Contacts of the helix formed by residues 14 - 20 (chain C) in PDB entry 1I8F
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 ALA 14 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C THR* 1.3 67.2 + - - +
16C LEU* 3.4 6.8 - - - +
17C GLN* 3.8 13.5 + - - +
18C ASP* 3.2 27.3 + - - +
41C PHE* 5.7 4.0 - - - -
48D LEU* 6.4 2.5 - - + -
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Residues in contact with THR 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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14C ALA* 1.3 80.4 - - - +
16C LEU* 1.3 66.5 + - - +
18C ASP* 3.3 16.2 + - - +
19C SER* 3.2 15.9 + - - -
78C PRO* 4.5 10.6 - - - +
48D LEU* 4.5 21.8 - - - -
65D THR* 4.1 17.8 - - - +
67D VAL* 4.6 19.9 - - - +
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Residues in contact with LEU 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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14C ALA 3.4 3.2 - - - +
15C THR* 1.3 79.0 - - - +
17C GLN* 1.3 56.1 + - - +
19C SER* 2.7 28.6 + - - -
20C ILE 3.1 9.5 + - - -
38C LEU* 3.6 16.3 - - + +
41C PHE* 3.5 46.9 - - + -
42C ASP 5.5 0.4 - - - +
45C VAL* 4.8 10.5 - - + -
47C LEU* 4.5 3.1 - - + -
76C ILE* 4.0 45.5 - - + -
78C PRO* 6.3 1.3 - - + -
67D VAL* 4.3 17.7 - - + -
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Residues in contact with GLN 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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14C ALA* 3.8 15.3 + - - +
15C THR 3.3 0.4 - - - -
16C LEU* 1.3 78.9 - - - +
18C ASP* 1.3 64.3 + - - +
19C SER 3.4 0.5 + - - -
20C ILE* 3.6 21.4 + - - +
41C PHE* 3.4 28.2 - - + -
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Residues in contact with ASP 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 ALA 3.2 17.1 + - - +
15C THR* 3.3 11.8 + - - +
16C LEU 3.0 0.6 - - - -
17C GLN* 1.3 82.1 - - - +
19C SER* 1.3 60.2 + - - +
20C ILE 3.4 4.3 + - - +
22C LYS* 4.4 6.2 - - - +
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Residues in contact with SER 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 THR* 3.2 11.3 + - - -
16C LEU* 2.7 13.6 + - - +
18C ASP* 1.3 78.0 - - - +
20C ILE* 1.3 65.8 + - - -
21C GLY 3.0 0.3 + - - -
22C LYS* 2.9 30.2 + - - +
24C VAL* 4.1 20.2 - - - -
38C LEU* 3.7 11.0 - - - +
78C PRO* 3.1 30.5 - - - +
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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 LEU 3.1 3.3 + - - +
17C GLN* 3.6 30.5 - - - +
18C ASP 3.4 4.5 - - - +
19C SER* 1.3 77.3 - - - +
21C GLY* 1.3 64.6 + - - +
22C LYS* 3.5 5.0 + - - +
38C LEU* 3.4 10.8 - - + +
39C ARG* 3.7 32.5 - - - +
40C SER* 4.1 2.7 - - - -
41C PHE* 3.7 30.5 - - + -
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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