Contacts of the helix formed by residues 24 - 36 (chain B) in PDB entry 1TBX
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 ALA 24 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B GLY 3.6 2.2 + - - -
23B ILE* 1.3 76.1 - - - +
25B THR* 1.3 67.0 + - - +
26B TYR* 4.5 4.0 - - + +
27B ASP* 3.0 29.8 + - - +
28B LEU 2.9 18.4 + - - -
64B GLU* 3.3 36.3 - - + +
65B LYS* 3.1 9.2 - - + +
66B ARG* 4.1 6.9 - - - +
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Residues in contact with THR 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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23B ILE 3.6 2.4 + - - -
24B ALA* 1.3 70.5 - - - +
26B TYR* 1.3 57.3 + - - +
28B LEU* 3.1 5.8 + - - +
29B TYR 3.0 24.3 + - - -
43B PHE* 3.5 22.1 - - + -
44B TYR* 3.9 16.6 - - + +
47B LYS* 3.8 17.9 - - + -
58B GLU* 3.0 22.7 + - - +
65B LYS* 2.9 22.5 + - + +
67B LEU* 3.5 31.0 - - + +
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Residues in contact with TYR 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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24B ALA* 3.2 5.1 - - + -
25B THR* 1.3 79.0 - - - +
27B ASP* 1.3 72.3 + - - +
29B TYR* 3.1 31.8 + + + +
30B LYS* 3.2 53.7 + - + +
44B TYR* 4.4 12.1 + - - +
64B GLU* 5.7 3.4 - - - +
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Residues in contact with ASP 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 ILE* 3.9 16.9 - - + +
24B ALA* 3.0 27.0 + - - +
26B TYR* 1.3 94.5 - - - +
28B LEU* 1.3 64.2 + - - +
30B LYS* 3.4 18.3 + - - +
31B LYS* 3.2 25.1 + - - +
64B GLU* 5.7 0.3 - - - -
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Residues in contact with LEU 28 (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 VAL* 4.1 21.1 - - + +
16B TYR* 3.9 37.7 - - + +
17B LEU* 4.1 15.3 - - + +
20B ASN* 4.5 6.5 - - - +
23B ILE* 3.6 30.0 - - + +
24B ALA 2.9 6.6 + - - +
25B THR 3.1 9.4 + - - +
27B ASP* 1.3 71.9 - - - +
29B TYR* 1.3 67.9 + - - +
31B LYS* 3.3 5.4 + - + +
32B VAL* 3.0 34.5 + - + +
43B PHE* 3.9 4.9 - - + -
67B LEU* 3.4 27.1 - - + -
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Residues in contact with TYR 29 (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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25B THR 3.0 12.3 + - - +
26B TYR* 3.1 17.7 + + + +
28B LEU* 1.3 77.3 - - - +
30B LYS* 1.3 71.7 + - + +
32B VAL* 3.3 2.0 + - + +
33B ASN* 2.9 55.9 + - + +
38B MSE 2.5 34.4 + - + -
39B SER* 3.8 17.6 - - - -
40B THR* 4.0 21.6 + - + +
43B PHE* 3.4 40.6 - + + -
44B TYR* 5.5 3.8 - + + -
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Residues in contact with LYS 30 (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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26B TYR* 3.2 59.4 + - + +
27B ASP* 3.8 16.3 + - - +
28B LEU 3.3 0.2 - - - -
29B TYR* 1.3 88.4 - - + +
31B LYS* 1.3 61.3 + - - +
33B ASN* 3.2 5.8 + - - +
34B ALA* 3.2 21.1 + - - +
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Residues in contact with LYS 31 (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 TYR* 2.9 39.6 - - + -
20B ASN* 3.5 27.6 - - - +
23B ILE* 4.4 12.8 - - + -
27B ASP 3.2 14.8 + - - +
28B LEU* 3.6 10.3 - - + +
30B LYS* 1.3 72.0 - - - +
32B VAL* 1.3 67.6 + - + +
34B ALA* 3.2 21.6 + - - +
35B GLU* 3.9 8.0 + - - +
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Residues in contact with VAL 32 (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* 3.9 21.5 - - + -
13B VAL* 4.5 11.9 - - + -
16B TYR* 3.8 33.9 - - + -
28B LEU* 3.0 31.5 + - + +
29B TYR* 3.5 5.6 - - - +
31B LYS* 1.3 76.0 - - - +
33B ASN* 1.3 59.7 + - - +
34B ALA 3.2 0.7 + - - -
35B GLU* 3.4 1.4 + - - +
36B PHE* 2.9 32.9 + - - +
38B MSE 3.9 27.1 - - - -
43B PHE* 4.3 7.9 - - + -
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Residues in contact with ASN 33 (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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29B TYR* 2.9 49.3 + - + +
30B LYS* 3.6 5.8 - - - +
31B LYS 3.2 0.2 - - - -
32B VAL* 1.3 79.5 - - - +
34B ALA* 1.3 60.8 + - - +
36B PHE 3.5 5.4 - - - -
37B PRO* 2.8 29.0 - - - +
38B MSE 2.7 31.5 + - - +
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Residues in contact with ALA 34 (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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30B LYS 3.2 10.0 + - - +
31B LYS* 3.2 15.1 + - - +
32B VAL 3.2 0.4 + - - -
33B ASN* 1.3 78.0 - - - +
35B GLU* 1.3 67.5 + - - +
37B PRO* 4.9 3.6 - - - +
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Residues in contact with GLU 35 (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 TYR* 3.0 34.7 + - + +
31B LYS* 3.9 6.2 + - - +
32B VAL 3.4 2.0 + - - -
34B ALA* 1.3 89.7 - - - +
36B PHE* 1.3 78.1 + - + +
37B PRO* 3.4 9.3 - - - +
88B LYS* 3.5 28.2 + - + +
91B LYS* 5.8 2.3 + - - -
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Residues in contact with PHE 36 (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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4B THR* 3.4 40.4 - - + +
7B PHE* 5.3 2.0 - + - -
12B ILE* 3.9 38.1 - - + -
16B TYR* 3.6 26.9 - + - -
32B VAL* 2.9 22.5 + - + +
33B ASN* 3.5 4.3 - - - -
35B GLU* 1.3 95.5 - - + +
37B PRO* 1.3 71.4 - - - +
38B MSE 3.2 8.9 + - + +
84B ILE* 3.9 24.2 - - + -
87B TYR* 4.6 13.9 - + - -
88B LYS* 4.3 16.2 - - + -
91B LYS* 5.8 4.9 - - - -
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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