Contacts of the helix formed by residues 10 - 19 (chain D) in PDB entry 1C03
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 10 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B GLU* 3.3 29.4 + - - +
9D ILE* 1.3 69.7 - - - +
11D TRP* 1.3 64.2 + - - +
12D THR* 3.3 31.9 + - - +
13D ILE* 3.3 8.6 + - + +
14D LEU* 3.2 20.3 + - - +
74D GLY* 2.6 26.8 + - - +
76D GLN* 3.8 25.3 - - + +
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Residues in contact with TRP 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D GLU* 5.6 4.5 - - - -
9D ILE* 3.4 36.2 + - + +
10D ASN* 1.3 72.9 - - - +
12D THR* 1.3 62.1 + - + +
14D LEU* 3.4 29.6 - - + +
15D ASN* 2.8 62.5 + - - +
18D ILE* 3.6 22.2 - - + -
158D GLU* 4.9 3.4 + - - -
159D LEU* 5.3 0.9 - - + -
162D TYR* 3.6 53.8 + + + -
163D TYR* 5.7 0.9 - + - -
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Residues in contact with THR 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B THR* 4.5 8.2 + - - +
13B ILE* 4.8 0.9 - - - +
16B GLU* 3.6 22.8 + - - +
10D ASN* 3.2 16.7 + - - +
11D TRP* 1.3 79.1 - - + +
13D ILE* 1.3 60.4 + - - +
15D ASN* 4.7 3.1 - - - +
16D GLU* 2.8 27.3 - - - +
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Residues in contact with ILE 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B THR 4.7 0.2 - - - +
13B ILE* 4.0 28.4 - - + +
16B GLU* 3.4 43.5 - - + +
17B ILE* 4.7 7.0 - - + -
10D ASN* 3.3 13.9 + - + +
12D THR* 1.3 81.8 + - - +
14D LEU* 1.3 66.4 + - - +
15D ASN 3.3 0.2 - - - -
16D GLU* 3.2 15.6 + - - +
17D ILE* 3.4 12.7 + - + +
71D ALA 3.6 17.5 - - - +
72D ALA* 3.5 24.2 - - - +
74D GLY* 3.9 14.1 - - - +
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Residues in contact with LEU 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ILE* 3.5 20.2 - - + -
10D ASN 3.2 14.0 + - - +
11D TRP* 3.4 34.5 - - + -
13D ILE* 1.3 78.3 - - - +
15D ASN* 1.3 60.7 + - - +
17D ILE* 3.1 17.4 + - + +
18D ILE* 2.9 43.2 + - + +
28D SER* 5.6 1.3 - - - -
32D ILE* 5.2 8.7 - - + -
73D LEU* 3.6 28.9 - - + +
75D LEU* 5.9 0.2 - - + -
159D LEU* 4.1 17.7 - - + -
163D TYR* 4.8 6.5 - - + +
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Residues in contact with ASN 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D TRP* 2.8 50.2 + - - +
12D THR* 4.7 5.8 - - - +
14D LEU* 1.3 76.9 - - - +
16D GLU* 1.3 61.1 + - - +
18D ILE* 3.4 11.7 + - - +
19D SER* 2.8 31.8 + - - -
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Residues in contact with GLU 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ASN* 3.3 25.3 + - - +
12B THR* 3.5 21.0 + - - +
13B ILE* 3.4 26.9 - - + +
12D THR* 2.8 21.3 - - - +
13D ILE 3.2 4.4 + - - +
14D LEU 3.2 0.4 - - - -
15D ASN* 1.3 80.8 - - - +
17D ILE* 1.3 64.8 + - - +
19D SER* 3.8 17.3 + - - +
20D MET* 4.2 14.0 - - - +
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Residues in contact with ILE 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ILE* 4.6 6.1 - - + -
71B ALA* 4.1 34.3 - - + +
72B ALA* 4.6 5.4 - - + +
13D ILE 3.7 13.2 - - - +
14D LEU* 3.1 19.9 + - + +
16D GLU* 1.3 75.4 - - - +
18D ILE* 1.3 64.5 + - - +
19D SER 3.3 0.4 - - - -
20D MET* 3.3 10.7 + - - +
21D ASP 4.2 0.2 + - - -
27D PHE* 3.7 25.2 - - + -
28D SER* 4.2 14.2 - - - -
31D LEU* 3.8 31.0 - - + -
72D ALA 4.2 20.2 - - - +
73D LEU* 5.1 5.2 - - + -
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Residues in contact with ILE 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D TRP* 3.6 32.1 - - + -
14D LEU* 2.9 23.4 + - + +
15D ASN* 3.7 12.8 - - - +
17D ILE* 1.3 73.9 - - - +
19D SER* 1.3 56.7 + - - +
20D MET 2.9 2.5 - - - -
21D ASP* 2.7 47.7 + - + +
22D ASP* 4.4 1.2 + - - +
28D SER* 4.3 5.2 - - - -
162D TYR* 6.4 0.7 - - + -
163D TYR* 3.7 26.9 - - + +
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Residues in contact with SER 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ASN* 2.8 22.4 + - - +
16D GLU* 3.8 15.7 - - - +
17D ILE 3.3 0.2 - - - -
18D ILE* 1.3 74.6 - - - +
20D MET* 1.3 60.1 + - - +
21D ASP 3.2 0.3 + - - -
22D ASP* 3.0 34.0 - - - +
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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