Contacts of the helix formed by residues 6 - 21 (chain A) in PDB entry 2AAO
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 MSE 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ASN* 1.3 78.1 + - - +
8A LYS* 2.9 9.8 - - - +
9A PHE* 2.8 17.3 + - - +
10A LYS* 2.7 50.3 + - - +
141B ASP* 4.0 36.3 + - - +
142B VAL* 3.9 14.4 - - + -
158B MSE 3.7 36.1 - - + +
160B GLN* 4.8 8.7 - - - +
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Residues in contact with ASN 7 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A MSE 1.3 93.8 - - - +
8A LYS* 1.3 56.3 + - - +
10A LYS* 3.5 21.6 + - + +
11A LYS* 2.9 44.6 + - - +
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Residues in contact with LYS 8 (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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6A MSE 2.9 8.1 - - - +
7A ASN* 1.3 75.6 - - - +
9A PHE* 1.3 66.1 + - - +
11A LYS* 3.0 12.5 + - + +
12A MSE 2.9 48.5 + - + +
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Residues in contact with PHE 9 (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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6A MSE 2.8 20.0 + - - +
8A LYS* 1.3 76.0 - - - +
10A LYS* 1.3 62.9 + - - +
12A MSE 3.0 17.4 + - + +
13A ALA* 2.9 21.1 + - - +
108B PHE* 3.8 36.8 - + - -
116B ILE* 4.3 8.3 - - + -
121B LEU* 3.4 37.5 - - + -
142B VAL* 5.4 2.5 - - + -
150B ILE* 4.2 17.7 - - + -
155B PHE* 4.1 19.7 - + - -
158B MSE 3.2 31.0 - - + -
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Residues in contact with LYS 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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6A MSE 2.7 24.1 + - - +
7A ASN* 3.5 29.1 + - - +
9A PHE* 1.3 72.0 - - - +
11A LYS* 1.3 62.4 + - + +
13A ALA* 3.1 4.5 + - - +
14A LEU* 3.0 36.6 + - + +
91A HIS* 5.8 5.2 - - + +
158B MSE 3.5 25.5 + - + +
159B MSE 3.7 40.2 + - + +
160B GLN* 3.8 23.2 + - - +
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Residues in contact with LYS 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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7A ASN* 2.9 30.1 + - - +
8A LYS* 3.5 8.3 - - + +
10A LYS* 1.3 75.9 - - + +
12A MSE 1.3 62.6 + - + +
14A LEU* 3.3 15.7 + - + +
15A ARG* 3.0 23.4 + - - +
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Residues in contact with MSE 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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8A LYS* 2.9 46.1 + - + +
9A PHE* 3.3 18.6 - - + +
11A LYS* 1.3 76.6 - - + +
13A ALA* 1.3 61.2 + - - +
15A ARG* 3.4 8.6 + - - +
16A VAL* 3.1 26.8 + - + +
107B TYR* 5.9 2.0 - - + -
108B PHE* 4.0 26.9 - - + -
121B LEU 5.5 7.6 - - - +
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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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9A PHE 2.9 12.3 + - - +
10A LYS 3.1 8.7 + - - +
12A MSE 1.3 73.6 - - - +
14A LEU* 1.3 66.3 + - - +
16A VAL* 3.1 4.6 + - - +
17A ILE* 3.0 28.4 + - - +
104B ALA* 4.1 3.3 - - + +
108B PHE* 3.9 24.2 - - + -
155B PHE* 4.1 12.6 - - + -
158B MSE 5.0 0.4 - - + -
159B MSE 3.8 25.1 - - + -
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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 LYS* 3.0 28.0 + - + +
11A LYS* 3.6 17.3 - - + +
13A ALA* 1.3 72.1 - - - +
15A ARG* 1.3 65.7 + - - +
17A ILE* 3.3 13.0 + - + +
18A ALA* 2.9 24.1 + - - +
90A LEU* 4.1 34.5 - - + +
91A HIS* 3.5 36.6 - - + +
159B MSE 3.7 21.8 - - + -
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Residues in contact with ARG 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 LYS 3.0 13.3 + - - +
12A MSE 3.6 11.7 - - - +
14A LEU* 1.3 77.1 - - - +
16A VAL* 1.3 62.9 + - + +
18A ALA* 3.3 5.3 + - - -
19A GLU* 2.3 68.9 + - - +
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Residues in contact with VAL 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 MSE 3.1 17.4 + - + +
13A ALA* 3.1 8.4 + - - +
15A ARG* 1.3 76.3 - - + +
17A ILE* 1.3 55.7 + - - +
19A GLU* 3.2 5.8 + - - +
20A SER* 2.6 45.8 + - - +
103B ALA 4.7 1.3 - - - +
104B ALA* 4.0 14.8 - - + -
107B TYR* 3.6 56.1 - - + -
108B PHE* 3.8 10.5 - - + -
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Residues in contact with ILE 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 17.5 + - - +
14A LEU* 3.5 24.0 - - + +
15A ARG 3.3 0.2 - - - -
16A VAL* 1.3 76.3 - - - +
18A ALA* 1.3 63.1 + - - +
20A SER* 3.0 16.6 + - - -
21A LEU* 3.2 16.0 + - + +
90A LEU* 3.7 31.0 - - + +
96A GLU* 4.7 6.5 - - - +
100B HIS* 3.8 40.2 - - + +
101B LEU* 4.2 28.0 - - + +
104B ALA* 3.9 9.0 - - + +
159B MSE 4.6 0.9 - - + -
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Residues in contact with ALA 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 2.9 17.4 + - - +
15A ARG* 3.7 5.2 - - - +
17A ILE* 1.3 76.1 - - - +
19A GLU* 1.3 73.6 + - - +
20A SER 3.3 0.7 + - - -
21A LEU* 3.3 27.0 + - + +
26A ILE* 5.0 2.9 - - - +
86A ILE* 5.5 4.9 - - + -
90A LEU* 3.6 20.9 - - + -
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Residues in contact with GLU 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 ARG* 2.3 63.2 + - - +
16A VAL* 3.8 5.8 - - - +
18A ALA* 1.3 84.1 - - - +
20A SER* 1.3 61.5 + - - +
21A LEU 3.3 6.2 + - - +
24B GLU* 4.9 4.9 - - - +
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Residues in contact with SER 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 VAL* 2.6 33.5 + - - +
17A ILE* 3.0 8.2 + - - -
19A GLU* 1.3 76.8 - - - +
21A LEU* 1.3 62.9 + - - +
22B SER* 2.6 29.3 + - - -
24B GLU* 3.4 36.7 - - - +
25B GLU* 3.4 12.5 - - - +
100B HIS* 6.4 0.7 - - - -
103B ALA* 5.4 7.7 + - - +
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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 ILE 3.2 14.1 + - - +
18A ALA* 3.4 22.9 - - + +
19A GLU 3.3 6.7 - - - +
20A SER* 1.3 79.0 - - - +
22A SER* 1.3 63.9 + - - +
23A GLU* 3.9 7.6 + - - +
25A GLU* 3.4 21.5 - - + +
26A ILE* 3.8 27.8 - - + +
29A LEU* 4.0 17.5 - - + -
86A ILE* 4.7 9.0 - - + -
90A LEU* 4.6 14.6 - - + -
99A ASP* 3.8 19.3 - - - +
22B SER* 4.5 0.6 - - - -
25B GLU* 4.2 1.1 - - - +
100B HIS* 3.9 13.2 - - + +
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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