Contacts of the helix formed by residues 11 - 24 (chain A) in PDB entry 2WPT
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 THR 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ASP 4.2 0.2 + - - -
10A TYR* 1.3 76.2 - - - +
12A GLU* 1.3 59.9 + - - +
13A ALA* 3.6 9.3 + - - +
14A GLU* 3.0 42.6 + - - +
15A PHE* 2.9 27.4 + - - +
83A PHE* 4.1 0.9 - - - -
84A LYS* 3.4 34.0 - - - +
85A GLN 4.3 11.7 - - - +
1088A GOL 4.7 0.2 + - - -
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Residues in contact with GLU 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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11A THR* 1.3 73.3 - - - +
13A ALA* 1.3 60.1 + - - +
15A PHE* 3.3 2.1 + - - +
16A LEU* 2.9 30.3 + - + +
68A VAL* 4.0 17.2 - - + +
69A LYS* 5.9 0.7 - - - -
72A LYS* 2.7 46.0 + - - +
83A PHE* 3.6 34.5 - - + +
84A LYS 4.3 1.4 + - - -
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Residues in contact with ALA 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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11A THR* 3.6 7.3 + - - +
12A GLU* 1.3 74.8 - - - +
14A GLU* 1.3 65.1 + - - +
16A LEU* 3.3 5.2 + - - -
17A GLU 3.0 10.9 + - - -
1088A GOL 2.6 48.0 + - - +
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Residues in contact with GLU 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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4A LYS* 2.9 35.3 + - - -
9A ASP 4.0 0.9 - - - +
10A TYR* 3.6 12.7 - - + -
11A THR* 3.0 45.8 + - - +
13A ALA* 1.3 75.6 - - - +
15A PHE* 1.3 58.3 + - - +
17A GLU* 3.2 4.8 + - - +
18A PHE* 3.0 27.9 + - - +
84A LYS* 4.5 3.6 + - - -
1088A GOL 3.5 18.2 - - - +
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Residues in contact with PHE 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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7A ILE* 3.9 21.8 - - + -
10A TYR* 4.0 17.8 - + + -
11A THR 2.9 12.2 + - - +
12A GLU 3.7 2.7 - - - +
14A GLU* 1.3 77.8 - - - +
16A LEU* 1.3 62.0 + - - +
18A PHE* 3.2 27.4 + + - +
19A VAL* 3.0 36.0 + - + +
40A PHE* 3.9 16.8 - + - -
43A LEU* 4.3 11.2 - - + -
44A THR* 3.7 23.6 - - + -
68A VAL* 3.9 14.6 - - + -
71A ILE* 4.3 17.5 - - + -
83A PHE* 3.5 34.1 - + + -
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Residues in contact with LEU 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 GLU* 2.9 19.0 + - + +
13A ALA* 3.3 7.2 + - - +
15A PHE* 1.3 76.4 - - - +
17A GLU* 1.3 56.4 + - - +
19A VAL* 3.3 0.9 + - - -
20A LYS* 2.9 53.1 + - - +
64A PRO* 3.7 39.0 - - + +
65A GLU* 3.8 15.3 - - + +
68A VAL* 3.7 18.6 - - + -
1088A GOL 4.0 11.4 - - - +
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Residues in contact with GLU 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 ALA 3.0 7.0 + - - +
14A GLU* 3.6 7.2 - - - +
16A LEU* 1.3 76.7 - - - +
18A PHE* 1.3 58.9 + - - +
20A LYS* 3.4 36.7 + - - +
21A LYS* 3.0 28.2 + - - +
24A ARG* 5.3 2.8 + - - -
1088A GOL 2.5 56.9 + - - -
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Residues in contact with PHE 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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10A TYR* 4.6 14.6 - + + -
14A GLU 3.0 12.6 + - - +
15A PHE* 3.4 41.5 - + - +
17A GLU* 1.3 78.8 - - - +
19A VAL* 1.3 63.2 + - + +
21A LYS* 3.1 14.6 + - + +
22A ILE* 3.1 31.0 + - + +
36A LEU* 3.5 43.1 - - + -
39A GLU* 3.6 30.1 - - + -
40A PHE* 3.6 27.4 - + + -
43A LEU* 4.3 4.0 - - + -
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Residues in contact with VAL 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 PHE* 3.0 44.5 + - + +
16A LEU 3.3 4.2 + - - +
18A PHE* 1.3 76.1 - - + +
20A LYS* 1.3 51.9 + - - +
22A ILE* 3.1 9.2 + - + +
23A ALA* 2.7 34.5 + - + +
40A PHE* 4.0 20.2 - - + -
53A ILE* 5.3 4.5 - - + -
64A PRO* 3.8 17.3 - - + +
67A ILE* 3.8 35.0 - - + -
68A VAL* 3.9 9.6 - - + -
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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 LEU* 2.9 39.4 + - - +
17A GLU* 3.4 40.9 + - - +
19A VAL* 1.3 75.9 - - - +
21A LYS* 1.3 62.3 + - - +
23A ALA* 3.2 0.7 + - - -
24A ARG* 2.9 66.9 + - - +
64A PRO* 3.8 25.8 - - + -
1088A GOL 5.0 0.4 + - - -
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Residues in contact with LYS 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 GLU 3.0 14.4 + - - +
18A PHE* 3.1 15.8 + - - +
20A LYS* 1.3 74.6 - - - +
22A ILE* 1.3 63.5 + - - +
24A ARG 3.3 0.9 + - - -
25A ALA 3.1 3.6 + - - -
26A GLU* 2.9 64.0 + - + +
27A GLY* 4.5 1.7 + - - -
32A ASP* 5.8 0.4 - - - +
36A LEU* 3.9 32.7 - - + +
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Residues in contact with ILE 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 PHE* 3.1 31.9 + - + +
19A VAL* 3.1 9.7 + - - +
21A LYS* 1.3 75.4 - - - +
23A ALA* 1.3 65.1 + - - +
25A ALA* 2.9 16.6 + - - +
33A ASP* 5.1 5.3 - - + +
36A LEU* 3.5 48.9 - - + +
37A VAL* 3.8 14.4 - - + +
40A PHE* 3.9 15.3 - - + -
53A ILE* 4.0 22.2 - - + -
54A TYR* 3.6 25.8 + - - +
74B SER 4.9 1.6 - - - +
78B SER* 5.3 0.2 + - - -
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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 VAL* 2.7 22.6 + - + +
20A LYS 3.8 3.6 - - - +
22A ILE* 1.3 76.5 - - - +
24A ARG* 1.3 60.0 + - + +
25A ALA 3.3 0.4 - - - -
53A ILE* 5.3 2.0 - - + -
64A PRO* 3.8 25.6 - - + -
67A ILE* 5.4 1.8 - - + -
73B PRO 4.7 0.3 - - - -
74B SER* 3.3 34.4 - - - +
77B SER* 3.0 22.0 + - - -
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Residues in contact with ARG 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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17A GLU* 5.3 2.8 + - - -
20A LYS* 2.9 59.4 + - - +
21A LYS 4.1 0.2 - - - +
23A ALA* 1.3 81.0 - - + +
25A ALA* 1.3 70.4 + - - +
26A GLU* 3.3 37.9 + - + +
64A PRO* 5.8 2.4 - - + +
77B SER* 3.7 13.6 + - - +
81B LYS* 3.3 13.3 - - - -
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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