Contacts of the helix formed by residues 6 - 17 (chain C) in PDB entry 4PAR
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 6 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C LYS* 3.0 13.5 + - - -
5C ALA* 1.3 76.3 - - - +
7C SER* 1.3 59.8 + - - +
8C ASP 3.2 2.7 - - - -
9C LEU* 3.8 16.9 + - - +
10C THR* 3.3 10.2 + - - -
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Residues in contact with SER 7 (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 ALA* 4.3 8.8 + - - -
6C SER* 1.3 78.3 - - - +
8C ASP* 1.3 65.8 + - - +
9C LEU 3.3 1.1 - - - -
10C THR* 3.3 13.5 + - - -
11C ASP* 2.9 28.9 + - - +
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Residues in contact with ASP 8 (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 ALA* 3.9 13.3 - - - +
6C SER 3.2 0.2 - - - -
7C SER* 1.3 85.5 + - - +
9C LEU* 1.3 56.7 + - - +
11C ASP* 3.5 5.7 + - - +
12C TYR* 2.9 29.2 + - - +
168C ILE* 3.8 18.6 - - + +
169C GLU* 2.8 36.8 - - - +
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Residues in contact with LEU 9 (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 ALA 5.2 0.2 + - - -
6C SER* 3.8 12.6 + - - +
7C SER 3.3 0.4 - - - -
8C ASP* 1.3 78.0 - - - +
10C THR* 1.3 65.6 + - - +
12C TYR* 3.3 3.3 + - - +
13C VAL* 2.9 37.6 + - + +
40C PHE* 4.6 23.6 - - + +
166C TRP* 3.7 34.5 - - + -
168C ILE* 4.6 9.7 - - + +
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Residues in contact with THR 10 (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 SER 3.3 5.5 + - - -
7C SER* 3.3 24.8 - - - -
9C LEU* 1.3 79.6 - - - +
11C ASP* 1.3 64.9 + - - +
13C VAL* 3.7 4.4 - - - +
14C ILE* 2.9 32.5 + - + +
25D TYR* 3.8 34.8 - - + +
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Residues in contact with ASP 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C SER 2.9 15.7 + - - +
8C ASP* 3.8 7.4 - - - +
10C THR* 1.3 76.5 - - - +
12C TYR* 1.3 63.1 + - - +
14C ILE* 3.9 4.6 - - - +
15C ARG* 2.9 53.0 + - - +
24D ARG* 2.5 37.5 + - - +
25D TYR* 5.7 0.6 + - - -
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Residues in contact with TYR 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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8C ASP 2.9 18.7 + - - +
9C LEU* 3.5 7.6 - - - +
10C THR 3.2 0.2 - - - -
11C ASP* 1.3 78.4 + - - +
13C VAL* 1.3 64.9 + - + +
15C ARG* 3.3 3.6 + - - +
16C GLN* 2.9 67.6 + - + +
43C LYS* 3.4 26.8 - - + -
44C PHE* 2.8 31.0 + + - -
45C VAL* 3.8 5.0 - - - +
166C TRP* 3.4 29.8 - + - -
168C ILE* 4.3 15.9 - - + -
171C GLU* 5.7 0.2 - - - -
172C TYR* 5.5 3.8 - - - -
278C ASN* 4.8 3.4 + - - -
279C LEU* 4.5 9.6 - - + +
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Residues in contact with VAL 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 LEU* 2.9 35.2 + - + +
10C THR* 3.8 4.0 - - - +
12C TYR* 1.3 76.1 - - + +
14C ILE* 1.3 67.9 + - + +
16C GLN* 3.2 1.4 + - - +
17C LEU* 3.0 36.8 + - + +
34C ILE* 5.5 0.2 - - + -
40C PHE* 3.7 27.6 - - + -
44C PHE* 4.2 17.9 - - + -
28D TYR* 3.6 32.5 - - + -
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Residues in contact with ILE 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 THR* 2.9 25.7 + - + +
11C ASP* 3.9 5.4 - - - +
13C VAL* 1.3 78.4 - - + +
15C ARG* 1.3 60.7 + - + +
17C LEU* 3.4 3.8 + - + +
18C GLY* 2.8 28.8 + - - -
24D ARG* 3.9 46.7 - - + +
25D TYR* 4.5 27.4 - - + -
28D TYR* 3.5 39.7 - - + +
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Residues in contact with ARG 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 ASP* 2.9 48.8 + - - +
12C TYR 3.8 0.2 - - - +
14C ILE* 1.3 78.5 - - + +
16C GLN* 1.3 61.7 + - - +
18C GLY* 3.4 9.2 + - - +
19C ARG* 3.6 16.1 + - - +
279C LEU* 3.6 43.6 - - + +
280C SER* 3.7 39.4 - - - +
24D ARG* 4.4 9.2 - - - +
13F T 4.8 10.7 + - - -
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Residues in contact with GLN 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 TYR* 2.9 61.9 + - + +
13C VAL 3.8 3.4 - - - +
15C ARG* 1.3 77.2 - - - +
17C LEU* 1.3 61.4 + - - +
18C GLY 3.1 1.1 + - - -
19C ARG* 3.3 18.2 + - - +
44C PHE* 3.8 21.8 - - + -
45C VAL* 3.8 1.2 - - - -
46C THR* 2.7 57.8 + - - +
278C ASN* 3.4 26.1 + - - +
279C LEU* 3.5 13.2 - - + +
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Residues in contact with LEU 17 (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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13C VAL* 3.0 35.3 + - + +
14C ILE* 3.6 3.8 - - - +
16C GLN* 1.3 75.5 - - - +
18C GLY* 1.3 58.0 + - - +
19C ARG 3.6 2.3 + - - +
27C ALA* 5.7 4.9 - - - +
30C VAL* 3.9 26.2 - - + -
31C SER* 4.8 11.2 - - - -
34C ILE* 4.1 17.7 - - + -
35C HIS* 4.7 8.1 - - + +
44C PHE* 3.8 22.7 - - + -
46C THR* 4.6 1.1 - - + -
27D ALA* 5.5 7.1 - - + +
28D TYR* 3.8 23.3 - - + -
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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