Contacts of the helix formed by residues 30 - 41 (chain C) in PDB entry 2AG1
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 30 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C LEU 3.8 16.6 - - - +
27C GLY 3.4 17.5 - - - +
28C ALA 3.1 0.2 - - - -
29C HIS* 1.3 81.4 - - - +
31C ASP* 1.3 62.2 + - - +
32C THR 3.2 3.1 - - - -
33C ILE* 3.3 16.5 + - + +
34C PHE* 3.5 23.8 + - + -
71C LEU* 3.4 31.6 - - + +
72C VAL* 3.6 34.1 - - - +
73C THR* 3.7 8.3 - - - +
99C THR 4.5 1.1 - - - -
100C GLY* 3.6 21.3 - - - +
166C LEU* 4.2 13.5 - - + -
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Residues in contact with ASP 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C HIS* 2.9 35.2 - - + +
27C GLY 3.3 3.0 + - - +
28C ALA* 3.1 18.0 + - - +
29C HIS 3.6 0.8 - - - -
30C ILE* 1.3 75.2 - - - +
32C THR* 1.3 60.5 + - - +
33C ILE 3.2 0.2 - - - -
34C PHE* 3.3 5.4 + - - +
35C GLN* 2.9 56.1 + - - +
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Residues in contact with THR 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C THR* 3.8 18.9 + - + +
7C GLY* 3.3 24.7 - - - -
8C GLU 4.4 0.3 + - - -
29C HIS 5.0 0.8 + - - +
30C ILE 4.6 0.7 - - - -
31C ASP* 1.3 80.0 - - + +
33C ILE* 1.3 59.0 + - - +
35C GLN* 4.0 7.1 - - - +
36C ALA* 3.1 27.4 + - - +
166C LEU* 3.5 34.0 - - + +
167C MSE 4.1 23.1 - - + -
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Residues in contact with ILE 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C GLY* 4.0 23.6 - - - +
10C VAL* 4.1 20.0 - - + -
11C VAL* 3.6 15.7 - - + +
22C LEU* 4.3 11.7 - - + -
30C ILE* 3.3 11.8 + - + +
31C ASP 3.2 0.8 - - - -
32C THR* 1.3 75.6 + - - +
34C PHE* 1.3 59.1 + - - +
36C ALA 3.4 0.9 + - - -
37C CYS* 2.8 31.4 + - - -
71C LEU* 3.8 42.4 - - + -
98C LEU* 4.8 2.2 - - + -
161C LEU* 4.3 11.0 - - + -
166C LEU* 4.1 25.1 - - + -
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Residues in contact with PHE 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C GLY 5.1 0.4 - - - -
25C LEU* 4.1 5.4 - - - -
26C HIS* 3.6 55.4 - + + +
30C ILE* 3.5 24.2 - - + -
31C ASP* 3.3 17.4 + - - +
33C ILE* 1.3 74.1 - - - +
35C GLN* 1.3 68.1 + - - +
37C CYS* 3.2 2.8 + - - +
38C LEU* 3.0 24.0 + - - +
44C ILE* 3.5 40.3 - - + +
46C ASP* 5.1 9.2 - - + -
71C LEU* 3.7 18.4 - - + -
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Residues in contact with GLN 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ASP* 2.9 52.8 + - - +
32C THR* 4.0 7.9 - - - +
34C PHE* 1.3 73.7 - - - +
36C ALA* 1.3 63.3 + - - +
38C LEU* 3.2 20.0 + - - +
39C ASP* 3.1 29.4 + - - +
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Residues in contact with ALA 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C GLY 3.9 6.7 - - - +
8C GLU* 3.3 28.9 - - + +
11C VAL* 3.5 30.1 - - + -
32C THR 3.1 15.5 + - - +
34C PHE 3.3 0.2 - - - -
35C GLN* 1.3 78.9 - - - +
37C CYS* 1.3 56.6 - - - +
39C ASP* 3.2 5.3 + - - +
40C HIS* 2.9 32.7 + - - +
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Residues in contact with CYS 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C VAL* 3.7 19.3 - - - -
22C LEU* 4.3 13.5 - - - -
33C ILE 2.8 24.5 + - - +
34C PHE 3.2 4.0 + - - +
36C ALA* 1.3 72.3 - - - +
38C LEU* 1.3 57.1 - - - +
40C HIS 4.5 0.2 - - - +
41C ASP* 2.9 10.2 + - - -
42C VAL* 2.8 65.9 + - - +
44C ILE* 3.9 25.6 - - + -
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Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C PHE 3.0 12.3 + - - +
35C GLN* 3.3 24.0 - - - +
37C CYS* 1.3 74.5 - - - +
39C ASP* 1.3 70.5 + - - +
40C HIS 3.4 0.5 + - - -
41C ASP* 3.5 15.6 + - - +
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Residues in contact with ASP 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C GLU* 4.7 7.1 - - - +
35C GLN* 3.1 17.7 + - - +
36C ALA* 3.4 10.5 - - - +
38C LEU* 1.3 83.9 - - - +
40C HIS* 1.3 70.0 + - + +
41C ASP* 3.7 2.8 + - - -
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Residues in contact with HIS 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C GLU* 3.3 33.1 + - - -
11C VAL* 4.2 8.4 - - + +
12C ARG* 4.3 20.1 + - + +
15C ILE* 3.9 30.5 - - + +
36C ALA 2.9 23.3 + - - +
39C ASP* 1.3 84.2 - - + +
41C ASP* 1.3 71.0 + - - +
42C VAL* 3.2 9.8 + - + +
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Residues in contact with ASP 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C CYS 2.9 5.6 + - - -
38C LEU* 3.5 10.2 + - - +
39C ASP 3.4 5.0 - - - -
40C HIS* 1.3 80.1 - - - +
42C VAL* 1.3 59.2 + - - +
43C PRO* 3.3 11.7 - - - +
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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