Contacts of the helix formed by residues 45 - 53 (chain N) in PDB entry 1KD1
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 ARG 45 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A A 4.0 15.8 + - - +
381A G 2.7 34.8 + - - -
8N ILE* 4.3 2.9 - - - -
9N ARG* 6.0 1.8 - - - +
12N TRP* 3.4 67.1 + - + +
43N PRO* 3.1 4.0 - - - -
44N THR* 1.3 80.2 - - - +
46N LEU* 1.3 62.8 + - - +
47N ASP* 3.3 14.0 + - - +
48N ARG* 2.9 44.5 + - + +
49N ALA* 3.0 12.6 + - - +
118N TYR* 3.6 17.7 + - + +
119N SER 3.0 33.3 + - - +
120N VAL* 4.3 2.0 - - + -
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Residues in contact with LEU 46 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A U 3.3 29.8 - - - +
264A G 3.2 28.0 - - - +
59H ILE* 4.0 16.8 - - + -
5N TYR* 3.8 11.2 - - + -
8N ILE* 3.7 17.8 - - + +
42N ARG* 6.2 1.1 - - - -
43N PRO* 3.8 15.7 + - + +
44N THR 3.7 4.6 + - - -
45N ARG* 1.3 72.2 - - - +
47N ASP* 1.3 63.6 + - - +
49N ALA* 3.4 3.9 + - + -
50N ARG* 3.1 44.9 + - + +
54N TYR* 4.3 13.0 - - + -
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Residues in contact with ASP 47 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A A 4.6 1.6 + - - -
380A A 4.8 2.4 + - - -
5N TYR* 3.8 37.4 - - + +
8N ILE* 3.1 23.2 - - + +
9N ARG* 3.3 42.1 + - + +
45N ARG* 3.6 10.0 + - - +
46N LEU* 1.3 76.0 - - - +
48N ARG* 1.3 76.4 + - - +
50N ARG* 3.5 3.1 + - - +
51N SER* 2.9 32.4 + - - -
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Residues in contact with ARG 48 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A G 4.2 1.1 + - - -
380A A 3.2 32.4 + - - +
381A G 3.0 33.6 + - - -
430A A 3.9 3.6 + - - -
431A G 2.5 45.7 + - - -
45N ARG* 2.9 48.0 + - + +
47N ASP* 1.3 86.1 - - - +
49N ALA* 1.3 56.8 + - - +
51N SER* 3.2 11.3 + - - -
52N LEU* 2.9 48.0 + - - +
117N SER 5.6 0.6 + - - -
118N TYR* 3.9 23.2 - - + +
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Residues in contact with ALA 49 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43N PRO* 3.8 24.9 - - + -
45N ARG 3.0 6.9 + - - +
46N LEU 3.7 6.5 - - - +
48N ARG* 1.3 73.1 - - - +
50N ARG* 1.3 62.2 + - - +
52N LEU* 2.8 19.9 + - - +
53N GLY 2.9 1.4 + - - -
54N TYR* 2.9 41.0 + - + +
118N TYR* 4.2 10.3 - - + -
132N ILE* 3.9 13.7 - - + -
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Residues in contact with ARG 50 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A C 5.4 0.3 + - - -
241A A 3.7 36.5 + - - +
242A A 3.2 29.4 + - - -
264A G 3.0 33.0 + - - -
265A U 2.6 38.6 + - - -
5N TYR* 3.4 25.6 + - - -
46N LEU* 3.1 40.0 + - + +
47N ASP* 4.0 2.5 - - - +
49N ALA* 1.3 77.4 - - - +
51N SER* 1.3 64.1 + - - +
53N GLY* 3.0 14.7 + - - -
54N TYR* 3.5 27.1 + - + +
55N LYS* 4.4 3.2 - - - +
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Residues in contact with SER 51 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A A 3.6 18.6 + - - -
379A G 2.9 69.0 + - - +
431A G 3.4 11.8 + - - +
47N ASP 2.9 20.4 + - - -
48N ARG* 3.4 11.0 + - - -
49N ALA 3.1 0.2 - - - -
50N ARG* 1.3 77.2 - - - +
52N LEU* 1.3 62.5 + - - +
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Residues in contact with LEU 52 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A G 3.1 51.0 + - - +
432A G 4.9 1.7 - - - +
48N ARG* 2.9 24.4 + - - +
49N ALA 2.8 9.4 + - - +
51N SER* 1.3 81.4 - - - +
53N GLY* 1.3 55.1 + - - +
54N TYR 3.8 0.2 - - - -
115N LEU* 2.9 21.2 - - - +
116N ASN* 3.3 40.7 + - + +
117N SER* 3.5 26.2 - - - +
118N TYR* 4.0 15.3 - - + -
132N ILE* 3.8 7.4 - - + -
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Residues in contact with GLY 53 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A C 5.4 7.6 - - - -
241A A 6.3 0.2 - - - -
49N ALA 2.9 0.6 + - - -
50N ARG 3.0 8.6 + - - -
52N LEU* 1.3 79.5 - - - +
54N TYR* 1.3 67.9 + - - +
55N LYS* 3.6 8.7 + - - +
60N ILE* 4.9 0.9 - - - +
115N LEU* 4.0 13.2 - - - +
132N ILE* 5.4 0.7 - - - -
134N ILE* 5.6 0.9 - - - +
147N LEU* 4.1 22.6 - - - +
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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