Contacts of the helix formed by residues 13 - 21 (chain C) in PDB entry 3DOY
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 PHE 13 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C GLN* 3.9 31.9 - - + -
12C PHE* 1.3 77.9 - - - +
14C ILE* 1.3 67.2 + - + +
15C GLU* 3.2 23.8 - - - +
16C HIS* 3.0 26.1 + + - +
17C ILE* 2.9 21.8 + - - +
31C ASP 4.0 2.9 - - - -
32C ARG* 3.5 46.7 - - - -
114E THR* 5.7 2.0 - - - -
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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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13C PHE* 1.3 76.7 - - + +
15C GLU* 1.3 70.8 + - - +
17C ILE* 4.2 4.9 - - + -
18C LEU* 2.9 34.2 + - + +
28C LEU* 4.1 13.0 - - + -
30C VAL 3.8 20.4 - - - +
31C ASP* 3.4 18.1 + - - +
32C ARG* 5.7 0.2 - - - +
50E PHE* 3.7 46.2 - - + -
63E PRO* 4.3 11.2 - - + +
114E THR* 5.1 5.2 - - - +
115E PRO* 4.2 30.2 + - + +
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Residues in contact with GLU 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C PHE* 3.2 26.6 - - - +
14C ILE* 1.3 92.9 + - + +
16C HIS* 1.3 79.8 + - + +
18C LEU* 3.6 11.4 + - - +
19C GLN* 3.3 30.7 + - - +
61E ASN 4.9 10.8 - - - +
62E LYS* 6.3 1.3 - - + -
63E PRO* 5.4 3.7 - - + +
114E THR* 5.9 1.9 - - - +
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Residues in contact with HIS 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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9C GLN* 4.3 20.6 + - - -
11C GLN 4.8 0.2 - - - -
12C PHE* 3.7 20.2 - + + -
13C PHE* 3.0 42.4 + + - +
15C GLU* 1.3 92.8 - - + +
17C ILE* 1.3 66.3 + - - +
19C GLN* 3.1 15.2 + - - -
20C ILE* 3.4 10.2 + - - +
80C PHE* 5.0 1.3 - - - -
89C PHE* 3.5 42.7 - + + -
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Residues in contact with ILE 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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12C PHE* 4.5 1.8 - - + +
13C PHE 2.9 13.8 + - - +
14C ILE* 3.7 8.1 - - + +
16C HIS* 1.3 74.8 - - - +
18C LEU* 1.3 63.8 + - - +
20C ILE* 3.1 1.7 + - - +
21C LEU* 3.0 37.4 + - + +
28C LEU* 4.0 23.1 - - + -
30C VAL* 3.3 40.8 - - + +
31C ASP 3.5 24.0 - - - +
32C ARG* 3.5 13.9 - - - +
33C ILE* 4.2 17.0 - - + -
80C PHE* 4.3 12.6 - - + -
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Residues in contact with LEU 18 (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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14C ILE* 2.9 22.0 + - + +
15C GLU* 3.7 12.8 - - - +
16C HIS 3.2 0.2 - - - -
17C ILE* 1.3 79.3 - - - +
19C GLN* 1.3 58.7 + - + +
21C LEU 3.3 10.8 - - - +
24C ARG* 2.9 56.7 + - - +
28C LEU* 3.5 27.6 - - + -
50E PHE* 3.8 23.3 - - + -
61E ASN* 4.7 15.9 - - - +
63E PRO* 4.3 17.7 - - + -
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Residues in contact with GLN 19 (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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15C GLU* 3.3 25.9 + - - +
16C HIS* 3.1 14.0 + - - +
18C LEU* 1.3 77.9 - - + +
20C ILE* 1.3 61.0 + - - +
21C LEU 4.7 0.2 - - - -
89C PHE* 3.9 19.7 - - + -
91C PRO* 3.4 41.0 - - + +
94C ALA* 3.5 15.9 - - - +
95C LYS* 5.6 2.3 - - - +
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Residues in contact with ILE 20 (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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16C HIS 3.7 11.0 - - - +
17C ILE 3.1 2.7 + - - +
19C GLN* 1.3 87.0 - - - +
21C LEU* 1.3 68.2 + - + +
22C PRO* 4.0 1.0 - - - +
80C PHE* 3.6 36.1 - - + -
83C PHE* 3.6 47.3 - - + -
84C THR* 4.9 1.6 - - + -
88C GLY 4.7 0.2 - - - +
89C PHE* 3.8 28.5 - - + -
90C ASP 3.9 14.6 - - - +
91C PRO 4.2 0.9 - - - -
94C ALA* 3.6 18.2 - - + +
158C ARG* 5.1 0.7 + - - -
3002C 2BE 4.0 12.6 - - + +
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Residues in contact with LEU 21 (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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17C ILE* 3.0 24.4 + - + +
18C LEU 3.3 8.8 - - - +
19C GLN 4.7 0.2 - - - -
20C ILE* 1.3 80.4 - - + +
22C PRO* 1.3 65.5 - - + +
23C HIS* 3.2 10.1 - - + +
24C ARG* 3.1 19.6 + - - -
28C LEU* 3.9 26.5 - - + -
30C VAL* 4.9 4.7 - - + -
76C GLN* 4.2 36.8 - - + +
80C PHE* 4.3 20.9 - - + +
158C ARG* 5.4 0.2 - - - -
3002C 2BE 3.1 33.0 - - + +
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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