Contacts of the helix formed by residues 6 - 18 (chain A) in PDB entry 3C8P
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A CYS* 3.3 2.5 + - - +
5A PRO* 1.3 84.9 - - - +
7A THR* 1.3 65.0 + - - +
8A THR* 3.4 10.6 + - - -
9A GLY* 3.0 20.6 + - - -
10A ARG 3.0 18.4 + - - -
46A LYS* 3.6 18.8 - - - +
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Residues in contact with THR 7 (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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6A SER* 1.3 73.1 - - - +
8A THR* 1.3 62.6 + - - +
10A ARG* 3.2 9.2 + - + +
11A ASN* 2.9 39.7 + - - +
46A LYS* 4.0 24.4 + - - +
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Residues in contact with THR 8 (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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6A SER* 3.2 9.1 + - - -
7A THR* 1.3 77.2 - - - +
9A GLY* 1.3 58.8 + - - +
11A ASN* 3.1 10.6 + - + +
12A ILE* 2.9 47.8 + - + +
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Residues in contact with GLY 9 (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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4A CYS* 4.6 1.3 - - - -
5A PRO* 4.7 1.8 - - - -
6A SER* 3.0 19.6 + - - -
8A THR* 1.3 76.5 - - - +
10A ARG* 1.3 60.9 + - - +
12A ILE* 3.3 3.6 + - - -
13A TYR* 2.9 21.7 + - - +
30A SER* 3.3 33.2 - - - -
32A CYS* 3.8 8.7 - - - -
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Residues in contact with ARG 10 (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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2A SER* 2.8 43.0 + - - -
4A CYS* 3.5 21.0 - - + +
6A SER 3.0 12.2 + - - +
7A THR* 3.5 12.8 - - + +
9A GLY* 1.3 75.9 - - - +
11A ASN* 1.3 62.1 - - - +
13A TYR* 3.4 11.6 + - - +
14A ASN* 2.9 59.7 + - - +
40A CYS* 5.4 0.4 - - - -
46A LYS* 2.8 45.7 + - + +
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Residues in contact with ASN 11 (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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7A THR* 2.9 35.4 + - - +
8A THR* 3.6 7.7 - - + +
10A ARG* 1.3 81.1 - - - +
12A ILE* 1.3 61.5 + - + +
14A ASN* 3.4 7.7 + - - +
15A THR* 2.9 36.1 + - - +
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Residues in contact with ILE 12 (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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8A THR* 2.9 39.7 + - + +
9A GLY* 3.7 4.5 - - - +
11A ASN* 1.3 75.4 - - + +
13A TYR* 1.3 63.6 + - - +
15A THR* 3.8 4.5 - - - -
16A CYS* 2.9 26.0 + - + +
26A CYS 5.0 0.2 - - - +
29A LEU* 3.6 38.6 - - + +
30A SER* 3.7 12.8 - - - +
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Residues in contact with TYR 13 (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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2A SER* 3.5 22.2 - - - -
4A CYS* 4.2 1.6 - - - -
9A GLY 2.9 17.7 + - - +
10A ARG* 3.7 20.0 - - - +
12A ILE* 1.3 78.1 - - - +
14A ASN* 1.3 68.9 + - - +
16A CYS* 3.3 3.1 + - - +
17A ARG* 2.9 46.6 + - + +
23A ARG* 3.3 46.1 + - - +
26A CYS* 3.6 33.4 - - + -
27A ALA* 3.8 3.6 - - - -
30A SER* 3.6 13.2 - - - +
32A CYS* 3.9 12.6 - - + -
34A ILE* 3.7 12.8 - - + +
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Residues in contact with ASN 14 (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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10A ARG* 2.9 55.2 + - - +
11A ASN* 4.0 8.4 + - - +
13A TYR* 1.3 84.6 - - - +
15A THR* 1.3 62.6 + - - +
17A ARG* 3.3 14.2 + - - +
18A LEU* 3.4 17.9 + - - +
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Residues in contact with THR 15 (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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11A ASN* 2.9 21.4 + - - +
12A ILE* 3.8 5.2 - - - +
14A ASN* 1.3 74.8 - - - +
16A CYS* 1.3 65.6 + - - +
18A LEU* 3.0 31.8 + - + +
19A THR* 3.8 8.5 + - + +
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Residues in contact with CYS 16 (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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12A ILE* 2.9 21.8 + - + +
13A TYR 3.6 2.2 - - - +
15A THR* 1.3 76.6 - - - +
17A ARG* 1.3 60.0 + - - +
19A THR* 2.6 32.9 + - - -
21A SER* 3.9 13.3 + - - -
25A THR* 4.4 1.8 - - - -
26A CYS* 2.1 56.3 - - + +
29A LEU* 4.2 20.6 - - + -
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Residues in contact with ARG 17 (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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13A TYR* 2.9 48.7 + - + +
14A ASN* 3.7 7.9 - - - +
15A THR 3.2 0.6 - - - -
16A CYS* 1.3 75.4 - - - +
18A LEU* 1.3 61.7 + - + +
19A THR 3.4 0.7 + - - -
20A GLY* 3.6 10.2 + - - -
21A SER 2.9 27.1 + - - +
22A SER* 3.7 2.8 - - - +
23A ARG* 3.3 60.3 - - - +
26A CYS* 3.8 11.4 - - - -
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Residues in contact with LEU 18 (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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14A ASN 3.4 15.9 + - - +
15A THR* 3.0 21.4 + - + +
17A ARG* 1.3 77.2 - - + +
19A THR* 1.3 60.9 + - + +
20A GLY 3.3 1.2 + - - -
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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