Contacts of the helix formed by residues 33 - 45 (chain H) in PDB entry 1XK4
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 33 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26H LEU* 4.2 25.3 + - - +
27H GLY* 4.9 3.8 - - - +
31H THR* 3.9 1.2 + - - +
32H LEU* 1.3 75.7 - - - +
34H GLN* 1.3 65.9 + - - +
35H GLY* 3.3 4.8 + - - -
36H GLU* 2.9 47.1 + - - +
37H PHE* 3.0 21.0 + - - +
63H MET* 3.8 2.7 - - - -
72H LYS 4.2 10.5 - - - +
73H GLN* 4.6 7.0 - - + +
4512H CA 4.4 0.4 - - - -
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Residues in contact with GLN 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H ASN* 1.3 76.4 - - - +
35H GLY* 1.3 58.7 + - - +
37H PHE* 3.4 2.0 + - + +
38H LYS* 3.0 67.9 + - + +
60H GLU* 3.6 24.5 + - + +
63H MET* 3.6 27.9 - - + +
64H GLU* 5.3 5.9 + - - +
72H LYS 4.3 3.5 + - - +
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Residues in contact with GLY 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H ASN* 3.3 6.0 + - - -
34H GLN* 1.3 78.0 - - - +
36H GLU* 1.3 58.1 + - - +
38H LYS* 3.4 11.1 + - - +
39H GLU* 3.0 30.1 + - - +
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Residues in contact with GLU 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H TYR* 3.1 31.5 - - + +
25H LYS* 3.8 9.9 - - + +
26H LEU* 3.0 40.9 + - + +
31H THR 3.4 3.1 - - - +
32H LEU* 3.6 13.4 - - + -
33H ASN* 2.9 36.0 + - - +
35H GLY* 1.3 74.8 - - - +
37H PHE* 1.3 64.0 + - - +
39H GLU* 3.3 8.6 + - - +
40H LEU* 3.0 24.4 + - - +
4512H CA 2.6 22.0 - - - -
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Residues in contact with PHE 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H LEU* 4.1 23.6 - - + +
33H ASN 3.0 16.9 + - - +
34H GLN* 3.7 3.4 - - + +
36H GLU* 1.3 75.0 - - - +
38H LYS* 1.3 60.7 + - + +
40H LEU* 3.3 4.0 + - + +
41H VAL* 2.9 54.3 + - + +
59H ILE* 3.8 28.5 - - + -
62H ILE* 4.0 15.0 - - + -
63H MET* 3.7 36.8 - - + -
66H LEU* 4.2 4.9 - - + -
74H LEU* 3.6 24.7 - - + -
79H PHE* 4.5 7.0 - + - -
82H LEU* 3.9 24.5 - - + -
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Residues in contact with LYS 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H GLN* 3.0 41.7 + - + +
35H GLY* 3.6 10.1 - - - +
37H PHE* 1.3 78.0 - - + +
39H GLU* 1.3 56.7 + - - +
41H VAL* 3.4 1.4 + - - +
42H ARG* 2.9 32.4 + - - +
53H ASN* 5.0 0.5 - - - +
56H GLU* 2.6 38.8 + - + +
59H ILE* 4.1 21.9 - - + +
60H GLU* 2.7 44.4 + - - +
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Residues in contact with GLU 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H TYR* 3.5 25.0 - - + -
25H LYS* 3.5 19.5 - - - +
35H GLY 3.0 17.5 + - - +
36H GLU* 3.6 8.3 - - - +
37H PHE 3.3 0.2 - - - -
38H LYS* 1.3 72.3 - - - +
40H LEU* 1.3 67.5 + - - +
42H ARG* 3.4 16.4 + - - +
43H LYS* 3.0 41.8 + - - +
7J LYS* 3.5 19.8 + - - +
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Residues in contact with LEU 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F LEU* 4.2 10.1 - - + -
18H THR* 4.1 17.3 - - + +
19H PHE* 4.3 4.0 - - - -
22H TYR* 3.7 36.4 - - + -
32H LEU* 4.2 12.1 - - + -
36H GLU 3.0 16.6 + - - +
37H PHE* 3.7 5.4 - - + +
39H GLU* 1.3 77.0 - - - +
41H VAL* 1.3 63.6 + - + +
44H ASP* 2.7 33.6 + - - +
45H LEU* 4.1 21.3 - - + -
79H PHE* 3.9 35.4 - - + -
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Residues in contact with VAL 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H PHE* 2.9 55.0 + - + +
38H LYS 3.9 3.4 - - - +
40H LEU* 1.3 80.4 - - + +
42H ARG* 1.3 61.8 + - - +
45H LEU* 3.3 31.1 + - + -
49H LEU* 3.6 27.4 - - + -
53H ASN* 3.2 31.0 + - - +
59H ILE* 3.9 18.8 - - + -
82H LEU* 4.9 0.2 - - + -
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Residues in contact with ARG 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H LYS 2.9 19.4 + - - +
39H GLU* 3.8 14.8 + - - +
41H VAL* 1.3 77.1 - - - +
43H LYS* 1.3 73.6 + - - +
46H GLN* 3.3 22.5 - - - +
53H ASN* 3.4 18.1 + - + +
1J MET* 2.8 53.1 - - + +
2J LEU 5.7 0.2 + - - -
7J LYS* 5.5 1.8 - - - +
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Residues in contact with LYS 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F THR* 3.6 4.2 - - - +
2008F FLC 3.7 20.7 - - - +
22H TYR* 3.6 13.0 - - - +
39H GLU* 3.0 26.8 + - - +
42H ARG* 1.3 90.0 - - + +
44H ASP* 1.3 64.7 + - - +
45H LEU 3.4 0.7 - - - -
46H GLN* 2.9 31.4 + - - +
1J MET* 3.7 21.5 - - + -
2J LEU 2.9 29.1 + - - +
3J THR* 3.9 2.9 - - - -
4J GLU* 2.5 31.3 + - - +
7J LYS* 2.9 24.5 - - - +
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Residues in contact with ASP 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F THR* 2.6 27.5 + - - +
5F LEU* 3.7 25.3 - - + +
6F GLU* 3.6 5.4 - - - +
2008F FLC 2.7 38.0 + - - +
18H THR* 3.8 15.5 - - + +
22H TYR* 2.6 40.4 + - - -
40H LEU* 2.7 19.6 + - + +
43H LYS* 1.3 72.4 - - - +
45H LEU* 1.3 61.7 + - - +
46H GLN 3.5 1.1 - - - -
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Residues in contact with LEU 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F LEU* 3.4 24.0 - - + -
6F GLU* 3.2 21.1 - - + -
9F LEU* 4.4 8.7 - - + -
40H LEU* 3.5 17.4 + - + -
41H VAL* 3.3 23.8 + - + +
44H ASP* 1.3 80.3 - - - +
46H GLN* 1.3 64.7 + - - +
47H ASN 3.1 3.1 - - - -
48H PHE* 4.4 3.6 - - + -
49H LEU* 3.0 40.8 + - + +
53H ASN* 3.5 6.9 + - - -
82H LEU* 4.4 2.7 - - + -
83H MET* 4.1 13.0 - - + -
86H LEU* 3.7 32.5 - - + -
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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