Contacts of the helix formed by residues 32 - 49 (chain B) in PDB entry 1TKD
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 CYS 32 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286A TYR* 4.0 3.5 - - - -
287A PRO* 5.1 0.9 - - - -
327A THR* 3.2 27.8 - - - +
29B ALA 3.3 6.5 + - - +
30B GLU 3.4 2.9 + - - +
31B TRP* 1.3 81.6 - - + +
33B GLY* 1.3 69.6 + - - +
34B PRO* 3.5 6.3 - - - -
35B CYS* 3.3 43.8 - - + +
36B LYS* 3.2 17.7 + - - +
75B ILE* 3.5 28.7 - - + -
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Residues in contact with GLY 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A PHE* 3.4 32.5 - - - -
286A TYR* 3.7 19.5 - - - -
287A PRO* 5.1 2.2 + - - +
289A ILE* 5.6 0.6 - - - +
327A THR* 4.3 1.4 + - - -
32B CYS* 1.3 69.3 - - - +
34B PRO* 1.3 72.2 - - - +
36B LYS* 3.0 17.9 + - - +
37B MET* 3.2 11.6 + - - +
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Residues in contact with PRO 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A PHE* 3.8 11.4 - - + -
289A ILE* 4.0 7.0 - - + -
325A PRO* 3.1 46.2 - - + +
326A TYR* 3.7 10.5 - - - +
327A THR* 3.5 7.4 - - - +
32B CYS* 3.5 8.7 - - - -
33B GLY* 1.3 88.3 - - - +
35B CYS* 1.3 60.7 + - - +
37B MET* 3.1 18.0 + - - +
38B ILE* 3.1 13.3 + - - +
76B PRO* 3.5 17.0 - - + -
93B ALA* 3.5 13.4 - - + +
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Residues in contact with CYS 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ASP* 5.6 0.3 - - - +
28B TRP* 3.6 35.2 - - + +
29B ALA 3.7 12.3 - - - +
32B CYS* 3.2 39.9 + - + +
33B GLY 3.2 0.8 - - - -
34B PRO* 1.3 78.7 - - - +
36B LYS* 1.3 62.6 + - - +
38B ILE* 3.6 5.3 - - - +
39B ALA* 3.3 22.2 + - - +
75B ILE* 3.9 3.4 - - - -
76B PRO* 3.5 33.7 - - - -
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Residues in contact with LYS 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A PHE* 6.5 1.1 - - + -
276A HIS* 5.1 13.1 - - - -
286A TYR* 4.0 22.5 + - + +
30B GLU* 5.8 3.8 - - - +
32B CYS 3.2 7.8 + - - +
33B GLY* 3.0 12.1 + - - +
35B CYS* 1.3 79.1 - - - +
37B MET* 1.3 61.8 + - + +
39B ALA* 3.7 7.1 - - + +
40B PRO* 3.3 18.4 - - - +
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Residues in contact with MET 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A PHE* 4.0 20.4 - - + -
277A PRO* 3.8 37.5 - - + -
325A PRO* 4.2 18.6 - - + -
33B GLY 3.2 10.9 + - - +
34B PRO* 3.1 15.1 + - - +
36B LYS* 1.3 78.1 - - + +
38B ILE* 1.3 58.8 + - - +
40B PRO* 3.1 19.1 - - - +
41B ILE* 3.8 10.4 - - - +
93B ALA* 4.3 13.2 - - + +
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Residues in contact with ILE 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ASP* 4.6 3.6 - - - +
34B PRO 3.1 10.7 + - - +
35B CYS* 3.6 11.0 - - - +
37B MET* 1.3 77.8 - - - +
39B ALA* 1.3 67.8 + - - +
40B PRO 3.4 0.4 - - - -
41B ILE* 3.1 17.3 + - + -
42B LEU* 3.0 40.4 + - + +
76B PRO* 4.2 17.7 - - + -
78B LEU* 3.7 36.6 - - + -
92B GLY 3.9 5.8 - - - +
93B ALA* 4.1 6.1 - - - -
94B LEU* 3.9 31.4 - - + +
99B LEU* 4.8 6.1 - - + -
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Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 5.3 0.2 - - - +
26B ASP* 5.7 0.4 - - - -
35B CYS 3.3 13.5 + - - +
36B LYS* 3.7 8.1 - - + +
37B MET 3.2 0.2 - - - -
38B ILE* 1.3 81.2 - - - +
40B PRO* 1.3 70.0 - - + +
42B LEU* 3.2 20.5 + - - +
43B ASP* 3.3 18.6 + - - +
57B LYS* 4.4 19.5 + - - +
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Residues in contact with PRO 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LYS 3.3 8.7 - - - +
37B MET 3.1 17.3 - - - +
39B ALA* 1.3 93.4 - - + +
41B ILE* 1.3 65.9 + - + +
43B ASP* 3.3 22.0 + - + +
44B GLU* 3.4 22.4 + - - +
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Residues in contact with ILE 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B MET 3.8 7.2 - - - +
38B ILE* 3.1 30.7 + - + +
40B PRO* 1.3 80.3 - - + +
42B LEU* 1.3 58.0 + - - +
44B GLU* 3.3 8.0 + - - +
45B ILE* 3.0 32.8 + - + +
94B LEU 4.5 6.7 - - - +
95B SER* 4.3 3.1 - - - -
96B LYS* 3.5 51.1 - - + +
99B LEU* 3.8 20.4 - - + -
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 3.9 13.3 - - + +
24B LEU* 4.5 16.4 - - + -
26B ASP* 3.1 39.5 - - + +
38B ILE* 3.0 33.1 + - + +
39B ALA* 3.5 10.1 - - - +
40B PRO 3.2 0.2 - - - -
41B ILE* 1.3 74.1 - - - +
43B ASP* 1.3 59.1 + - - +
45B ILE* 3.7 4.5 - - + +
46B ALA* 2.8 31.2 + - - +
55B VAL* 4.4 12.1 - - + +
57B LYS* 4.1 11.7 - - + -
78B LEU* 4.6 8.3 - - + -
99B LEU* 3.9 22.4 - - + -
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Residues in contact with ASP 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 3.2 23.5 - - - +
39B ALA* 3.3 15.4 + - - +
40B PRO* 3.6 14.1 - - - +
41B ILE 3.3 0.2 - - - -
42B LEU* 1.3 78.8 - - - +
44B GLU* 1.3 57.1 + - + +
46B ALA* 3.5 6.2 - - - +
47B ASP* 2.7 28.8 - - - +
57B LYS* 5.7 1.9 + - - -
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Residues in contact with GLU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B PRO* 3.4 15.5 + - - +
41B ILE* 3.3 9.5 + - - +
42B LEU 3.2 0.4 - - - -
43B ASP* 1.3 77.4 - - + +
45B ILE* 1.3 64.9 + - - +
47B ASP* 3.1 17.4 + - - +
48B GLU* 3.2 21.0 + - - +
96B LYS* 2.7 41.8 + - - +
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Residues in contact with ILE 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LEU* 5.2 1.8 - - + -
41B ILE* 3.0 22.6 + - + +
42B LEU* 3.7 7.4 - - + +
44B GLU* 1.3 76.2 - - - +
46B ALA* 1.3 65.2 + - - +
48B GLU* 4.7 2.2 - - - +
49B TYR* 3.0 36.7 + - + +
53B LEU* 4.5 0.9 - - + -
55B VAL* 4.3 14.1 - - + -
96B LYS* 4.0 20.0 - - + +
99B LEU* 3.5 28.5 - - + -
100B LYS* 3.9 28.0 - - + -
103B LEU* 3.4 27.8 - - + -
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Residues in contact with ALA 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B LYS* 3.6 26.8 - - + +
4B ILE* 3.6 25.1 - - + +
42B LEU 2.8 17.4 + - - +
43B ASP 3.5 7.0 - - - +
45B ILE* 1.3 77.7 - - - +
47B ASP* 1.3 67.0 + - - +
49B TYR* 4.0 1.1 - - - -
50B GLN* 3.3 12.0 + - - -
53B LEU 4.7 4.4 - - - +
55B VAL* 3.9 17.9 - - + +
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Residues in contact with ASP 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B LYS* 3.7 27.0 + - - +
43B ASP 2.7 25.4 - - - +
44B GLU* 3.1 9.3 + - - +
46B ALA* 1.3 73.8 - - - +
48B GLU* 1.3 59.6 + - + +
50B GLN* 2.6 38.0 + - - +
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Residues in contact with GLU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B GLU* 3.2 13.1 + - - +
45B ILE* 4.1 1.1 - - - +
47B ASP* 1.3 80.4 - - + +
49B TYR* 1.3 76.2 + - + +
50B GLN 3.2 5.4 + - - +
52B LYS* 5.2 3.3 - - - -
96B LYS* 3.1 34.8 + - - -
100B LYS* 4.1 20.3 - - - +
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Residues in contact with TYR 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ILE* 3.0 27.1 + - + +
46B ALA* 4.0 2.9 - - - -
48B GLU* 1.3 89.5 - - + +
50B GLN* 1.3 64.1 + - - +
52B LYS* 3.1 25.5 + - + +
53B LEU* 3.0 41.0 + - + +
100B LYS* 3.4 31.2 - - + +
103B LEU* 3.7 31.2 - - + -
104B ASP* 2.8 40.8 + - - -
107B LEU* 3.9 22.7 - - + -
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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