + +
7A ARG 3.1 5.5 + - - +
8A ALA* 1.3 79.0 - - - +
10A PRO* 1.3 59.2 - - - +
11A ARG 3.6 1.6 - - - -
12A VAL* 4.3 18.4 - - + -
13A SER* 2.7 36.1 + - - +
62A ALA* 3.8 3.0 - - - +
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Residues in contact with PRO 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 ALA 3.4 8.5 - - - +
9A ALA* 1.3 88.9 - - - +
11A ARG* 1.3 61.5 + - + +
14A LEU* 3.0 30.5 + - - +
62A ALA 3.1 23.5 - - - +
63A PHE* 3.7 6.4 - - + -
67A PHE* 3.7 22.2 - - + -
68A PRO* 3.8 14.1 - - + +
69A GLY 4.0 3.8 - - - +
70A GLY* 3.9 8.3 - - - -
73A ALA* 3.7 24.9 - - + +
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Residues in contact with ARG 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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9A ALA 3.6 0.4 - - - -
10A PRO* 1.3 85.6 - - + +
12A VAL* 1.3 65.6 + - + +
14A LEU* 3.3 7.9 + - + +
15A GLU* 3.1 22.9 + - - +
68A PRO 5.7 4.5 + - - -
69A GLY* 5.4 10.7 - - - +
73A ALA* 5.3 3.4 - - + -
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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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5A GLY* 5.5 2.0 - - - -
6A MSE 5.2 14.4 - - + -
9A ALA* 3.7 19.8 + - + +
10A PRO 3.4 0.2 - - - -
11A ARG* 1.3 78.3 - - + +
13A SER* 1.3 59.2 + - - +
15A GLU* 3.3 10.2 + - - +
16A ALA* 3.0 29.4 + - + +
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Residues in contact with SER 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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4A VAL* 5.1 0.3 - - - +
5A GLY* 3.9 15.7 - - - -
6A MSE 2.9 30.3 + - - -
9A ALA* 2.7 23.6 + - - +
10A PRO 3.8 0.4 - - - -
12A VAL* 1.3 74.2 - - - +
14A LEU* 1.3 62.0 + - - +
16A ALA* 3.3 2.1 + - - +
17A LEU* 2.9 29.6 + - - +
59A VAL* 3.9 6.8 - - - +
62A ALA* 3.3 14.1 - - - +
63A PHE* 3.8 13.4 - - - -
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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 PRO 3.0 18.7 + - - +
11A ARG* 3.7 7.2 - - - +
13A SER* 1.3 76.7 - - - +
15A GLU* 1.3 58.5 + - - +
17A LEU* 3.3 3.0 + - + +
18A LYS* 3.0 58.2 + - - +
63A PHE* 4.0 10.2 - - + -
73A ALA* 4.4 10.8 - - + +
76A GLU* 3.5 35.7 - - + +
77A LEU* 3.9 36.3 - - + +
80A LEU* 4.4 11.0 - - + -
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Residues in contact with GLU 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 ARG 3.1 13.2 + - - +
12A VAL* 3.7 12.4 - - - +
14A LEU* 1.3 79.3 - - - +
16A ALA* 1.3 60.7 + - - +
18A LYS* 3.3 13.1 + - + +
19A ALA* 3.0 24.8 + - + +
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Residues in contact with ALA 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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4A VAL* 4.0 10.9 - - + +
5A GLY* 3.8 25.6 - - - +
12A VAL* 3.0 18.7 + - + +
13A SER 3.7 4.3 - - - +
15A GLU* 1.3 73.6 - - - +
17A LEU* 1.3 66.3 + - - +
19A ALA* 3.3 7.4 + - - +
20A ALA* 3.1 23.2 + - - +
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Residues in contact with LEU 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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4A VAL* 4.2 5.8 - - - +
13A SER 2.9 16.8 + - - +
14A LEU* 3.6 6.7 - - + +
15A GLU 3.2 0.2 - - - -
16A ALA* 1.3 77.5 - - - +
18A LYS* 1.3 58.0 + - - +
20A ALA* 3.2 2.2 + - - -
21A LEU* 2.8 37.7 + - + +
48A LEU* 3.8 14.8 - - + -
50A LEU* 4.7 9.6 - - + -
57A LEU* 3.8 34.3 - - + -
59A VAL* 4.5 7.4 - - + -
63A PHE* 5.4 2.0 - - + -
77A LEU* 2.9 39.3 - - + -
80A LEU* 4.1 14.8 - - + -
81A LEU* 4.7 4.0 - - + -
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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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14A LEU* 3.0 45.7 + - - +
15A GLU* 3.3 14.1 + - + +
17A LEU* 1.3 76.3 - - - +
19A ALA* 1.3 57.4 + - - +
21A LEU* 3.9 1.9 - - - +
22A GLY* 3.0 28.8 + - - +
76A GLU* 5.4 3.5 + - - +
80A LEU* 3.5 37.7 - - + -
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Residues in contact with ALA 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 GLU* 3.0 18.2 + - + +
16A ALA* 3.7 7.6 - - - +
17A LEU 3.2 0.2 - - - -
18A LYS* 1.3 79.2 - - - +
20A ALA* 1.3 62.4 + - - +
22A GLY* 3.9 6.2 + - - -
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Residues in contact with ALA 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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2A VAL* 5.9 2.0 - - + -
4A VAL* 4.4 12.8 - - + -
16A ALA 3.1 16.1 + - - +
17A LEU 3.8 1.3 - - - +
19A ALA* 1.3 78.1 - - - +
21A LEU* 1.3 62.6 + - - +
24A LEU* 6.0 0.2 - - - +
55A LYS* 5.2 7.8 + - - -
57A LEU* 3.6 27.6 - - + -
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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 LEU* 2.8 23.7 + - + +
18A LYS 3.9 2.5 - - - +
20A ALA* 1.3 80.3 - - - +
22A GLY* 1.3 70.5 + - - +
23A GLY 3.3 0.3 + - - -
24A LEU* 3.1 52.7 + - + +
26A LEU* 3.9 18.4 - - + -
50A LEU* 4.2 11.4 - - + -
57A LEU* 5.2 2.0 - - + +
80A LEU* 4.1 24.2 - - + -
81A LEU* 4.2 16.2 - - + -
84A GLN* 3.7 26.2 - - + +
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Residues in contact with GLY 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 3.0 15.7 + - - +
19A ALA 3.9 5.3 + - - -
20A ALA 3.5 2.0 - - - -
21A LEU* 1.3 79.3 - - - +
23A GLY* 1.3 51.2 + - - -
80A LEU* 5.9 0.9 - - - +
84A GLN* 2.7 25.8 + - - -
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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