Contacts of the helix formed by residues 19 - 28 (chain A) in PDB entry 1TAQ
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 GLY 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A VAL 3.0 6.1 + - - -
18A ASP* 1.3 72.4 - - - +
20A HIS* 1.3 56.5 + - - +
23A ALA* 2.8 34.7 + - - +
47A PHE* 3.4 22.4 - - - -
64A VAL* 3.6 8.0 - - - +
65A VAL 2.9 13.9 + - - -
66A PHE* 3.5 16.4 - - - -
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Residues in contact with HIS 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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18A ASP* 3.1 0.8 - - - +
19A GLY* 1.3 76.9 - - - +
21A HIS* 1.3 84.3 + + - +
23A ALA* 3.7 3.4 - - - +
24A TYR* 3.2 25.4 + + + +
65A VAL 3.1 4.9 + - - -
66A PHE* 3.7 12.4 - - - -
67A ASP* 3.6 39.1 + - + +
88A THR* 6.5 1.3 - - + -
92A PHE* 4.7 20.6 - + - -
96A LEU* 4.9 9.2 - - + +
118A ALA* 3.6 29.6 - - + -
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Residues in contact with HIS 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ASP* 2.9 25.2 + - - +
20A HIS* 1.3 102.2 + + - +
22A LEU* 1.3 63.0 + - + +
24A TYR* 3.8 14.6 - + - +
25A ARG* 3.0 28.6 + - - +
118A ALA* 4.8 2.9 - - + +
119A ASP* 3.2 32.3 + - - -
140A THR* 5.1 1.1 - - - +
142A ASP* 4.7 15.5 - - + +
900A ZN 3.6 2.2 - - - -
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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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17A VAL* 3.3 30.3 - - + -
18A ASP* 2.8 27.4 + - + +
21A HIS* 1.3 79.1 - - + +
23A ALA* 1.3 59.0 + - - +
24A TYR 3.3 0.2 + - - -
25A ARG* 3.3 8.6 + - - +
26A THR* 3.0 35.6 + - + +
47A PHE* 3.8 19.3 - - + +
50A SER* 4.7 12.6 - - - +
51A LEU* 5.7 1.1 - - - +
139A LEU* 3.6 39.0 - - + +
140A THR* 3.9 15.9 - - - +
141A ALA* 4.4 3.1 - - + +
158A PRO* 4.3 11.2 - - + -
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Residues in contact with ALA 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 GLY 2.8 20.0 + - - +
20A HIS 3.7 3.1 - - - +
22A LEU* 1.3 79.2 - - - +
24A TYR* 1.3 59.1 + - - +
26A THR* 3.7 5.8 + - - -
27A PHE* 3.4 22.2 + - - +
43A ALA* 4.0 7.0 - - + +
47A PHE* 3.7 15.0 - - + -
92A PHE* 3.5 8.1 - - + -
96A LEU* 3.5 29.8 - - + -
99A ILE* 4.7 7.2 - - + -
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Residues in contact with TYR 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 HIS* 3.2 20.4 + + + +
21A HIS* 3.8 16.8 - - - +
22A LEU 3.2 0.4 - - - -
23A ALA* 1.3 76.1 - - - +
25A ARG* 1.3 68.1 + - - +
27A PHE* 3.2 9.2 + - - +
28A HIS* 3.2 52.7 + + - -
88A THR* 5.4 7.2 - - + -
89A PRO* 4.6 18.9 - - + +
92A PHE* 3.6 24.0 - + + -
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Residues in contact with ARG 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 HIS 3.0 18.0 + - - +
22A LEU* 3.6 9.0 - - - +
24A TYR* 1.3 79.4 - - - +
26A THR* 1.3 70.9 + - + +
28A HIS* 3.1 28.9 + - - +
29A ALA* 3.6 5.9 + - + +
141A ALA* 3.2 25.9 - - + +
157A HIS* 4.1 14.6 - - - -
158A PRO* 3.5 38.9 - - - +
159A GLU* 4.2 11.1 - - - +
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Residues in contact with THR 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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22A LEU* 3.0 18.2 + - + +
23A ALA* 3.7 6.1 + - - -
25A ARG* 1.3 86.7 - - + +
27A PHE* 1.3 63.4 + - - +
28A HIS 3.2 0.2 - - - -
29A ALA* 3.1 28.6 - - + +
42A GLN 3.2 12.3 - - - +
43A ALA* 2.9 22.5 + - - -
46A GLY* 3.5 36.3 - - - +
47A PHE* 3.5 4.4 + - - +
50A SER* 4.7 5.6 - - - +
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Residues in contact with PHE 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 ALA 3.4 15.9 + - - +
24A TYR 3.2 10.5 + - - +
25A ARG 3.2 0.8 - - - -
26A THR* 1.3 78.0 - - - +
28A HIS* 1.3 80.1 + + + +
29A ALA 3.3 1.5 + - - +
31A LYS* 4.9 4.0 - - - +
42A GLN* 3.5 33.8 - - - +
43A ALA* 3.7 16.8 - - + -
89A PRO* 3.8 32.3 - - + -
91A ASP* 3.8 21.3 - - + -
92A PHE* 3.6 39.3 - + + -
95A GLN* 4.1 2.2 - - + -
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Residues in contact with HIS 28 (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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24A TYR* 3.2 64.4 + + - -
25A ARG* 3.1 10.9 + - - +
27A PHE* 1.3 102.4 - + - +
29A ALA* 1.3 56.3 + - - +
31A LYS* 3.4 33.7 + - - +
89A PRO* 4.4 8.3 - - + +
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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