Contacts of the helix formed by residues 5 - 21 (chain E) in PDB entry 5AKF
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 GLU 5 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E ASN* 1.3 76.0 + - - +
7E VAL* 3.0 36.0 + - + +
8E SER* 3.1 32.6 + - - +
9E GLY 3.3 4.5 + - - -
104E ARG* 3.2 44.1 + - - +
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Residues in contact with ASN 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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5E GLU* 1.3 79.3 + - - +
7E VAL* 1.3 57.5 + - - +
9E GLY* 3.3 2.3 + - - -
10E ILE* 3.0 56.8 + - - +
58E PHE* 4.1 17.1 - - + -
104E ARG* 4.5 12.2 + - - +
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Residues in contact with VAL 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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5E GLU* 3.0 34.3 - - + +
6E ASN* 1.3 77.7 - - - +
8E SER* 1.3 54.3 + - - +
10E ILE* 4.1 5.1 - - - +
11E SER* 2.6 37.9 + - - -
58E PHE* 4.7 14.5 - - + -
59E LEU* 4.0 17.2 - - + +
62E GLU* 4.8 15.9 - - + -
63E LEU* 4.9 6.5 - - + -
90E TYR* 4.0 15.3 - - - +
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Residues in contact with SER 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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5E GLU* 3.1 35.5 + - - +
7E VAL* 1.3 80.7 - - - +
9E GLY* 1.3 60.8 + - - +
11E SER* 3.5 7.7 - - - -
12E ALA* 3.1 23.0 + - - +
90E TYR* 5.1 1.6 - - - -
94E MET* 3.8 6.8 - - - +
102E ASN* 5.2 3.9 + - - -
104E ARG* 4.7 3.6 - - - -
105E GLU* 4.3 25.4 - - - +
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Residues in contact with GLY 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 3.3 9.6 + - - -
6E ASN* 3.3 3.1 + - - -
7E VAL 3.3 0.4 - - - -
8E SER* 1.3 80.0 + - - +
10E ILE* 1.3 66.5 + - - +
12E ALA* 3.0 2.8 + - - -
13E TYR* 2.9 20.8 + - - +
104E ARG* 5.0 13.2 - - - -
105E GLU* 5.3 1.3 - - - -
108E ALA* 3.2 21.1 - - - +
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Residues in contact with ILE 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 ASN* 3.0 34.7 + - - +
7E VAL* 4.1 4.5 - - - +
9E GLY* 1.3 73.8 - - - +
11E SER* 1.3 57.4 + - - +
13E TYR* 3.2 7.7 + - - +
14E LEU* 2.9 48.2 + - + +
55E LEU* 3.9 39.3 - - + +
58E PHE* 3.5 34.5 - - + -
59E LEU* 4.7 7.4 - - + -
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Residues in contact with SER 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 VAL 2.6 21.1 + - - -
8E SER* 3.5 2.2 - - - -
10E ILE* 1.3 77.9 - - - +
12E ALA* 1.3 56.2 - - - +
14E LEU* 3.4 0.6 + - - -
15E LEU* 2.8 28.2 + - - +
59E LEU* 3.9 12.0 - - - +
90E TYR* 2.6 34.1 + - - -
91E PHE* 3.5 13.2 - - - -
94E MET* 3.5 25.7 - - - +
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Residues in contact with ALA 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 SER 3.1 10.0 + - - +
9E GLY 3.0 8.5 + - - +
11E SER* 1.3 76.5 - - - +
13E TYR* 1.3 67.6 + - - +
15E LEU* 3.1 7.7 + - - +
16E GLY 3.0 18.2 + - - -
94E MET* 4.1 7.4 - - + -
101E PHE* 3.9 16.4 - - + -
105E GLU* 3.5 29.4 - - + +
108E ALA* 3.6 4.5 - - + -
109E PHE* 3.3 13.2 - - - +
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Residues in contact with TYR 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 GLY 2.9 11.6 + - - +
10E ILE* 3.4 12.1 - - - +
12E ALA* 1.3 76.2 - - - +
14E LEU* 1.3 66.9 + - + +
16E GLY* 3.0 12.8 + - - -
17E LEU* 3.1 31.6 + - + +
51E HIS* 2.7 29.0 + + - -
55E LEU* 3.5 34.5 - - + -
108E ALA* 3.3 18.4 - - + +
111E LYS* 4.0 24.7 - - + -
112E GLY* 3.5 32.9 - - - -
115E VAL* 3.8 19.7 - - + +
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Residues in contact with LEU 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 ILE* 2.9 33.2 + - + +
11E SER 3.6 5.2 - - - +
13E TYR* 1.3 79.7 - - + +
15E LEU* 1.3 52.0 + - - +
17E LEU* 3.1 25.2 + - + +
18E ILE* 2.7 42.6 + - + +
40E ILE* 4.3 12.6 - - + -
52E ILE* 4.3 8.3 - - + +
55E LEU* 4.2 15.9 - - + -
56E MET* 4.0 26.7 - - + +
59E LEU* 3.7 27.6 - - + -
91E PHE* 4.1 10.1 - - + -
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Residues in contact with LEU 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 SER 2.8 18.4 + - - +
12E ALA* 3.1 8.0 + - - +
14E LEU* 1.3 75.4 - - - +
16E GLY* 1.3 57.2 + - - +
18E ILE* 4.3 9.4 - - + -
19E ILE* 2.8 51.1 + - + +
24E LEU* 4.8 4.3 - - + -
91E PHE* 4.0 30.9 - - + +
94E MET* 4.2 8.5 - - + -
95E LEU* 4.1 32.5 - - + +
98E ILE* 5.0 0.7 - - + -
101E PHE* 4.0 26.0 - - + -
109E PHE* 4.0 12.8 - - + -
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Residues in contact with GLY 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 ALA 3.0 6.9 + - - -
13E TYR 3.0 8.9 + - - -
15E LEU* 1.3 75.3 - - - +
17E LEU* 1.3 56.6 + - - +
19E ILE* 3.9 1.4 - - - +
20E GLY* 2.9 27.7 + - - -
109E PHE* 3.6 20.5 - - - -
112E GLY 3.8 0.4 - - - -
113E LEU* 3.5 31.1 - - - +
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Residues in contact with LEU 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 TYR* 3.1 38.5 + - + +
14E LEU* 3.1 21.4 + - + +
16E GLY* 1.3 74.4 - - - +
18E ILE* 1.3 58.4 + - - +
21E ASP* 2.8 35.6 + - + +
22E GLY 3.5 1.0 + - - -
40E ILE* 3.9 18.6 - - + +
51E HIS* 5.3 0.4 - - + -
52E ILE* 4.3 28.3 - - + -
112E GLY* 3.5 20.4 - - - +
115E VAL* 3.9 23.6 - - + -
116E ALA* 4.3 9.9 - - + -
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Residues in contact with ILE 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 LEU 2.7 24.0 + - - +
15E LEU* 3.2 8.3 + - + +
17E LEU* 1.3 71.0 - - - +
19E ILE* 1.3 61.7 + - + +
22E GLY 2.8 34.1 + - - -
23E GLY* 3.2 31.4 + - - +
24E LEU* 3.9 15.3 - - + -
38E VAL* 3.5 25.8 - - + -
39E VAL 3.9 7.6 - - - +
40E ILE* 3.6 20.0 - - + -
56E MET* 4.6 3.8 - - + -
91E PHE* 3.8 35.2 - - + -
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Residues in contact with ILE 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 LEU* 2.8 35.1 + - + +
16E GLY* 3.9 3.6 - - - +
18E ILE* 1.3 79.1 - - + +
20E GLY* 1.3 63.5 + - - +
22E GLY 4.3 5.8 - - - +
23E GLY* 5.8 1.1 - - - -
24E LEU* 5.3 3.8 - - + -
95E LEU* 3.8 38.1 - - + -
109E PHE* 4.4 9.2 - - + -
113E LEU* 4.2 10.8 - - + -
117E GLU* 4.2 2.6 - - - +
129E ASN* 4.4 6.8 + - - +
134E LEU* 4.0 26.2 - - + -
15G G 4.6 5.7 + - - -
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Residues in contact with GLY 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 GLY 2.9 16.0 + - - -
17E LEU 3.9 0.2 - - - -
19E ILE* 1.3 80.5 - - - +
21E ASP* 1.3 66.8 + - - +
22E GLY 3.7 0.2 - - - -
113E LEU* 4.1 2.7 - - - -
116E ALA* 3.9 2.0 - - - -
117E GLU* 3.2 45.7 - - - +
15G G 3.3 13.7 + - - +
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Residues in contact with ASP 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 LEU* 2.8 16.6 + - + +
20E GLY* 1.3 73.9 - - - +
22E GLY* 1.3 57.6 + - - +
40E ILE* 4.6 5.4 - - + -
41E THR* 2.8 46.9 + - - +
42E ALA* 5.8 0.5 - - - +
116E ALA* 3.3 19.8 - - + +
1182E MN 2.6 34.1 + - - -
14F A 3.0 27.9 + - - +
15G G 3.7 10.4 - - - +
16H C 3.1 3.6 + - - -
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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