Contacts of the helix formed by residues 4 - 23 (chain E) in PDB entry 5WC9
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 PRO 4 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3E SER* 1.3 89.9 - - - +
5E GLU* 1.3 59.3 + - + +
7E ARG* 3.8 6.7 + - + +
8E GLU* 3.3 20.8 + - - +
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Residues in contact with GLU 5 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E SER* 3.1 8.6 + - - +
4E PRO* 1.3 77.8 - - - +
6E ILE* 1.3 61.0 + - - +
7E ARG 3.3 0.4 - - - -
8E GLU* 3.3 9.3 + - - +
9E LEU* 2.8 30.8 + - + +
57E PHE* 3.5 32.3 - - + -
61E CYS* 4.4 14.7 - - - -
64E LYS* 4.2 16.8 + - - -
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Residues in contact with ILE 6 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E SER* 3.1 29.2 + - - +
5E GLU* 1.3 73.1 - - - +
7E ARG* 1.3 60.6 + - - +
9E LEU* 3.0 8.4 + - + +
10E GLU* 2.8 34.5 + - + +
57E PHE* 4.1 24.2 - - + -
149E VAL* 4.4 23.6 - - + +
150E LYS* 4.1 30.1 - - - +
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Residues in contact with ARG 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E SER 3.1 15.2 + - - +
4E PRO* 4.0 7.9 - - + +
6E ILE* 1.3 77.8 - - - +
8E GLU* 1.3 62.4 + - - +
9E LEU 3.2 0.2 + - - -
10E GLU* 3.3 14.0 + - - +
11E LYS* 3.1 29.1 + - + +
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Residues in contact with GLU 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E PRO 3.3 16.0 + - - +
5E GLU* 3.7 11.7 - - - +
6E ILE 3.3 0.2 - - - -
7E ARG* 1.3 77.7 - - - +
9E LEU* 1.3 62.1 + - - +
11E LYS* 4.1 7.6 - - - +
12E PHE* 3.5 19.8 + - - +
64E LYS* 4.6 16.0 + - - +
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Residues in contact with LEU 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E GLU* 2.8 18.5 + - - +
6E ILE* 3.0 12.7 + - - +
8E GLU* 1.3 77.2 - - - +
10E GLU* 1.3 63.9 + - - +
12E PHE* 3.5 5.2 + - - +
13E ALA* 3.1 21.8 + - - +
50E PHE* 5.5 3.4 - - + -
53E LEU* 4.4 16.5 - - + +
57E PHE* 4.3 26.5 - - + -
60E ALA* 3.6 37.9 - - + +
61E CYS* 4.5 13.2 - - - -
64E LYS* 3.8 28.7 - - + +
149E VAL* 4.8 8.1 - - + -
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Residues in contact with GLU 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E ILE* 2.8 26.7 + - + +
7E ARG* 3.7 12.8 - - - +
9E LEU* 1.3 73.7 - - - +
11E LYS* 1.3 63.0 + - + +
13E ALA* 3.1 3.5 + - - +
14E ASN* 2.9 37.1 + - - +
53E LEU* 3.7 21.5 - - + -
150E LYS* 3.5 27.3 + - - +
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Residues in contact with LYS 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ARG* 3.1 20.3 + - + +
8E GLU* 4.1 7.9 - - - +
9E LEU 3.3 0.2 - - - -
10E GLU* 1.3 77.3 - - + +
12E PHE* 1.3 57.6 + - - +
14E ASN* 3.4 8.4 + - - +
15E GLU* 2.8 41.5 + - + +
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Residues in contact with PHE 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E GLU 3.5 13.8 + - - +
9E LEU 3.5 4.8 + - - +
10E GLU 3.3 0.4 - - - -
11E LYS* 1.3 75.8 - - - +
13E ALA* 1.3 57.0 + - - +
15E GLU* 4.3 7.0 - - + +
16E PHE* 2.5 59.8 + + + +
50E PHE* 3.6 35.9 - + + -
64E LYS* 3.8 30.3 - - + -
67E LEU* 4.2 6.3 - - + -
68E SER* 3.6 43.3 - - - -
71E LEU* 4.8 11.4 - - + -
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Residues in contact with ALA 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E LEU 3.1 13.9 + - - +
10E GLU* 3.1 9.7 + - - +
12E PHE* 1.3 76.1 - - - +
14E ASN* 1.3 66.1 + - - +
16E PHE* 4.0 1.9 - - - +
17E LYS* 3.1 23.7 + - - +
50E PHE* 3.9 28.3 - - + +
51E GLU* 3.8 27.8 - - - +
53E LEU* 4.4 11.0 - - + -
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Residues in contact with ASN 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E GLU* 2.9 25.9 + - - +
11E LYS* 3.7 6.4 - - - +
13E ALA* 1.3 79.5 - - - +
15E GLU* 1.3 64.8 + - + +
17E LYS* 3.3 7.7 + - - +
18E VAL* 3.2 30.0 + - + +
51E GLU 4.9 3.6 - - - +
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Residues in contact with GLU 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E LYS* 2.8 28.5 + - + +
12E PHE* 3.8 9.0 - - + +
14E ASN* 1.3 76.4 - - + +
16E PHE* 1.3 62.7 + - - +
18E VAL* 3.5 4.7 + - - +
19E ARG* 3.0 37.9 + - + +
71E LEU* 5.3 2.0 - - + -
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Residues in contact with PHE 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E PHE* 2.5 46.4 + + + +
13E ALA* 4.0 3.1 - - - +
15E GLU* 1.3 73.6 - - - +
17E LYS* 1.3 57.9 + - - +
20E ARG* 3.0 33.8 + - + +
30E VAL* 3.6 29.8 - - + -
47E ILE* 4.2 10.5 - - + -
50E PHE* 4.4 9.0 - + + -
51E GLU* 3.6 31.0 - - + -
67E LEU* 3.8 23.8 - - + -
70E TRP* 3.8 26.9 - + - -
71E LEU* 4.2 24.9 - - + +
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Residues in contact with LYS 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E ALA 3.1 17.9 + - - +
14E ASN* 3.6 8.1 - - - +
15E GLU 3.2 0.6 - - - -
16E PHE* 1.3 77.8 - - - +
18E VAL* 1.3 64.6 + - + +
20E ARG* 3.4 8.1 + - - +
21E ILE* 3.2 42.5 + - + +
27E GLN* 4.5 0.6 - - - +
51E GLU* 3.0 49.9 + - + +
52E ASN* 4.3 5.1 + - - +
179G C 4.7 2.8 + - - -
180G A 3.6 27.0 + - - -
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Residues in contact with VAL 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E ASN* 3.2 18.9 + - + +
15E GLU* 4.1 4.3 - - - +
17E LYS* 1.3 79.3 - - + +
19E ARG* 1.3 64.7 + - + +
21E ILE* 3.1 6.9 + - - +
22E LYS* 2.9 48.9 + - + +
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Residues in contact with ARG 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E GLU* 3.0 27.8 + - + +
16E PHE 4.2 0.7 - - - +
18E VAL* 1.3 83.2 - - + +
20E ARG* 1.3 60.4 + - - +
22E LYS* 3.2 40.5 - - - +
23E LEU* 3.2 35.0 + - - +
71E LEU* 4.0 27.4 - - + -
75E GLU* 3.8 22.6 + - - +
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Residues in contact with ARG 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E PHE* 3.0 30.9 + - + +
17E LYS* 3.6 8.2 - - - +
18E VAL 3.1 0.2 - - - -
19E ARG* 1.3 78.1 - - - +
21E ILE* 1.3 84.5 + - - +
23E LEU* 3.4 5.7 + - - +
24E GLY 3.3 3.6 + - - -
25E TYR* 3.0 49.7 + - + +
26E THR 4.3 3.6 - - - -
27E GLN* 3.2 20.7 - - - +
30E VAL* 3.6 32.1 - - + -
47E ILE* 5.4 0.2 - - - -
51E GLU* 2.1 53.2 + - - -
70E TRP* 5.4 2.7 - - + -
71E LEU* 5.0 2.6 - - - +
179G C 2.5 34.6 + - - -
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Residues in contact with ILE 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E LYS* 3.2 30.0 + - + +
18E VAL* 3.1 5.9 + - - +
20E ARG* 1.3 101.9 - - - +
22E LYS* 1.3 63.1 + - + +
23E LEU 3.1 1.6 - - - -
24E GLY* 2.7 21.7 + - - -
25E TYR 4.4 4.9 - - - +
179G C 4.7 4.5 - - - +
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Residues in contact with LYS 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E VAL* 2.9 30.3 + - + +
19E ARG* 3.2 37.0 - - - +
21E ILE* 1.3 78.1 - - + +
23E LEU* 1.3 62.2 + - + +
24E GLY 3.2 0.6 + - - -
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Residues in contact with LEU 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E ARG* 3.2 25.0 + - - +
20E ARG* 3.8 1.3 - - - +
21E ILE 3.1 0.6 - - - -
22E LYS* 1.3 77.9 - - + +
24E GLY* 1.3 61.1 + - - +
25E TYR* 3.5 28.8 + - + -
70E TRP* 5.8 1.1 - - + -
71E LEU* 4.3 12.6 - - + -
74E ALA* 3.3 26.5 - - + +
75E GLU* 3.8 31.6 - - - +
76E GLN 5.0 9.9 - - - +
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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
------------------------------------------------------------
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