Contacts of the helix formed by residues 19 - 27 (chain A) in PDB entry 2K1N
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 PRO 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ILE* 5.6 8.5 - - + -
8A ARG* 3.4 21.9 - - - +
18A ILE* 1.3 87.3 - - + +
20A ILE* 1.3 65.5 + - - +
21A GLU* 3.7 26.5 - - + +
22A LEU* 3.8 15.2 - - + +
23A ARG* 3.0 24.6 + - - +
36B ILE* 3.7 43.3 - - + -
38B VAL* 6.0 0.4 - - + -
43B ILE* 5.0 1.8 - - + -
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Residues in contact with ILE 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG* 4.1 11.7 - - - +
18A ILE 4.5 1.8 - - - +
19A PRO* 1.3 72.1 - - - +
21A GLU* 1.3 67.4 + - - +
23A ARG* 3.2 10.9 + - - +
24A ARG* 3.1 52.6 + - - +
21D GLU* 4.1 1.1 - - - -
24D ARG* 4.2 11.7 - - - +
15F T 3.2 51.6 - - - +
16F T 3.4 28.3 - - - +
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Residues in contact with GLU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ILE* 4.8 18.5 - - + +
8A ARG* 4.5 5.1 + - - -
19A PRO* 3.6 19.3 - - + +
20A ILE* 1.3 85.6 + - - +
22A LEU* 1.3 61.7 + - + +
25A THR* 2.6 37.9 + - - +
2D LYS* 5.9 2.5 - - - +
21D GLU* 3.4 22.9 - - + +
24D ARG* 2.8 37.6 + - - +
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ILE* 6.3 0.2 - - + -
19A PRO* 3.3 20.5 + - + +
21A GLU* 1.3 81.0 - - + +
23A ARG* 1.3 60.7 + - - +
25A THR* 4.1 10.1 - - + -
26A LEU* 2.8 57.3 + - + +
28A ILE* 4.0 9.1 - - + +
38B VAL* 4.1 36.8 - - + -
43B ILE* 3.9 37.0 - - + -
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Residues in contact with ARG 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ILE* 3.5 47.1 + - + +
19A PRO 3.0 12.9 + - - +
20A ILE* 3.3 14.6 - - - +
22A LEU* 1.3 78.5 - - - +
24A ARG* 1.3 59.0 + - + +
27A GLY* 2.9 6.4 + - - -
28A ILE* 2.9 41.8 + - + +
30A GLU* 2.7 32.7 + - - +
13B LEU 4.0 2.6 + - - -
14B GLY* 3.0 40.0 + - - -
15F T 2.8 53.2 + - - +
16F T 4.6 2.8 + - - -
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Residues in contact with ARG 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ILE* 3.1 37.1 + - - +
23A ARG* 1.3 79.8 - - + +
25A THR* 1.3 66.4 - - - +
26A LEU 3.4 0.2 - - - -
27A GLY* 3.6 7.7 + - - +
1D MET 5.2 9.2 + - - +
20D ILE* 3.4 41.5 - - - +
21D GLU* 2.6 47.5 + - - +
24D ARG* 4.3 1.2 - - - +
14F A 3.6 28.8 + - - -
15F T 3.8 8.7 + - - +
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Residues in contact with THR 25 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A GLU 2.6 28.2 + - - -
22A LEU* 3.9 11.7 - - + -
24A ARG* 1.3 79.8 - - - +
26A LEU* 1.3 60.7 + - - +
53C THR* 5.4 7.6 - - - +
1D MET 6.1 1.3 - - - +
2D LYS* 3.4 47.4 - - + +
21D GLU* 3.9 4.5 - - - +
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Residues in contact with LEU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LEU* 2.8 41.2 + - + +
25A THR* 1.3 76.8 - - + +
27A GLY* 1.3 65.5 + - - +
28A ILE* 3.8 22.7 - - + -
47A LYS* 6.2 3.1 - - + -
50A PRO* 5.6 14.6 - - + +
53A THR* 6.4 1.6 - - - -
54A CYS* 4.6 17.2 - - + -
38B VAL* 6.3 0.4 - - + -
40B ASP 4.9 12.1 - - - +
41B GLU* 5.2 11.9 - - + +
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Residues in contact with GLY 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ARG 2.9 11.0 + - - -
24A ARG* 3.6 7.6 + - - -
25A THR 3.4 2.2 - - - -
26A LEU* 1.3 83.8 - - - +
28A ILE* 1.3 63.6 + - - +
29A ALA* 3.5 4.1 + - - +
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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