Contacts of the helix formed by residues 5 - 21 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I ASN* 1.3 76.3 + - + +
7I VAL* 3.2 36.3 - - + +
8I SER* 3.1 26.3 + - - +
9I GLY 3.4 2.1 + - - -
62I GLU* 4.5 7.6 - - - +
102I ASN* 5.9 2.2 - - - +
104I ARG* 2.9 38.5 + - - +
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Residues in contact with ASN 6 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I GLU* 1.3 79.7 - - + +
7I VAL* 1.3 58.0 + - + +
9I GLY* 3.7 1.0 + - - -
10I ILE* 3.2 39.9 + - - +
58I PHE* 3.8 23.3 - - + -
104I ARG* 4.0 12.0 + - - +
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Residues in contact with VAL 7 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I GLU* 3.2 30.7 - - + +
6I ASN* 1.3 75.5 - - + +
8I SER* 1.3 60.7 + - - +
9I GLY 3.2 1.8 - - - -
10I ILE* 4.1 1.4 - - - +
11I SER* 2.6 40.3 + - - +
58I PHE* 3.6 26.7 - - + -
59I LEU* 4.6 11.3 - - + +
62I GLU* 3.4 36.6 - - + -
90I TYR* 5.0 4.5 - - - +
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Residues in contact with SER 8 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I GLU* 3.1 27.7 + - - -
7I VAL* 1.3 83.1 - - - +
9I GLY* 1.3 60.4 + - - +
11I SER* 3.3 7.6 - - - -
12I ALA* 2.9 28.8 + - - +
90I TYR* 5.1 2.0 - - - -
94I MET* 4.0 4.6 - - - +
102I ASN* 5.4 2.1 + - - -
104I ARG* 4.0 7.6 - - - -
105I GLU* 3.6 27.0 - - - +
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Residues in contact with GLY 9 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I GLU 3.4 8.5 + - - -
6I ASN 4.1 2.0 - - - -
7I VAL 3.2 0.6 - - - -
8I SER* 1.3 78.7 + - - +
10I ILE* 1.3 64.8 + - - +
11I SER 3.0 1.1 - - - -
12I ALA* 3.1 2.6 + - - -
13I TYR* 3.0 21.0 + - - +
104I ARG* 4.6 15.0 - - - -
105I GLU* 5.1 0.9 - - - -
108I ALA* 3.2 21.2 - - - +
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Residues in contact with ILE 10 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I ASN* 3.2 30.3 + - - +
7I VAL* 4.1 3.8 - - - +
9I GLY* 1.3 75.0 - - - +
11I SER* 1.3 56.4 + - - +
13I TYR* 3.4 7.1 + - - +
14I LEU* 2.9 46.7 + - + +
55I LEU* 4.1 39.9 - - + +
58I PHE* 3.5 35.0 - - + -
59I LEU* 5.3 3.8 - - + -
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Residues in contact with SER 11 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I VAL 2.6 23.3 + - - -
8I SER* 3.3 7.9 - - - -
10I ILE* 1.3 78.2 - - - +
12I ALA* 1.3 57.2 + - - +
14I LEU* 3.3 1.8 + - - -
15I LEU* 2.9 29.8 + - - +
59I LEU* 3.7 10.6 - - - +
90I TYR* 2.7 33.4 + - - -
91I PHE* 3.6 13.2 - - - -
94I MET* 3.5 18.3 - - - +
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Residues in contact with ALA 12 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I SER 2.9 16.7 + - - +
9I GLY 3.6 5.2 - - - +
11I SER* 1.3 75.5 - - - +
13I TYR* 1.3 62.7 + - - +
15I LEU* 3.2 3.5 + - - +
16I GLY 3.1 16.6 + - - -
94I MET* 3.4 12.0 - - + +
101I PHE* 4.2 2.5 - - + -
105I GLU* 3.3 39.3 - - + +
108I ALA* 3.7 4.7 - - + -
109I PHE* 3.4 20.3 - - + +
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Residues in contact with TYR 13 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I GLY 3.0 11.9 + - - +
10I ILE* 3.6 9.9 - - - +
12I ALA* 1.3 77.2 - - - +
14I LEU* 1.3 65.9 + - + +
16I GLY* 3.0 12.6 + - - -
17I LEU* 3.2 36.8 + - + +
51I HIS* 2.7 34.8 + + - -
55I LEU* 3.8 24.0 - - + -
108I ALA* 3.4 18.9 - - + +
111I LYS* 4.0 26.0 - - + -
112I GLY* 3.6 30.3 - - - -
115I VAL* 4.1 18.0 - - + +
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Residues in contact with LEU 14 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I ILE* 2.9 38.8 + - + +
11I SER 3.8 3.4 - - - +
13I TYR* 1.3 85.6 - - + +
15I LEU* 1.3 58.1 + - - +
17I LEU* 3.3 7.0 + - + +
18I ILE* 2.8 38.3 + - + +
40I ILE* 4.3 17.5 - - + -
52I ILE* 4.3 13.5 - - + +
55I LEU* 4.1 17.0 - - + +
56I MET* 3.9 37.5 - - + +
59I LEU* 4.3 13.2 - - + -
91I PHE* 4.0 10.5 - - + -
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Residues in contact with LEU 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I SER 2.9 18.6 + - - +
12I ALA* 3.6 6.1 - - - +
14I LEU* 1.3 77.7 - - - +
16I GLY* 1.3 57.2 + - - +
18I ILE* 3.6 8.2 - - + +
19I ILE* 2.8 52.2 + - + +
24I LEU* 4.6 7.0 - - + -
91I PHE* 4.0 33.3 - - + +
94I MET* 4.0 19.7 - - + -
95I LEU* 4.0 30.7 - - + +
98I ILE* 4.9 0.9 - - + -
101I PHE* 4.1 13.9 - - + -
109I PHE* 3.9 15.0 - - + -
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Residues in contact with GLY 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I ALA 3.1 6.9 + - - -
13I TYR 3.0 8.6 + - - -
15I LEU* 1.3 72.9 - - - +
17I LEU* 1.3 59.1 + - - +
19I ILE* 3.9 1.5 - - - +
20I GLY* 2.8 28.9 + - - -
109I PHE* 3.7 19.2 - - - -
112I GLY 3.7 9.4 - - - +
113I LEU* 3.7 21.6 - - - +
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Residues in contact with LEU 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I TYR* 3.2 38.8 + - + +
14I LEU* 3.5 9.6 - - + +
16I GLY* 1.3 75.0 - - - +
18I ILE* 1.3 55.2 + - - +
21I ASP* 2.6 39.1 + - + +
22I GLY 3.6 0.5 + - - -
40I ILE* 3.8 19.3 - - + +
51I HIS* 4.9 0.7 - - + +
52I ILE* 4.0 38.6 - - + -
112I GLY* 3.3 23.6 - - - +
115I VAL* 4.0 22.4 - - + -
116I ALA* 4.1 8.7 - - + -
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Residues in contact with ILE 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I LEU* 2.8 36.8 + - + +
15I LEU* 3.6 9.2 - - + +
16I GLY 3.2 0.2 - - - -
17I LEU* 1.3 69.9 - - - +
19I ILE* 1.3 65.6 + - + +
22I GLY 2.8 34.8 + - - +
23I GLY* 3.8 28.8 - - - +
24I LEU* 4.0 15.7 - - + -
38I VAL* 3.5 26.2 - - + -
39I VAL 3.9 8.3 - - - +
40I ILE* 3.6 19.1 - - + -
56I MET* 4.6 2.2 - - + -
91I PHE* 3.9 26.7 - - + -
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Residues in contact with ILE 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I LEU* 2.8 35.7 + - + +
16I GLY* 3.9 4.0 - - - +
18I ILE* 1.3 79.7 - - + +
20I GLY* 1.3 63.4 + - - +
22I GLY 4.5 3.9 - - - +
23I GLY* 5.7 1.3 - - - -
24I LEU* 5.4 2.5 - - + -
95I LEU* 3.8 39.5 - - + -
109I PHE* 4.4 8.1 - - + -
113I LEU* 4.4 8.7 - - + -
117I GLU* 4.4 2.3 - - - +
129I ASN* 4.5 7.9 + - - +
134I LEU* 3.9 27.6 - - + -
15K G 4.3 7.8 + - - -
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Residues in contact with GLY 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I GLY 2.8 17.1 + - - -
19I ILE* 1.3 80.5 - - - +
21I ASP* 1.3 67.5 + - - +
22I GLY 3.8 0.2 - - - -
113I LEU* 4.3 3.6 - - - -
116I ALA* 3.7 3.8 - - - -
117I GLU* 3.1 42.0 - - - +
15K G 3.3 12.9 + - - +
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Residues in contact with ASP 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I LEU* 2.6 19.9 + - + +
20I GLY* 1.3 78.8 - - - +
22I GLY* 1.3 54.9 + - - +
40I ILE* 4.5 6.5 - - + -
41I THR* 2.7 46.0 + - - +
42I ALA* 5.6 1.6 - - - +
115I VAL 4.8 0.5 - - - +
116I ALA* 3.4 19.0 - - + +
1180I MN 2.6 33.8 + - - -
14J A 3.3 18.2 + - - +
15K G 3.8 9.4 - - - -
16L C 3.2 7.3 + - - -
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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
------------------------------------------------------------
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