Contacts of the helix formed by residues 13 - 24 (chain C) in PDB entry 3O9Z
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 ILE 13 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C TYR* 1.3 76.0 - - + +
14C ALA* 1.3 70.6 + - - +
15C PRO* 3.2 3.1 - - - -
16C ARG* 2.9 60.7 + - - +
17C HIS* 3.5 8.7 - - + -
77C ALA* 3.6 21.5 - - + -
100C GLU* 3.5 18.8 - - - +
264C HIS* 3.8 7.6 - - + +
311C NAD 3.0 68.9 + - + +
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Residues in contact with ALA 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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6C LEU* 4.5 8.7 - - + -
8C GLY 3.4 18.2 - - - +
9C LEU* 3.4 34.8 - - + +
11C GLY 3.7 3.0 + - - +
12C TYR 3.5 0.4 - - - -
13C ILE* 1.3 81.1 - - - +
15C PRO* 1.4 61.8 - - + +
17C HIS* 2.8 30.3 + - - +
18C LEU* 2.9 15.7 + - + +
77C ALA* 4.8 3.4 - - + -
311C NAD 4.6 0.2 + - - -
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Residues in contact with PRO 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU 5.1 1.8 - - - +
11C GLY 3.5 11.4 - - - +
12C TYR 3.3 18.2 - - - +
13C ILE 3.3 1.1 - - - -
14C ALA* 1.4 91.0 - - + +
16C ARG* 1.3 56.2 + - - +
18C LEU* 3.4 13.9 + - + +
19C LYS* 3.0 28.6 + - - +
40C LEU* 3.6 28.0 - - + -
44C PHE* 4.5 4.4 - - + -
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Residues in contact with ARG 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* 3.2 29.5 + - - -
13C ILE* 2.9 36.5 + - + +
15C PRO* 1.3 79.6 - - - +
17C HIS* 1.3 58.9 + - - +
19C LYS* 3.8 20.8 - - - +
20C ALA* 2.9 28.2 + - - +
129C GLN* 4.3 2.8 + - - -
260C PHE 4.2 3.4 + - - -
261C THR* 3.4 55.1 + - - +
262C ASP* 6.1 0.2 - - - -
264C HIS* 3.5 46.5 + - + +
265C THR* 5.1 0.3 + - - -
311C NAD 4.4 4.9 + - - -
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Residues in contact with HIS 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU* 4.0 20.6 - - + +
13C ILE* 3.5 24.5 - - + -
14C ALA* 2.8 10.1 + - - +
16C ARG* 1.3 75.8 - - - +
18C LEU* 1.3 60.3 + - - +
20C ALA* 3.2 4.9 + - - +
21C ILE* 2.9 36.4 + - + +
75C SER* 4.4 6.9 - - - -
76C ILE 4.8 3.8 - - - -
77C ALA* 4.2 6.5 - - + +
98C LEU 5.2 2.9 - - - -
100C GLU* 2.7 43.6 + - + +
127C VAL* 4.1 9.0 - - + -
264C HIS* 3.7 11.5 - + - -
268C TYR* 2.7 37.1 + + - +
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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
----------------------------------------------------------
6C LEU* 3.7 16.6 - - + -
9C LEU* 3.9 20.4 - - + +
14C ALA* 2.9 14.5 + - + +
15C PRO* 3.7 19.5 - - + +
17C HIS* 1.3 74.9 - - - +
19C LYS* 1.3 64.8 + - - +
21C ILE* 3.3 7.0 + - + +
22C LYS* 3.1 23.7 + - - +
28C LEU* 3.7 30.5 - - + -
40C LEU* 4.4 8.3 - - + -
41C VAL* 4.2 15.7 - - + +
44C PHE* 3.9 35.8 - - + -
45C PHE* 4.0 8.8 - - + -
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Residues in contact with LYS 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 PRO 3.0 17.8 + - - +
16C ARG* 3.8 21.7 - - - +
18C LEU* 1.3 76.7 - - - +
20C ALA* 1.3 57.5 + - - +
22C LYS* 3.4 2.8 + - - +
23C GLU* 2.9 55.3 + - + +
44C PHE* 3.8 18.1 - - + -
261C THR 5.4 1.8 + - - -
262C ASP* 4.7 16.2 + - - +
264C HIS* 6.4 0.4 - - - -
265C THR* 4.6 9.2 - - - +
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Residues in contact with ALA 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 ARG 2.9 19.5 + - - +
17C HIS 3.2 4.5 + - - +
19C LYS* 1.3 77.0 - - - +
21C ILE* 1.3 62.9 + - - +
23C GLU* 3.2 1.0 + - - +
24C VAL* 3.0 30.6 + - - +
264C HIS 4.2 1.6 - - - +
265C THR* 3.5 26.4 + - - +
268C TYR* 3.4 35.9 - - + -
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Residues in contact with ILE 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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4C PHE* 3.8 37.9 - - + -
6C LEU* 5.0 4.7 - - + -
17C HIS* 2.9 29.3 + - + +
18C LEU* 3.8 7.9 - - + +
20C ALA* 1.3 71.4 - - - +
22C LYS* 1.3 58.4 + - - +
24C VAL* 3.4 7.6 - - - +
25C GLY 3.3 2.6 + - - -
26C GLY 2.8 46.1 + - - -
27C VAL 3.9 6.1 - - - +
28C LEU* 4.4 15.7 - - + -
45C PHE* 3.6 22.7 - - + -
75C SER* 4.4 6.1 - - - +
268C TYR* 3.7 23.6 - - + +
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Residues in contact with LYS 22 (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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18C LEU 3.1 17.5 + - - +
19C LYS* 3.5 5.8 - - - +
21C ILE* 1.3 76.0 - - - +
23C GLU* 1.3 65.4 + - + +
25C GLY* 3.0 21.1 + - - -
26C GLY 4.7 2.2 - - - +
43C SER 4.3 4.2 + - - -
44C PHE* 2.8 51.9 + - + +
45C PHE* 3.8 20.6 - - + -
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Residues in contact with GLU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LYS* 2.9 41.6 + - + +
20C ALA 3.2 0.2 + - - -
22C LYS* 1.3 82.3 - - + +
24C VAL* 1.3 59.7 + - - +
25C GLY 3.3 1.0 + - - -
265C THR* 2.6 44.2 + - + +
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Residues in contact with VAL 24 (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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2C THR* 5.6 1.7 + - - -
4C PHE* 4.5 5.6 - - + -
20C ALA 3.0 19.9 + - - +
21C ILE* 3.4 14.8 - - - +
23C GLU* 1.3 77.2 - - - +
25C GLY* 1.3 59.8 + - - +
26C GLY* 4.0 4.2 - - - +
265C THR* 4.3 11.2 - - + -
268C TYR* 4.0 11.9 - - + -
269C ARG* 4.0 32.5 - - + +
272C LEU* 3.7 28.9 - - + +
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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