Contacts of the helix formed by residues 12 - 27 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B TYR* 4.0 24.0 - - + +
9B VAL* 3.7 9.0 - - + +
11B ASP* 1.3 72.1 + - - +
13B GLY* 1.3 66.6 + - - +
15B ALA* 3.0 22.4 + - + +
90B ALA* 3.8 12.1 - - - +
93B ALA* 3.7 16.6 - - + -
94B LYS* 3.6 38.4 - - + +
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Residues in contact with GLY 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ASP* 2.8 18.3 + - - -
12B ILE* 1.3 85.1 - - - +
14B LEU* 1.3 57.8 + - - +
15B ALA* 3.0 6.0 + - - +
16B ALA* 3.9 11.3 + - - +
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Residues in contact with LEU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ALA* 5.7 0.4 - - + -
11B ASP* 2.8 48.5 + - + +
13B GLY* 1.3 75.7 - - - +
15B ALA* 1.3 64.2 + - - +
16B ALA 3.1 1.8 + - - -
17B TRP* 3.1 23.4 + - + +
18B GLY* 2.7 21.3 + - - -
86B ASN* 3.7 30.7 - - + +
87B HIS* 3.5 23.6 - - + +
90B ALA* 4.1 3.4 - - + -
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Residues in contact with ALA 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ILE* 3.0 18.5 + - + +
13B GLY 3.0 1.5 - - - +
14B LEU* 1.3 76.6 - - - +
16B ALA* 1.3 65.5 - - - +
18B GLY* 3.0 8.8 + - - -
19B ARG* 3.0 15.0 + - - +
90B ALA* 3.7 2.0 - - - +
91B ALA* 4.0 20.8 - - - +
94B LYS* 3.6 41.5 - - + +
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Residues in contact with ALA 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLY 3.9 8.3 + - - +
14B LEU 3.2 0.6 - - - -
15B ALA* 1.3 81.1 - - - +
17B TRP* 1.3 63.3 + - - +
19B ARG* 3.1 15.4 + - - +
20B LYS* 3.2 16.5 + - + +
94B LYS* 5.7 2.9 - - - +
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Residues in contact with TRP 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU* 3.1 25.1 + - + +
16B ALA* 1.3 75.3 - - - +
18B GLY* 1.3 68.4 + - - +
20B LYS* 3.1 30.2 - - + +
21B ALA* 3.1 7.0 + - - +
87B HIS* 3.5 47.6 + + + -
351B MSE 5.8 7.9 - - + -
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Residues in contact with GLY 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU 2.7 10.7 + - - -
15B ALA 3.0 5.1 + - - -
17B TRP* 1.3 79.2 - - - +
19B ARG* 1.3 63.2 + - - +
21B ALA* 3.0 3.3 + - - +
22B LEU* 2.9 22.7 + - - +
87B HIS* 3.3 34.9 - - - +
88B ALA* 4.4 1.1 - - - -
91B ALA* 3.8 8.3 - - - -
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Residues in contact with ARG 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ALA 3.0 13.0 + - - +
16B ALA* 3.5 8.7 - - - +
18B GLY* 1.3 72.9 - - - +
20B LYS* 1.3 58.6 + - - +
22B LEU* 3.0 21.7 + - - +
23B ASP* 2.6 57.9 + - - +
26B GLU* 4.6 6.9 + - - -
65B GLU* 2.7 45.6 + - - -
91B ALA* 4.0 12.8 + - + +
92B ILE* 5.2 0.2 - - - +
94B LYS* 6.2 4.0 - - + +
95B ALA* 4.1 21.0 - - - +
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Residues in contact with LYS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ALA* 3.4 16.4 - - + +
17B TRP* 3.1 28.2 + - + +
19B ARG* 1.3 80.7 - - - +
21B ALA* 1.3 62.2 + - - +
23B ASP* 3.3 16.2 + - - +
24B ILE* 3.1 28.7 + - + +
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B TRP* 3.1 6.8 + - - +
18B GLY 3.0 8.4 + - - +
20B LYS* 1.3 77.4 - - - +
22B LEU* 1.3 67.4 + - - +
24B ILE* 3.0 8.6 + - - +
25B ALA* 2.8 22.3 + - - +
58B VAL* 3.7 28.0 - - + +
87B HIS* 3.8 16.4 - - + +
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLY 2.9 26.1 + - - +
19B ARG* 3.4 23.3 - - - +
21B ALA* 1.3 71.9 - - - +
23B ASP* 1.3 65.9 + - - +
25B ALA* 2.8 4.0 + - - +
26B GLU* 2.8 31.8 + - + +
58B VAL* 3.7 25.8 - - + +
61B ALA* 3.4 33.9 - - + -
62B VAL* 4.6 7.2 - - + -
65B GLU* 3.2 27.6 - - - +
88B ALA* 4.4 11.7 - - + -
91B ALA* 4.1 11.2 - - + -
92B ILE* 4.7 1.3 - - + -
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Residues in contact with ASP 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ARG* 2.6 53.4 + - - +
20B LYS* 3.3 20.1 + - - +
22B LEU* 1.3 72.8 - - - +
24B ILE* 1.3 62.9 + - + +
26B GLU* 3.7 23.2 + - - +
27B ASN* 3.9 9.5 + - - +
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Residues in contact with ILE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LYS* 3.6 15.3 - - + +
21B ALA* 3.0 9.8 + - - +
23B ASP* 1.3 77.8 - - + +
25B ALA* 1.3 67.8 + - - +
26B GLU 3.1 0.2 - - - -
27B ASN* 3.0 21.0 + - + +
28B GLU* 3.6 11.6 + - + +
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Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ALA 2.8 13.2 + - - +
22B LEU 3.5 6.7 - - - +
24B ILE* 1.3 78.8 - - - +
26B GLU* 1.3 62.4 + - - +
28B GLU* 3.0 13.0 + - - +
29B MSE 3.1 38.5 - - + +
58B VAL* 3.5 23.6 - - + -
62B VAL* 4.2 4.7 - - + -
355B SER* 3.8 15.7 - - - +
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Residues in contact with GLU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ARG* 4.6 7.4 + - - -
22B LEU* 2.8 24.7 + - - +
23B ASP* 3.9 21.3 - - - +
24B ILE 3.1 0.2 - - - -
25B ALA* 1.3 76.9 - - - +
27B ASN* 1.3 61.6 + - - +
28B GLU 3.2 1.0 + - - -
29B MSE 3.2 19.5 + - - +
30B PRO* 4.4 0.5 - - - +
33B MSE 3.2 41.1 - - + +
36B ARG* 3.4 21.3 + - - -
62B VAL* 4.0 19.5 - - + +
65B GLU* 4.5 8.3 - - - +
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Residues in contact with ASN 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ASP 3.9 6.7 + - - +
24B ILE* 3.0 14.2 + - + +
26B GLU* 1.3 77.7 - - - +
28B GLU* 1.3 60.8 + - + +
29B MSE 3.5 0.4 - - - -
30B PRO* 4.7 2.1 - - - +
401B LYS* 2.9 38.3 + - - +
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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
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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