Contacts of the helix formed by residues 34 - 49 (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 GLN 34 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TYR* 2.7 29.0 + - + +
32A HIS* 4.3 10.5 - - + +
33A GLU* 1.3 78.7 - - - +
35A PHE* 1.3 63.9 + - - +
36A ASP* 3.0 13.1 + - - +
37A ALA* 2.9 37.6 + - + +
38A ALA* 3.0 10.4 + - - +
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Residues in contact with PHE 35 (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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30A ALA* 3.3 41.1 - - + -
33A GLU* 3.1 38.9 + - + -
34A GLN* 1.3 76.5 - - - +
36A ASP* 1.3 62.6 + - - +
38A ALA* 3.4 8.3 - - + +
39A LEU* 2.9 29.7 + - - +
61A LYS* 3.5 34.3 - - + -
62A THR* 3.3 37.8 - - + +
65A GLY* 3.5 31.0 - - - -
66A GLN* 4.2 7.2 - - + +
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Residues in contact with ASP 36 (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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34A GLN* 3.0 12.8 + - - +
35A PHE* 1.3 80.0 - - - +
37A ALA* 1.3 59.7 + - - +
39A LEU* 3.5 13.0 + - - +
40A PRO* 3.2 20.8 - - - +
66A GLN* 4.5 19.6 + - + +
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Residues in contact with ALA 37 (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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29A TYR* 4.2 19.6 - - + -
34A GLN* 2.9 31.7 + - + +
36A ASP* 1.3 80.5 - - - +
38A ALA* 1.3 66.3 + - - +
40A PRO* 3.2 19.7 - - - +
41A HIS* 3.9 9.0 + - - +
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Residues in contact with ALA 38 (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* 4.3 2.5 - - - +
29A TYR* 3.7 23.7 - - + +
30A ALA* 4.2 9.9 - - + +
34A GLN 3.0 12.0 + - - +
35A PHE* 3.2 16.4 + - - +
37A ALA* 1.3 77.3 - - - +
39A LEU* 1.3 55.7 + - - +
41A HIS* 3.1 2.3 + - - -
42A LEU* 2.7 56.9 + - + +
62A THR* 4.6 2.0 - - + -
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Residues in contact with LEU 39 (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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35A PHE 2.9 18.7 + - - +
36A ASP* 3.6 9.6 - - - +
38A ALA* 1.3 75.1 - - - +
40A PRO* 1.4 64.4 - - + +
42A LEU* 3.9 3.5 - - - +
43A ARG* 2.9 32.6 + - - +
59A LEU* 4.5 11.1 - - + +
62A THR* 3.5 22.4 - - + -
63A LEU* 4.4 17.9 - - + -
66A GLN* 3.6 35.4 - - - +
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Residues in contact with PRO 40 (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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36A ASP 3.2 16.4 - - - +
37A ALA* 3.2 18.4 - - - +
39A LEU* 1.4 93.0 - - + +
41A HIS* 1.3 55.2 + - - +
43A ARG* 3.5 8.6 + - + +
44A ALA* 3.0 28.4 + - - +
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Residues in contact with HIS 41 (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* 2.8 34.6 + - + +
25A LEU* 3.3 33.3 - - + +
26A GLY* 3.6 17.0 - - - -
29A TYR* 3.9 20.1 + + + -
37A ALA 4.0 9.6 - - - +
38A ALA 3.1 7.7 + - - +
40A PRO* 1.3 79.4 - - + +
42A LEU* 1.3 65.0 + - + +
44A ALA* 3.4 7.8 + - + +
45A ALA* 3.3 17.7 + - - +
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Residues in contact with LEU 42 (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* 4.8 19.3 - - + +
26A GLY* 3.8 29.8 - - - +
27A LYS* 4.6 1.1 - - - +
30A ALA* 5.2 2.7 - - + -
38A ALA* 2.7 38.5 + - + +
39A LEU* 4.1 2.9 - - - +
41A HIS* 1.3 71.0 - - + +
43A ARG* 1.3 59.6 + - - +
45A ALA* 3.2 9.1 + - + +
46A LEU* 2.9 35.3 + - + +
55A ALA* 5.7 4.0 - - + -
58A TRP* 4.7 12.8 - - + -
59A LEU* 3.9 28.0 - - + -
62A THR* 3.7 23.8 - - + +
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Residues in contact with ARG 43 (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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39A LEU 2.9 19.8 + - - +
40A PRO* 3.7 8.1 - - - +
42A LEU* 1.3 78.3 - - - +
44A ALA* 1.3 61.4 + - - +
46A LEU* 3.3 13.3 + - + +
47A ASP* 3.1 22.3 + - - +
59A LEU* 5.9 1.5 - - + +
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Residues in contact with ALA 44 (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* 5.5 3.4 - - - +
40A PRO 3.0 18.1 + - - +
41A HIS* 3.5 9.6 - - - +
42A LEU 3.2 0.2 - - - -
43A ARG* 1.3 74.9 - - - +
45A ALA* 1.3 59.4 + - - +
47A ASP* 3.4 11.3 + - - +
48A PHE* 3.0 33.0 - - + -
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Residues in contact with ALA 45 (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* 3.9 39.7 - - + +
23A PHE* 5.0 5.2 - - + +
41A HIS 3.3 9.0 + - - +
42A LEU* 3.2 14.2 + - + +
44A ALA* 1.3 80.0 - - - +
46A LEU* 1.3 54.5 + - + +
48A PHE* 3.0 3.5 + - - -
49A ASP* 2.8 45.5 + - - +
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Residues in contact with LEU 46 (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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42A LEU* 2.9 21.7 + - + +
43A ARG* 3.3 10.1 + - + +
45A ALA* 1.3 76.1 - - + +
47A ASP* 1.3 61.0 + - - +
49A ASP 3.9 7.4 - - - +
50A PRO* 3.1 43.0 - - + +
55A ALA* 4.0 27.4 - - + -
56A TRP* 4.5 13.7 - - + -
59A LEU* 3.8 32.5 - - + -
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Residues in contact with ASP 47 (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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43A ARG 3.1 12.1 + - - +
44A ALA* 3.4 13.5 - - - +
45A ALA 3.1 0.6 - - - -
46A LEU* 1.3 79.4 - - - +
48A PHE* 1.3 73.6 - - + +
50A PRO* 4.6 3.3 - - - +
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Residues in contact with PHE 48 (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* 3.9 41.7 - - - +
44A ALA* 3.0 29.2 - - + -
45A ALA 3.0 4.1 + - - +
47A ASP* 1.3 94.4 - - + +
49A ASP* 1.3 71.7 + - - +
50A PRO* 3.8 5.0 - - - +
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Residues in contact with ASP 49 (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* 3.4 51.1 - - + +
22A ARG* 4.0 11.5 + - - -
23A PHE* 6.1 1.0 - - - +
45A ALA* 2.8 27.2 + - - +
46A LEU* 3.7 8.1 - - - +
48A PHE* 1.3 87.3 - - - +
50A PRO* 1.3 62.9 - - - +
51A THR* 3.2 10.5 + - - +
52A TYR* 3.9 13.7 + - - +
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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