Contacts of the helix formed by residues 30 - 42 (chain F) 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 TYR 30 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23F LYS* 3.4 40.2 - - + -
24F GLY* 4.0 3.6 - - - -
25F ASN* 3.0 21.3 + - - +
28F ALA* 3.7 11.9 - - + -
29F VAL* 1.3 76.8 - - - +
31F ARG* 1.3 68.3 + - - +
32F ASP* 3.3 11.0 - - - +
33F ASP* 3.0 24.3 + - - +
34F LEU* 2.8 20.4 + - - +
55F PHE* 3.8 1.3 - - - -
64F GLY 3.5 19.1 - - - +
65F ALA* 4.0 7.2 - - + -
2006F CL 4.2 16.5 - - + +
2512F CA 3.5 7.0 - - - -
68G THR 2.6 29.6 + - - -
69G ASN* 4.4 5.5 - - + -
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Residues in contact with ARG 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F TYR* 1.3 75.0 - - - +
32F ASP* 1.3 64.1 + - - +
34F LEU* 3.2 12.0 + - - +
35F LYS* 3.2 12.1 + - - +
51F ALA* 5.3 4.6 - - + +
52F ASP* 3.6 31.4 + - - +
55F PHE* 3.4 57.2 - - + +
56F LYS* 5.7 1.6 - - - +
64F GLY* 4.7 2.4 + - - -
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Residues in contact with ASP 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F LYS* 2.8 37.2 + - - -
30F TYR* 3.8 8.5 - - - +
31F ARG* 1.3 77.2 + - - +
33F ASP* 1.3 63.6 + - - -
35F LYS* 3.3 13.2 + - + +
36F LYS* 3.3 32.7 + - - +
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Residues in contact with ASP 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F TYR* 3.9 24.5 - - + +
22F ILE* 3.6 23.2 - - + +
23F LYS* 2.9 26.8 + - - +
28F ALA 4.4 0.9 - - - +
29F VAL* 3.7 15.2 - - + +
30F TYR* 3.0 39.4 + - - +
32F ASP* 1.3 78.6 + - - +
34F LEU* 1.3 57.0 + - - +
36F LYS* 3.4 10.0 + - - +
37F LEU* 3.0 26.0 + - - +
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Residues in contact with LEU 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F VAL* 3.7 13.9 - - + +
30F TYR 2.8 11.3 + - - +
31F ARG 3.2 9.4 + - - +
33F ASP* 1.3 72.3 - - - +
35F LYS* 1.3 61.9 + - - +
37F LEU* 3.1 21.0 + - + +
38F LEU* 2.8 48.3 + - + +
51F ALA* 4.0 7.2 - - + +
54F TRP* 4.1 4.9 - - + -
55F PHE* 3.6 47.3 - - + +
58F LEU* 4.1 21.1 - - + -
66F VAL* 4.7 8.3 - - + -
71F PHE* 5.7 1.1 - - + -
74F LEU* 4.7 4.7 - - + -
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Residues in contact with LYS 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F ARG 3.2 9.0 + - - +
32F ASP* 3.5 14.4 - - + +
34F LEU* 1.3 80.2 - - - +
36F LYS* 1.3 57.3 - - + +
38F LEU* 3.4 2.4 + - - +
39F GLU* 2.9 57.6 + - + +
51F ALA* 3.9 29.8 - - + +
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Residues in contact with LYS 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F TYR* 3.9 11.4 - - + -
22F ILE* 4.5 19.1 - - + -
32F ASP* 3.3 18.4 + - - +
33F ASP* 3.6 10.1 - - - +
34F LEU 3.2 0.4 - - - -
35F LYS* 1.3 76.0 - - + +
37F LEU* 1.3 59.5 + - - +
39F GLU* 3.5 9.0 + - - +
40F THR* 2.9 37.8 + - - +
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Residues in contact with LEU 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F VAL* 5.0 2.5 - - + +
16F TYR* 5.2 3.6 - - + -
19F TYR* 3.6 43.6 - - + -
29F VAL* 4.9 8.1 - - + -
33F ASP 3.0 14.4 + - - +
34F LEU* 3.1 19.7 + - + +
36F LYS* 1.3 76.7 - - - +
38F LEU* 1.3 59.2 + - + +
41F GLU* 2.7 52.0 + - + +
42F SER* 5.6 1.3 - - - -
71F PHE* 3.7 31.0 - - + -
74F LEU* 3.9 24.7 - - + -
8H LEU* 4.9 2.7 - - + -
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Residues in contact with LEU 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F LEU* 2.8 33.6 + - + +
35F LYS 3.9 3.1 - - - +
37F LEU* 1.3 76.1 - - + +
39F GLU* 1.3 61.6 + - + +
42F SER* 2.9 39.9 + - - +
46F ILE* 4.2 3.8 - - + +
47F ARG* 3.2 17.0 - - + +
50F GLY 4.9 0.2 - - - -
51F ALA* 3.8 32.8 - - + +
54F TRP* 3.9 35.7 - - + -
74F LEU* 3.9 30.7 - - + -
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Residues in contact with GLU 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F LYS* 2.9 57.4 + - + +
36F LYS* 3.8 9.6 - - - +
38F LEU* 1.3 77.6 - - + +
40F THR* 1.3 61.5 + - - +
42F SER 4.7 0.7 - - - +
47F ARG* 3.6 24.6 + - - +
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Residues in contact with THR 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F LYS* 5.7 1.6 - - - +
19F TYR* 3.1 29.3 + - - +
36F LYS* 2.9 16.2 + - - +
39F GLU* 1.3 79.6 - - - +
41F GLU* 1.3 65.0 + - - +
42F SER 5.3 0.2 - - - -
6H SER* 3.5 14.0 - - - -
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Residues in contact with GLU 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F VAL* 3.8 15.0 - - + -
18F LYS* 2.9 27.8 + - - -
19F TYR* 2.9 32.5 + - + +
37F LEU* 2.7 32.7 + - + +
40F THR* 1.3 81.5 - - - +
42F SER* 1.3 57.6 + - - +
78F MET* 4.1 2.5 - - - +
6H SER* 2.7 28.0 + - - -
7H GLN* 3.7 4.0 + - - +
8H LEU* 3.3 39.9 + - + +
9H GLU* 3.5 9.6 - - - +
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Residues in contact with SER 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F LEU* 5.6 0.9 - - - -
38F LEU* 2.9 29.2 + - - -
39F GLU 4.7 1.0 - - - +
40F THR 3.8 0.4 - - - -
41F GLU* 1.3 80.0 - - - +
43F PRO* 1.3 70.2 + - - +
46F ILE* 3.5 22.9 - - - +
47F ARG* 2.8 40.7 + - - +
78F MET* 4.0 12.8 - - - -
9H GLU* 3.6 3.1 - - - -
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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