Contacts of the helix formed by residues 20 - 36 (chain A) in PDB entry 3TR7
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 GLU 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A GLU 4.4 2.9 - - - +
17A GLU* 2.9 35.3 + - - +
18A LYS 3.8 1.0 - - - +
19A GLN* 1.3 76.4 - - - +
21A PRO* 1.3 75.7 - - - +
22A TYR* 3.4 32.1 - - + -
23A PHE* 2.9 27.5 + - - +
24A GLN* 4.1 1.4 + - - +
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Residues in contact with PRO 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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19A GLN 3.2 8.9 - - - +
20A GLU* 1.3 93.4 - - - +
22A TYR* 1.3 61.2 + - - +
23A PHE 3.2 0.9 + - - -
24A GLN* 3.5 8.8 + - + +
25A GLU* 3.2 34.3 + - - +
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Residues in contact with TYR 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 GLU* 2.7 30.5 + - + +
20A GLU* 3.1 39.1 + - + -
21A PRO* 1.3 80.2 - - - +
23A PHE* 1.3 72.2 + + + +
25A GLU* 3.3 16.5 + - - +
26A ILE* 3.0 50.5 + - + +
142A GLY* 4.1 0.4 - - - -
145A ARG* 3.5 47.5 - - + +
146A PHE* 3.4 28.9 + - + +
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Residues in contact with PHE 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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17A GLU 4.4 6.5 - - - +
18A LYS* 3.8 38.1 - - + +
20A GLU 2.9 15.2 + - - +
22A TYR* 1.3 90.1 - + + +
24A GLN* 1.3 69.4 + - + +
26A ILE* 3.2 17.2 + - + +
27A LEU* 3.2 33.6 + - + +
48A PHE* 4.0 26.9 - + - -
143A TRP* 4.8 6.3 - + - -
146A PHE* 3.6 48.5 - + + -
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Residues in contact with GLN 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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18A LYS 5.8 1.6 - - - +
20A GLU 4.1 1.9 + - - +
21A PRO* 3.5 9.5 + - + +
23A PHE* 1.3 85.6 - - + +
25A GLU* 1.3 52.4 + - + +
27A LEU* 3.2 26.7 + - - +
28A ASP* 2.6 62.8 + - - +
31A LYS* 5.9 1.4 + - - -
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Residues in contact with GLU 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 PRO* 3.2 21.3 + - + +
22A TYR* 3.5 22.2 + - - +
23A PHE 3.1 0.4 - - - -
24A GLN* 1.3 75.3 - - + +
26A ILE* 1.3 59.2 + - + +
28A ASP* 3.6 10.9 - - - +
29A PHE* 2.9 30.0 + - - +
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Residues in contact with ILE 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 TYR* 3.0 35.2 + - + +
23A PHE* 3.2 8.9 + - + +
25A GLU* 1.3 75.8 - - - +
27A LEU* 1.3 62.9 + - - +
29A PHE* 3.2 7.3 + - - +
30A VAL* 3.1 27.2 + - - +
141A ILE* 3.9 26.5 - - + +
142A GLY* 3.5 31.9 - - - +
143A TRP* 3.5 51.1 - - + +
146A PHE* 5.3 1.6 - - + -
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Residues in contact with LEU 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 PHE* 3.2 35.8 + - + +
24A GLN* 3.2 33.3 + - - +
26A ILE* 1.3 75.8 - - - +
28A ASP* 1.3 63.9 + - - +
30A VAL* 3.5 6.2 + - + +
31A LYS* 3.1 35.3 + - - +
44A GLN* 4.5 17.6 - - - +
48A PHE* 4.3 17.7 - - + -
143A TRP* 3.9 25.6 - - + -
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Residues in contact with ASP 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 GLN* 2.6 45.5 + - - +
25A GLU* 3.6 10.3 - - - +
27A LEU* 1.3 73.7 - - - +
29A PHE* 1.3 62.9 + - - +
31A LYS* 3.2 17.6 + - - +
32A LYS* 3.0 26.0 + - + +
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Residues in contact with PHE 29 (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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25A GLU 2.9 18.5 + - - +
26A ILE* 3.2 5.8 + - - +
28A ASP* 1.3 76.1 - - - +
30A VAL* 1.3 65.5 + - + +
32A LYS* 3.0 45.9 - - - +
33A GLU* 3.0 56.3 + - + +
138A HIS* 4.1 19.1 - + - -
141A ILE* 4.1 35.2 - - + -
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Residues in contact with VAL 30 (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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26A ILE 3.1 16.0 + - - +
27A LEU* 3.8 7.6 - - + +
29A PHE* 1.3 85.7 - - + +
31A LYS* 1.3 63.4 + - - +
33A GLU* 3.3 8.0 + - - +
34A ARG* 3.1 52.0 + - - +
40A ILE* 4.0 18.4 - - + -
44A GLN* 3.4 8.1 - - - +
129A THR* 4.0 26.7 - - + +
138A HIS* 4.8 2.9 - - + -
141A ILE* 4.5 5.4 - - + -
143A TRP* 4.5 9.6 - - + -
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Residues in contact with LYS 31 (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 GLN* 5.9 1.6 + - - -
27A LEU* 3.1 24.8 + - - +
28A ASP* 3.4 20.7 + - - +
29A PHE 3.2 0.2 - - - -
30A VAL* 1.3 77.2 - - - +
32A LYS* 1.3 63.3 + - - +
34A ARG* 3.0 10.4 + - - +
35A LYS* 3.0 26.9 + - + +
44A GLN* 4.5 21.5 - - + +
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Residues in contact with LYS 32 (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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28A ASP 3.0 11.1 + - - +
29A PHE* 3.0 53.4 - - - +
31A LYS* 1.3 76.4 - - - +
33A GLU* 1.3 64.8 + - - +
35A LYS* 3.4 10.5 + - - +
36A ALA* 3.0 27.5 + - - +
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Residues in contact with GLU 33 (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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29A PHE* 3.0 56.9 + - + +
30A VAL* 3.4 11.2 - - - +
32A LYS* 1.3 86.4 - - - +
34A ARG* 1.3 60.9 + - - +
36A ALA* 3.1 16.7 + - - +
38A LYS* 2.8 59.4 + - + +
40A ILE* 4.0 16.8 - - + -
131A GLU* 4.4 4.5 - - - +
138A HIS* 5.1 5.2 + - - +
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Residues in contact with ARG 34 (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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30A VAL* 3.1 25.3 + - - +
31A LYS* 3.0 10.4 + - - +
33A GLU* 1.3 73.1 - - - +
35A LYS* 1.3 62.4 + - + +
37A GLY* 3.0 19.6 + - - -
38A LYS 3.7 11.6 + - - +
40A ILE* 3.2 42.1 + - + +
42A PRO 2.6 31.1 + - - -
43A PRO* 3.5 2.4 - - - +
44A GLN* 2.1 57.3 + - - +
47A ILE* 4.4 2.6 - - - +
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Residues in contact with LYS 35 (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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31A LYS* 3.0 18.2 + - + +
32A LYS* 3.6 12.1 - - - +
33A GLU 3.3 0.2 - - - -
34A ARG* 1.3 77.2 - - + +
36A ALA* 1.3 56.7 + - - +
37A GLY* 3.1 4.7 + - - -
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Residues in contact with ALA 36 (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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32A LYS 3.0 14.0 + - - +
33A GLU* 3.1 17.8 + - - +
35A LYS* 1.3 76.4 - - - +
37A GLY* 1.3 58.5 + - - +
38A LYS* 3.4 17.1 + - + +
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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