Contacts of the helix formed by residues 48 - 59 (chain C) in PDB entry 3ECS
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 ASN 48 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C GLY* 2.8 28.1 + - - +
45C LEU* 4.0 13.3 - - - +
46C ARG 4.7 0.4 - - - +
47C ALA* 1.3 85.6 - - - +
49C LEU* 1.3 54.4 + - - +
50C THR 3.3 0.2 - - - -
51C SER* 2.9 8.9 + - - -
52C ALA* 2.7 34.8 + - - +
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Residues in contact with LEU 49 (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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33C PHE* 3.4 17.3 - - + -
37C ASP* 3.5 22.7 - - - +
40C GLU* 3.0 29.2 - - - +
45C LEU* 4.8 1.1 - - - +
46C ARG* 3.3 16.1 + - - +
48C ASN* 1.3 80.1 - - - +
50C THR* 1.3 60.7 + - - +
52C ALA* 3.3 12.5 + - + +
53C ILE* 3.2 22.0 + - - +
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Residues in contact with THR 50 (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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30C LEU* 3.4 18.5 + - - +
33C PHE* 4.0 16.0 - - - -
34C LEU* 5.6 6.2 - - - +
46C ARG* 2.9 35.7 + - - +
47C ALA* 3.3 19.3 - - - +
49C LEU* 1.3 76.5 - - - +
51C SER* 1.3 56.7 + - - +
53C ILE* 2.6 26.8 - - - +
54C GLU* 3.3 12.3 - - - +
72C PHE* 5.2 2.9 - - - -
73C LEU* 3.9 23.0 - - + +
76C ILE* 6.0 1.2 - - - +
93C MSE 5.4 5.4 - - + -
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Residues in contact with SER 51 (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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47C ALA 3.4 14.6 - - - -
48C ASN* 2.9 15.8 + - - -
50C THR* 1.3 80.7 - - - +
52C ALA* 1.3 58.1 + - - +
53C ILE 3.1 1.6 - - - -
54C GLU* 2.9 34.3 + - - +
55C THR* 3.5 6.9 + - - +
73C LEU* 5.1 6.3 - - - +
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Residues in contact with ALA 52 (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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48C ASN 2.7 17.7 + - - +
49C LEU* 3.7 13.0 - - + +
51C SER* 1.3 72.9 - - - +
53C ILE* 1.3 58.3 + - - +
55C THR* 2.6 26.0 + - - +
56C LEU* 3.0 21.3 - - + +
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Residues in contact with ILE 53 (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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6C LEU* 3.0 49.8 - - + -
29C THR* 4.7 3.8 - - - +
30C LEU* 3.4 28.7 - - + -
33C PHE* 3.4 27.4 - - + -
49C LEU 3.2 8.7 + - - +
50C THR* 2.6 39.0 - - - +
52C ALA* 1.3 73.9 - - - +
54C GLU* 1.3 59.7 + - - +
56C LEU* 3.3 11.0 - - + +
57C CYS* 3.0 29.1 + - - +
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Residues in contact with GLU 54 (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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30C LEU* 3.0 36.8 - - - +
50C THR 3.3 12.9 - - - +
51C SER* 2.9 18.2 + - - +
53C ILE* 1.3 74.1 - - - +
55C THR* 1.3 69.2 + - + +
56C LEU 2.9 1.8 + - - -
57C CYS* 3.0 7.4 + - - +
58C GLY* 2.9 19.2 + - - -
65C VAL* 4.0 12.1 - - - +
66C SER* 5.0 2.3 - - - +
69C GLY* 3.0 40.3 - - - +
70C GLU* 4.2 0.4 + - - -
72C PHE* 4.7 0.9 - - - -
73C LEU* 4.1 11.2 - - + +
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Residues in contact with THR 55 (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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51C SER 3.5 5.6 + - - +
52C ALA* 2.6 27.9 + - - +
54C GLU* 1.3 81.0 - - + +
56C LEU* 1.3 66.3 + - - +
58C GLY* 3.2 13.5 + - - +
59C VAL* 3.8 6.6 + - - +
249C LYS* 5.5 10.3 - - - +
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Residues in contact with LEU 56 (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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3C ASP* 2.9 45.5 - - - +
6C LEU* 3.5 15.3 - - + -
7C ILE* 5.6 11.0 - - + -
52C ALA* 3.0 20.1 + - + +
53C ILE* 3.3 24.5 - - + +
54C GLU 2.9 0.8 - - - -
55C THR* 1.3 75.2 + - - +
57C CYS* 1.3 54.3 + - - +
58C GLY 2.9 3.6 - - - -
59C VAL* 2.8 45.0 + - + +
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Residues in contact with CYS 57 (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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6C LEU* 5.6 6.5 - - - -
7C ILE* 6.1 4.2 - - - +
10C PHE* 4.4 32.1 - - + -
26C ALA* 4.6 5.2 - - + -
29C THR* 3.9 20.6 - - - -
30C LEU* 4.6 11.2 - - + -
53C ILE* 3.0 15.5 + - - +
54C GLU* 3.0 7.4 + - - +
56C LEU* 1.3 77.8 - - - +
58C GLY* 1.3 63.6 + - - +
59C VAL* 3.0 4.8 + - - +
60C ASP* 3.6 16.1 - - - +
65C VAL* 3.6 25.7 - - + +
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Residues in contact with GLY 58 (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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54C GLU 2.9 10.9 + - - -
55C THR* 3.5 10.5 - - - -
56C LEU 2.8 3.0 + - - -
57C CYS* 1.3 77.6 - - - +
59C VAL* 1.3 49.4 + - - +
60C ASP* 2.5 18.9 + - - +
61C SER* 2.6 18.4 + - - -
62C SER 3.9 4.8 + - - -
65C VAL* 3.9 11.0 - - - +
66C SER* 5.8 3.1 - - - -
249C LYS* 6.3 3.6 - - - -
250C PHE* 6.6 0.2 - - - -
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Residues in contact with VAL 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 4.7 22.4 - - + -
10C PHE* 5.6 1.7 - - - -
55C THR 3.8 5.7 + - - +
56C LEU* 2.8 28.2 + - + +
57C CYS* 3.8 3.9 - - - +
58C GLY* 1.3 70.7 - - - +
60C ASP* 1.3 60.6 + - - +
61C SER* 4.0 1.1 - - - +
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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