Contacts of the helix formed by residues 5 - 17 (chain C) in PDB entry 2D28
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 SER 5 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C ARG* 1.3 76.1 - - - +
6C ALA* 1.3 61.6 + - - +
7C GLU* 3.5 10.7 + - - +
8C THR* 3.0 32.7 + - - -
9C ARG* 3.1 21.5 + - - +
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Residues in contact with ALA 6 (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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4C ARG 3.8 0.8 + - - -
5C SER* 1.3 70.9 - - - +
7C GLU* 1.3 63.6 + - - +
9C ARG* 3.2 17.1 + - - +
10C ILE* 2.9 32.2 + - + +
61C VAL* 5.0 0.9 - - - -
62C LEU* 4.1 22.9 - - + -
114C TYR* 3.7 26.2 - - + +
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Residues in contact with GLU 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C SER* 3.3 8.3 + - - +
6C ALA* 1.3 78.2 - - - +
8C THR* 1.3 60.5 + - - +
10C ILE* 3.3 3.9 + - - +
11C VAL* 2.9 32.3 + - + +
38C GLY* 4.6 4.7 - - - -
39C LEU* 3.6 39.0 + - - +
40C LEU* 3.8 29.7 + - + +
114C TYR* 4.3 20.3 + - + +
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Residues in contact with THR 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ARG* 4.6 22.0 - - + +
5C SER* 3.0 29.9 + - - -
7C GLU* 1.3 75.3 + - - +
9C ARG* 1.3 60.4 + - - +
11C VAL* 3.5 7.1 + - - +
12C GLU* 2.9 28.5 + - + +
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Residues in contact with ARG 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ARG* 3.8 49.9 + - + +
5C SER 3.1 18.4 + - - +
6C ALA* 3.7 14.7 - - - +
8C THR* 1.3 76.0 - - - +
10C ILE* 1.3 58.7 + - - +
12C GLU* 3.7 11.4 - - - +
13C ALA* 3.0 28.9 + - - +
61C VAL* 3.4 51.8 + - + +
62C LEU* 4.7 8.3 - - - +
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Residues in contact with ILE 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ALA* 2.9 23.1 + - + +
7C GLU 3.6 4.3 - - - +
9C ARG* 1.3 74.8 - - - +
11C VAL* 1.3 58.7 + - - +
13C ALA 3.2 0.9 + - - -
14C LEU* 2.8 31.5 + - + +
40C LEU* 3.9 22.9 - - + -
54C HIS* 5.1 2.2 - - - +
57C THR* 3.5 19.9 - - + +
58C CYS* 3.8 36.3 - - - +
61C VAL* 3.8 27.1 - - + -
62C LEU* 4.9 3.8 - - + -
114C TYR* 3.8 25.6 - - + -
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Residues in contact with VAL 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C GLU* 2.9 23.0 + - + +
8C THR* 3.8 7.4 - - - +
10C ILE* 1.3 77.1 - - - +
12C GLU* 1.3 63.7 + - - +
14C LEU* 3.3 10.1 + - - +
15C LEU* 3.2 23.2 + - + +
20C LEU* 4.4 4.5 - - + -
25C LEU* 3.8 35.0 - - + -
39C LEU* 4.1 24.2 - - + -
40C LEU* 3.9 21.5 - - + -
43C LEU* 4.8 3.1 - - + -
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Residues in contact with GLU 12 (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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4C ARG* 2.9 43.9 + - - +
8C THR* 2.9 20.2 + - + +
9C ARG* 3.7 8.6 - - - +
11C VAL* 1.3 76.5 - - - +
13C ALA* 1.3 60.3 + - - +
15C LEU* 3.4 12.6 + - - +
16C GLU* 3.0 29.6 + - + +
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Residues in contact with ALA 13 (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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9C ARG 3.0 18.1 + - - +
12C GLU* 1.3 76.8 - - + +
14C LEU* 1.3 59.8 + - - +
16C GLU* 4.0 8.0 - - + +
17C ARG* 2.9 36.9 + - + +
57C THR* 3.5 22.7 - - + -
60C GLU* 4.5 8.1 - - - +
61C VAL* 4.1 10.5 - - + -
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Residues in contact with LEU 14 (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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10C ILE* 2.8 25.4 + - + +
11C VAL* 3.3 11.0 + - - +
13C ALA* 1.3 72.6 - - - +
15C LEU* 1.3 61.3 + - - +
18C ARG 3.1 2.3 + - - -
19C ARG* 2.8 51.9 + - + +
20C LEU* 3.4 18.6 + - + -
40C LEU* 3.8 28.5 - - + -
43C LEU* 5.0 0.2 - - + -
49C VAL* 3.9 31.2 - - + -
53C ASP 3.8 10.5 - - - +
54C HIS* 4.7 2.0 - - - +
57C THR* 3.4 24.6 - - + +
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Residues in contact with LEU 15 (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* 3.2 15.7 + - + +
12C GLU* 3.7 11.2 - - - +
14C LEU* 1.3 76.1 - - - +
16C GLU* 1.3 60.2 + - - +
18C ARG* 2.9 25.1 + - - +
20C LEU* 3.5 35.5 - - + +
22C ASP* 3.8 31.6 - - + +
25C LEU* 3.8 20.6 - - + -
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Residues in contact with GLU 16 (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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12C GLU* 3.0 18.4 + - + +
13C ALA* 4.0 8.7 - - + +
15C LEU* 1.3 80.6 - - - +
17C ARG* 1.3 97.6 + - + +
18C ARG* 3.3 9.9 + - - +
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Residues in contact with ARG 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ALA* 2.9 24.0 + - + +
16C GLU* 1.3 107.0 + - + +
18C ARG* 1.3 71.0 + - - +
19C ARG* 3.3 51.8 + - + +
60C GLU* 4.3 9.6 - - - +
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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