Contacts of the helix formed by residues 18 - 32 (chain A) in PDB entry 2KAT
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 ASN 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A LEU* 5.5 0.2 - - - +
16A THR* 3.1 31.1 + - - +
17A ASP* 1.3 82.5 + - - +
19A MET* 1.3 66.0 + - - +
20A LEU 3.6 1.1 - - - +
21A LEU* 3.5 30.0 + - + +
22A ARG* 3.2 27.9 + - - +
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Residues in contact with MET 19 (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 ASN* 1.3 71.1 - - - +
20A LEU* 1.3 78.0 + - + +
22A ARG* 3.0 35.0 + - - +
23A PHE* 3.5 4.4 + - + +
49A ASP* 3.4 46.6 - - + +
51A THR* 5.2 4.3 - - - +
52A TYR* 3.7 36.6 - - + +
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Residues in contact with LEU 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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18A ASN* 4.6 1.4 - - - +
19A MET* 1.3 100.5 - - + +
21A LEU* 1.3 62.6 + - + +
23A PHE* 3.0 12.9 + - + +
24A THR* 2.9 38.4 + - - +
52A TYR* 3.7 38.8 - - + +
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Residues in contact with LEU 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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8A LEU* 5.0 6.9 - - + +
11A MET* 3.7 35.0 - - + -
12A LEU* 3.8 28.3 - - + -
16A THR* 3.2 27.6 - - + +
18A ASN* 3.5 31.6 - - + +
19A MET 3.1 0.6 - - - -
20A LEU* 1.3 83.8 - - + +
22A ARG* 1.3 61.2 + - + +
24A THR* 4.5 4.8 - - - -
25A LEU* 3.3 32.0 + - - +
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Residues in contact with ARG 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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17A ASP* 4.1 31.3 + - - +
18A ASN 3.2 20.6 + - - +
19A MET* 3.0 9.3 + - - +
21A LEU* 1.3 77.8 - - + +
23A PHE* 1.3 61.6 + - - +
25A LEU* 5.1 0.9 - - - -
26A GLY* 3.4 1.9 + - - -
41A HIS* 2.8 36.3 + - - +
42A LEU* 5.4 0.3 - - - +
44A ALA* 5.2 3.2 + - - +
45A ALA* 3.9 29.2 - - + +
48A PHE* 3.9 44.5 - - - +
49A ASP* 4.0 19.7 + - - -
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Residues in contact with PHE 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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19A MET* 3.5 2.6 + - + +
20A LEU* 3.0 18.5 + - + +
22A ARG* 1.3 78.4 - - - +
24A THR* 1.3 72.8 + - - +
26A GLY* 2.9 5.2 + - - -
27A LYS* 2.9 47.5 + - + +
42A LEU* 5.0 11.0 - - + -
45A ALA* 5.3 6.5 - - + -
52A TYR* 3.6 42.6 - + + -
54A VAL* 3.5 12.8 - - + -
55A ALA* 3.8 19.1 - - + -
58A TRP* 3.3 40.8 - + + -
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Residues in contact with THR 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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4A ILE* 4.3 13.5 - - + -
8A LEU* 4.1 22.7 - - + -
20A LEU* 2.9 21.3 + - - +
21A LEU* 4.5 3.3 - - - -
23A PHE* 1.3 82.8 - - - +
25A LEU* 1.3 61.3 + - - +
27A LYS* 3.3 19.1 + - + +
28A THR* 3.2 18.7 + - - +
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Residues in contact with LEU 25 (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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4A ILE* 5.8 0.2 - - + -
5A THR* 3.7 32.6 - - + +
8A LEU* 3.5 28.9 - - + -
9A GLU* 4.6 11.9 - - - +
12A LEU* 4.4 25.1 - - + -
21A LEU 3.3 20.1 + - - +
22A ARG* 5.1 0.4 - - - -
23A PHE 3.2 0.6 - - - -
24A THR* 1.3 77.1 - - - +
26A GLY* 1.3 62.3 + - - +
28A THR* 3.5 15.0 + - - -
29A TYR* 3.2 20.6 - - + -
41A HIS* 3.3 28.9 - - + +
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Residues in contact with GLY 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 ARG 3.4 4.4 + - - -
23A PHE 2.9 7.8 + - - -
25A LEU* 1.3 78.0 - - - +
27A LYS* 1.3 65.0 + - - +
29A TYR* 3.2 19.2 + - - +
30A ALA* 3.2 12.3 + - - +
38A ALA* 4.3 4.4 - - - +
41A HIS* 3.6 18.8 + - - -
42A LEU* 3.8 19.8 - - - +
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Residues in contact with LYS 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 PHE* 2.9 40.3 + - + +
24A THR* 3.3 16.5 + - + +
26A GLY* 1.3 77.4 - - - +
28A THR* 1.3 57.3 + - - +
30A ALA* 3.0 8.1 + - - +
31A GLU* 2.8 49.1 + - + +
42A LEU* 4.6 1.5 - - - +
54A VAL* 5.6 1.7 - - - +
58A TRP* 3.6 38.8 - - + +
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Residues in contact with THR 28 (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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4A ILE* 4.6 16.0 - - + +
5A THR* 4.0 27.8 - - + +
24A THR* 3.2 13.9 + - - +
25A LEU* 3.7 9.0 + - - -
26A GLY 3.2 0.4 - - - -
27A LYS* 1.3 78.8 - - - +
29A TYR* 1.3 62.6 - - + +
31A GLU* 3.5 10.0 + - - +
32A HIS* 3.1 49.5 + - + +
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Residues in contact with TYR 29 (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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5A THR* 5.0 15.3 - - + +
25A LEU* 3.2 24.9 + - + -
26A GLY* 3.2 13.7 + - - +
28A THR* 1.3 78.5 - - + +
30A ALA* 1.3 57.4 + - - +
32A HIS* 3.2 8.4 + - - -
34A GLN* 2.7 49.7 + - + +
37A ALA* 4.2 19.3 - - + -
38A ALA* 3.7 24.5 - - + -
41A HIS* 3.9 24.9 + + + -
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Residues in contact with ALA 30 (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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26A GLY 3.2 8.6 + - - +
27A LYS* 3.0 9.2 + - - +
29A TYR* 1.3 76.6 - - - +
31A GLU* 1.3 65.2 + - - +
33A GLU* 3.1 9.5 + - - +
35A PHE* 3.3 40.6 - - + -
38A ALA* 4.2 7.2 - - + +
42A LEU* 5.2 1.8 - - + -
58A TRP* 3.7 32.2 - - + -
61A LYS* 5.5 0.7 + - - -
62A THR* 5.1 4.0 - - - +
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Residues in contact with GLU 31 (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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27A LYS* 2.8 42.3 + - + +
28A THR* 3.9 9.2 + - - +
30A ALA* 1.3 71.8 - - - +
32A HIS* 1.3 63.8 + - + +
33A GLU* 3.1 15.0 + - - +
58A TRP* 3.9 22.1 - - + -
61A LYS* 6.1 0.4 - - - +
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Residues in contact with HIS 32 (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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28A THR* 3.1 38.7 + - + +
29A TYR* 3.2 7.6 + - - +
30A ALA 3.2 0.4 - - - -
31A GLU* 1.3 83.2 - - + +
33A GLU* 1.3 70.8 + - - +
34A GLN* 3.1 9.9 + - + +
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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