Contacts of the helix formed by residues 22 - 32 (chain A) in PDB entry 5LXR
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 THR 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A LYS 3.4 15.4 + - - +
21A VAL* 1.3 76.2 - - - +
23A GLU* 1.3 64.3 + - - +
24A GLU* 3.6 11.1 + - - +
25A LEU* 3.1 25.6 + - - +
26A LEU* 3.1 26.0 + - - +
41A ILE* 3.8 6.5 - - - -
105A BR 3.7 17.3 - - + -
294B GLU* 4.7 8.8 + - - +
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Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A THR* 1.3 73.1 - - - +
24A GLU* 1.3 57.0 + - - +
26A LEU* 3.4 1.2 + - - +
27A PHE* 2.8 32.2 + - - +
39A VAL* 3.2 37.5 - - + +
40A LYS* 3.2 6.9 - - - +
41A ILE* 2.7 41.3 + - + +
105A BR 3.2 13.1 - - + +
107A CL 2.8 29.7 - - - +
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Residues in contact with GLU 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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22A THR* 3.2 9.8 + - - +
23A GLU* 1.3 79.0 - - - +
25A LEU* 1.3 62.6 + - - +
27A PHE* 3.2 8.1 + - - +
28A GLU* 3.1 23.4 + - + +
103A SM 2.5 31.3 - - - -
294B GLU* 4.3 17.5 - - - +
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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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20A LYS 5.1 1.1 - - - +
21A VAL* 4.4 16.4 - - + -
22A THR* 3.1 20.0 + - - +
24A GLU* 1.3 79.0 - - - +
26A LEU* 1.3 62.1 + - - +
28A GLU* 3.3 9.0 + - - +
29A LEU* 3.1 22.4 + - + +
75A LEU* 4.5 12.1 - - + -
76A TYR* 3.8 20.4 - - + +
294B GLU* 3.7 36.7 + - + +
295B LEU* 3.8 33.4 - - + +
298B ALA* 3.7 20.9 - - + -
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Residues in contact with LEU 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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14A VAL* 4.6 6.1 - - + -
17A LEU* 3.8 17.5 - - + -
21A VAL* 3.5 23.6 - - + -
22A THR 3.1 13.0 + - - +
23A GLU 3.9 2.9 - - - +
25A LEU* 1.3 73.4 - - - +
27A PHE* 1.3 66.6 + - - +
29A LEU* 4.5 3.6 - - + -
30A PHE* 3.0 53.2 + - + +
39A VAL* 3.9 15.0 - - + -
41A ILE* 4.3 4.3 - - + -
53A ALA* 3.6 31.0 - - + -
55A VAL* 5.1 1.3 - - + -
75A LEU* 3.8 26.7 - - + -
80A ILE* 5.2 0.2 - - + -
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Residues in contact with PHE 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 GLU 2.8 19.7 + - - +
24A GLU* 3.4 8.3 - - + +
26A LEU* 1.3 75.6 - - - +
28A GLU* 1.3 61.1 + - + +
30A PHE 3.8 0.2 - - - -
31A HIS* 2.8 57.6 + + + +
36A VAL* 3.4 43.2 - - + +
37A ILE 3.8 14.1 - - - -
38A LYS* 4.5 4.7 - - - -
39A VAL* 3.8 16.0 - - + +
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Residues in contact with GLU 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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24A GLU* 3.1 10.4 + - + +
25A LEU* 3.3 11.9 + - - +
27A PHE* 1.3 82.2 - - + +
29A LEU* 1.3 62.9 + - - +
31A HIS* 3.3 17.9 + - + +
32A GLN* 3.7 12.0 + - - +
290B VAL 4.8 1.4 - - - +
291B ILE* 3.5 8.9 - - + -
292B SER* 2.7 50.3 + - - -
294B GLU* 5.2 2.1 - - - +
295B LEU* 3.6 20.5 + - + +
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Residues in contact with LEU 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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25A LEU 3.1 16.8 + - - +
26A LEU* 3.9 4.3 - - + +
28A GLU* 1.3 76.5 - - - +
30A PHE* 1.3 73.0 + - + +
32A GLN* 3.1 27.5 + - - +
70A LEU* 3.7 35.2 - - + +
73A ILE* 4.8 4.9 - - + -
75A LEU* 4.1 33.0 - - + -
80A ILE* 4.5 8.5 - - + -
295B LEU* 3.9 16.3 - - + +
299B LEU* 4.3 11.2 - - + -
309B PHE* 3.7 26.5 - - + -
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Residues in contact with PHE 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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12A LEU* 4.2 10.5 - - + -
14A VAL* 3.5 29.2 - - + -
26A LEU* 3.0 45.4 + - + +
29A LEU* 1.3 77.2 - - + +
31A HIS* 1.3 59.5 + - - +
32A GLN 3.0 2.0 - - - -
33A ALA* 2.9 17.7 + - - +
34A GLY 3.3 0.5 - - - +
36A VAL* 3.6 9.9 - - + -
55A VAL* 4.1 15.7 - - + -
57A PHE* 3.3 41.5 - + + -
66A ALA* 4.2 3.4 - - + -
70A LEU* 3.5 26.5 - - + -
80A ILE* 4.0 13.9 - - + -
82A ILE* 3.9 24.9 - - + -
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Residues in contact with HIS 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 PHE* 2.8 41.0 + + - +
28A GLU* 3.3 12.6 - - - +
29A LEU 3.2 0.2 - - - -
30A PHE* 1.3 77.0 - - - +
32A GLN* 1.3 60.2 + - + +
33A ALA 3.2 0.2 - - - -
34A GLY 3.4 5.9 + - - -
35A PRO* 3.9 10.5 - - + -
36A VAL* 3.5 18.5 + - - +
286B PHE* 4.0 3.5 - + - -
322B TRP* 2.8 63.0 + + - -
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Residues in contact with GLN 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 GLU* 4.0 9.8 + - - +
29A LEU* 3.3 17.3 - - - +
30A PHE 3.0 0.6 - - - -
31A HIS* 1.3 81.4 - - - +
33A ALA* 1.3 59.6 + - - +
69A LEU* 4.2 7.9 - - + -
286B PHE* 3.6 17.7 - - - -
287B LYS 3.9 10.3 + - - -
288B PRO* 3.6 5.5 - - - +
289B GLY* 2.8 27.0 + - - +
290B VAL 3.7 21.2 + - - -
291B ILE* 4.2 6.8 - - + +
309B PHE* 3.6 33.9 - - + -
313B MET* 3.7 6.0 - - + +
319B PRO* 3.4 21.7 - - - +
322B TRP* 3.9 0.2 + - - -
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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