Contacts of the helix formed by residues 12 - 27 (chain A) in PDB entry 1A7A
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 ILE 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A TYR* 4.1 22.4 - - + +
9A VAL* 3.7 9.3 - - + +
11A ASP* 1.3 74.3 + - - +
13A GLY* 1.3 65.7 + - - +
14A LEU 3.1 0.4 - - - -
15A ALA* 2.9 21.7 + - + +
90A ALA* 3.8 12.1 - - - +
93A ALA* 3.7 15.7 - - + -
94A LYS* 3.6 39.3 - - + +
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Residues in contact with GLY 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 ASP* 2.8 16.9 + - - -
12A ILE* 1.3 85.1 - - - +
14A LEU* 1.3 60.4 + - - +
15A ALA* 3.0 5.2 + - - +
16A ALA* 3.9 11.4 + - - +
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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 ALA* 5.6 0.7 - - + -
11A ASP* 2.8 48.5 + - + +
13A GLY* 1.3 75.3 - - - +
15A ALA* 1.3 64.8 + - - +
16A ALA 3.1 1.8 + - - -
17A TRP* 3.1 24.3 + - + +
18A GLY* 2.8 20.4 + - - -
86A ASN* 3.7 31.2 - - + +
87A HIS* 3.5 23.6 - - + +
90A ALA* 4.1 2.7 - - + -
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Residues in contact with ALA 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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12A ILE* 2.9 17.1 + - + +
13A GLY 3.0 1.5 - - - +
14A LEU* 1.3 75.5 - - - +
16A ALA* 1.3 65.6 + - - +
18A GLY* 2.9 9.9 + - - -
19A ARG* 3.0 14.1 + - - +
90A ALA* 3.7 2.9 - - - +
91A ALA* 3.9 20.5 - - - +
94A LYS* 3.6 42.6 - - + +
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Residues in contact with ALA 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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13A GLY 3.9 9.2 + - - +
14A LEU 3.2 0.6 - - - -
15A ALA* 1.3 80.7 - - - +
17A TRP* 1.3 64.4 + - - +
19A ARG* 3.0 14.9 + - - +
20A LYS* 3.2 15.8 + - + +
94A LYS* 5.7 3.3 - - - +
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Residues in contact with TRP 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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14A LEU* 3.1 24.5 + - + +
16A ALA* 1.3 75.8 - - - +
18A GLY* 1.3 68.1 + - - +
20A LYS* 3.2 21.4 - - + +
21A ALA* 3.1 16.3 + - - +
87A HIS* 3.5 48.7 + + + -
351A MSE 5.8 7.2 - - + -
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Residues in contact with GLY 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 2.8 9.9 + - - -
15A ALA 2.9 4.9 + - - -
17A TRP* 1.3 79.8 - - - +
19A ARG* 1.3 63.6 + - - +
21A ALA* 3.0 3.6 + - - +
22A LEU* 3.0 21.7 + - - +
87A HIS* 3.2 35.6 - - - +
88A ALA* 4.4 0.9 - - - -
91A ALA* 3.8 9.0 - - - -
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Residues in contact with ARG 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 ALA 3.0 12.8 + - - +
16A ALA* 3.5 8.5 - - - +
18A GLY* 1.3 74.6 - - - +
20A LYS* 1.3 67.8 + - - +
22A LEU* 3.0 22.0 + - - +
23A ASP* 2.6 48.7 + - - +
26A GLU* 4.5 6.9 + - - -
65A GLU* 2.7 46.0 + - - -
91A ALA* 4.0 13.2 + - + +
94A LYS* 6.2 4.0 - - + +
95A ALA* 4.1 21.2 - - - +
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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 ALA* 3.5 16.4 - - + +
17A TRP* 3.2 26.5 - - + +
19A ARG* 1.3 81.7 - - - +
21A ALA* 1.3 62.4 + - - +
23A ASP* 3.2 16.9 + - - +
24A ILE* 3.1 28.3 + - + +
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Residues in contact with ALA 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 TRP* 3.1 6.7 + - - +
18A GLY 3.0 8.3 + - - +
20A LYS* 1.3 76.7 - - - +
22A LEU* 1.3 67.5 + - - +
24A ILE* 3.1 8.7 + - - +
25A ALA* 2.8 23.0 + - - +
58A VAL* 3.7 28.2 - - + +
87A HIS* 3.8 15.9 - - + +
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Residues in contact with LEU 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 GLY 3.0 26.3 + - - +
19A ARG* 3.3 24.5 - - - +
21A ALA* 1.3 70.4 - - - +
23A ASP* 1.3 64.5 + - - +
25A ALA* 2.8 4.1 + - - +
26A GLU* 2.8 32.7 + - + +
58A VAL* 3.7 25.1 - - + +
61A ALA* 3.4 35.0 - - + -
62A VAL* 4.6 7.0 - - + +
65A GLU* 3.1 28.3 - - - +
88A ALA* 4.4 11.7 - - + -
91A ALA* 4.1 11.0 - - + -
92A ILE* 4.7 1.1 - - + -
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Residues in contact with ASP 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 ARG* 2.6 53.2 + - - +
20A LYS* 3.2 19.5 + - - +
22A LEU* 1.3 73.7 - - - +
24A ILE* 1.3 63.6 + - + +
26A GLU* 3.7 23.9 + - - +
27A ASN* 3.8 9.9 + - - +
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Residues in contact with ILE 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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20A LYS* 3.1 15.9 + - + +
21A ALA* 3.1 11.1 + - - +
23A ASP* 1.3 77.0 - - + +
25A ALA* 1.3 66.6 + - - +
26A GLU 3.1 0.2 - - - -
27A ASN* 3.1 20.7 + - + +
28A GLU* 3.6 13.5 + - + +
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Residues in contact with ALA 25 (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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21A ALA 2.8 17.2 + - - +
22A LEU 3.5 6.5 - - - +
24A ILE* 1.3 74.1 - - - +
26A GLU* 1.3 63.2 + - - +
28A GLU* 3.0 13.0 + - - +
29A MSE 3.1 38.0 - - + +
58A VAL* 3.5 22.7 - - + -
62A VAL* 4.2 4.5 - - + -
355A SER* 3.8 16.2 - - - +
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Residues in contact with GLU 26 (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 ARG* 4.5 6.8 + - - -
22A LEU* 2.8 26.9 + - - +
23A ASP* 3.8 18.4 - - - +
24A ILE 3.1 0.2 - - - -
25A ALA* 1.3 78.1 - - - +
27A ASN* 1.3 57.6 - - - +
29A MSE 3.2 27.0 + - - +
30A PRO* 4.4 0.5 - - - +
33A MSE 3.2 41.9 - - + +
36A ARG* 3.5 21.3 + - - -
62A VAL* 4.0 16.1 - - + +
65A GLU* 4.5 8.7 - - - +
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Residues in contact with ASN 27 (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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23A ASP 3.8 6.8 + - - +
24A ILE* 3.1 14.7 + - + +
26A GLU* 1.3 77.3 - - - +
28A GLU* 1.3 58.4 + - - +
29A MSE 3.5 0.2 - - - -
30A PRO* 4.8 2.4 - - - +
401A LYS* 2.9 39.9 + - - +
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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
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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